Mercurial > repos > galaxyp > openms_idfileconverter
annotate IDFileConverter.xml @ 15:7d0eb300f360 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author | galaxyp |
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date | Thu, 01 Dec 2022 19:01:16 +0000 |
parents | 250d6a43f66b |
children | 5e9c35b8d194 |
rev | line source |
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bea4646ed591
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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1 <?xml version='1.0' encoding='UTF-8'?> |
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1dcffdad49c0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> |
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bea4646ed591
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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3 <!--Proposed Tool Section: [ID Processing]--> |
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7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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4 <tool id="IDFileConverter" name="IDFileConverter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> |
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bea4646ed591
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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5 <description>Converts identification engine file formats.</description> |
bea4646ed591
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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6 <macros> |
bea4646ed591
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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7 <token name="@EXECUTABLE@">IDFileConverter</token> |
bea4646ed591
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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8 <import>macros.xml</import> |
bea4646ed591
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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9 </macros> |
bea4646ed591
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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10 <expand macro="requirements"/> |
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43a1db77b7a6
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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11 <expand macro="stdio"/> |
43a1db77b7a6
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ |
43a1db77b7a6
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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13 @EXT_FOO@ |
43a1db77b7a6
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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14 #import re |
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bea4646ed591
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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15 |
11
43a1db77b7a6
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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16 ## Preprocessing |
43a1db77b7a6
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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17 mkdir in && |
43a1db77b7a6
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && |
43a1db77b7a6
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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19 mkdir out && |
43a1db77b7a6
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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20 #if $mz_file: |
43a1db77b7a6
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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21 mkdir mz_file && |
43a1db77b7a6
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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22 ln -s '$mz_file' 'mz_file/${re.sub("[^\w\-_]", "_", $mz_file.element_identifier)}.$gxy2omsext($mz_file.ext)' && |
3
066cf4d993f5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
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23 #end if |
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43a1db77b7a6
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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24 |
43a1db77b7a6
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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25 ## Main program call |
43a1db77b7a6
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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26 |
43a1db77b7a6
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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27 set -o pipefail && |
43a1db77b7a6
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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28 @EXECUTABLE@ -write_ctd ./ && |
43a1db77b7a6
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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29 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && |
43a1db77b7a6
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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30 @EXECUTABLE@ -ini @EXECUTABLE@.ctd |
43a1db77b7a6
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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31 -in |
43a1db77b7a6
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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32 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' |
43a1db77b7a6
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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33 -out |
43a1db77b7a6
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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34 'out/output.${out_type}' |
43a1db77b7a6
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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35 #if $mz_file: |
43a1db77b7a6
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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36 -mz_file |
43a1db77b7a6
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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37 'mz_file/${re.sub("[^\w\-_]", "_", $mz_file.element_identifier)}.$gxy2omsext($mz_file.ext)' |
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1dcffdad49c0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
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38 #end if |
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43a1db77b7a6
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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39 |
43a1db77b7a6
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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40 ## Postprocessing |
43a1db77b7a6
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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41 && mv 'out/output.${out_type}' '$out' |
43a1db77b7a6
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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42 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS |
43a1db77b7a6
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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43 && mv '@EXECUTABLE@.ctd' '$ctd_out' |
43a1db77b7a6
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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44 #end if]]></command> |
43a1db77b7a6
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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45 <configfiles> |
43a1db77b7a6
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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46 <inputs name="args_json" data_style="paths"/> |
43a1db77b7a6
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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47 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
43a1db77b7a6
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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48 </configfiles> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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49 <inputs> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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50 <param argument="-in" type="data" format="fasta,idxml,mascotxml,mzid,pepxml,protxml,psms,sqlite,tabular,xquest.xml" optional="false" label="Input file or directory containing the data to convert" help="This may be:. - a single file in OpenMS database format (.oms),. - a single file in a multi-purpose XML format (.idXML, .mzid, .pepXML, .protXML),. - a single file in a search engine-specific format (Mascot: .mascotXML, OMSSA: .omssaXML, X! Tandem: .xml, Percolator: .psms, xQuest: .xquest.xml),. - a single file in fasta format (can only be used to generate a theoretical mzML),. - a single text file (tab separated) with one line for all peptide sequences matching a spectrum (top N hits),. - for Sequest results, a directory containing .out files.. select fasta,idxml,mascotxml,mzid,pepxml,protxml,psms,sqlite,tabular,xquest.xml data sets(s)"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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51 <param argument="-out_type" type="select" optional="false" label="Output file type (default: determined from file extension)" help=""> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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52 <option value="fasta">fasta</option> |
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43a1db77b7a6
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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53 <option value="idXML">idxml</option> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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54 <option value="mzML">mzml</option> |
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bea4646ed591
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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55 <option value="mzid">mzid</option> |
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7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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56 <option value="oms">sqlite (oms)</option> |
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43a1db77b7a6
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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57 <option value="pepXML">pepxml</option> |
43a1db77b7a6
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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58 <option value="xquest.xml">xquest.xml</option> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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59 <expand macro="list_string_san" name="out_type"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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60 </param> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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61 <param argument="-mz_file" type="data" format="mzdata,mzml,mzxml" optional="true" label="[pepXML, Sequest, Mascot, X" help="Tandem, mzid, Percolator only] Retention times and native spectrum ids (spectrum_references) will be looked up in this file select mzdata,mzml,mzxml data sets(s)"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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62 <param argument="-mz_name" type="text" optional="true" value="" label="[pepXML only] Experiment filename/path (extension will be removed) to match in the pepXML file ('base_name' attribute)" help="Only necessary if different from 'mz_file'"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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63 <expand macro="list_string_san" name="mz_name"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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64 </param> |
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65 <param argument="-peptideprophet_analyzed" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[pepXML output only] Write output in the format of a PeptideProphet analysis result" help="By default a 'raw' pepXML is produced that contains only search engine results"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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66 <param argument="-score_type" type="select" optional="true" label="[Percolator only] Which of the Percolator scores to report as 'the' score for a peptide hit" help=""> |
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67 <option value="qvalue" selected="true">qvalue</option> |
bea4646ed591
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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68 <option value="PEP">PEP</option> |
bea4646ed591
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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69 <option value="score">score</option> |
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70 <expand macro="list_string_san" name="score_type"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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71 </param> |
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72 <section name="fasta_to_mzml" title="[FASTA input + MzML output only] Parameters used to adjust simulation of the theoretical spectra" help="" expanded="false"> |
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73 <param name="isotope_model" argument="-fasta_to_mzml:isotope_model" type="select" optional="true" label="Model to use for isotopic peaks ('none' means no isotopic peaks are added, 'coarse' adds isotopic peaks in unit mass distance, 'fine' uses the hyperfine isotopic generator to add accurate isotopic peaks" help="Note that adding isotopic peaks is very slow"> |
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74 <option value="none" selected="true">none</option> |
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75 <option value="coarse">coarse</option> |
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76 <option value="fine">fine</option> |
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77 <expand macro="list_string_san" name="isotope_model"/> |
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78 </param> |
15
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79 <param name="max_isotope" argument="-fasta_to_mzml:max_isotope" type="integer" optional="true" value="2" label="Defines the maximal isotopic peak which is added if 'isotope_model' is 'coarse'" help=""/> |
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80 <param name="max_isotope_probability" argument="-fasta_to_mzml:max_isotope_probability" type="float" optional="true" value="0.05" label="Defines the maximal isotopic probability to cover if 'isotope_model' is 'fine'" help=""/> |
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81 <param name="add_metainfo" argument="-fasta_to_mzml:add_metainfo" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Adds the type of peaks as metainfo to the peaks, like y8+, [M-H2O+2H]++" help=""/> |
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82 <param name="add_losses" argument="-fasta_to_mzml:add_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Adds common losses to those ion expect to have them, only water and ammonia loss is considered" help=""/> |
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83 <param name="sort_by_position" argument="-fasta_to_mzml:sort_by_position" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Sort output by position" help=""/> |
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84 <param name="add_precursor_peaks" argument="-fasta_to_mzml:add_precursor_peaks" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Adds peaks of the unfragmented precursor ion to the spectrum" help=""/> |
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85 <param name="add_all_precursor_charges" argument="-fasta_to_mzml:add_all_precursor_charges" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Adds precursor peaks with all charges in the given range" help=""/> |
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86 <param name="add_abundant_immonium_ions" argument="-fasta_to_mzml:add_abundant_immonium_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add most abundant immonium ions (for Proline, Cystein, Iso/Leucine, Histidin, Phenylalanin, Tyrosine, Tryptophan)" help=""/> |
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87 <param name="add_first_prefix_ion" argument="-fasta_to_mzml:add_first_prefix_ion" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set to true e.g. b1 ions are added" help=""/> |
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88 <param name="add_y_ions" argument="-fasta_to_mzml:add_y_ions" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Add peaks of y-ions to the spectrum" help=""/> |
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89 <param name="add_b_ions" argument="-fasta_to_mzml:add_b_ions" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Add peaks of b-ions to the spectrum" help=""/> |
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90 <param name="add_a_ions" argument="-fasta_to_mzml:add_a_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of a-ions to the spectrum" help=""/> |
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91 <param name="add_c_ions" argument="-fasta_to_mzml:add_c_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of c-ions to the spectrum" help=""/> |
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92 <param name="add_x_ions" argument="-fasta_to_mzml:add_x_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of x-ions to the spectrum" help=""/> |
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93 <param name="add_z_ions" argument="-fasta_to_mzml:add_z_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of z-ions to the spectrum" help=""/> |
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94 <param name="y_intensity" argument="-fasta_to_mzml:y_intensity" type="float" optional="true" min="0.0" value="1.0" label="Intensity of the y-ions" help=""/> |
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95 <param name="b_intensity" argument="-fasta_to_mzml:b_intensity" type="float" optional="true" min="0.0" value="1.0" label="Intensity of the b-ions" help=""/> |
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96 <param name="a_intensity" argument="-fasta_to_mzml:a_intensity" type="float" optional="true" min="0.0" value="1.0" label="Intensity of the a-ions" help=""/> |
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97 <param name="c_intensity" argument="-fasta_to_mzml:c_intensity" type="float" optional="true" min="0.0" value="1.0" label="Intensity of the c-ions" help=""/> |
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98 <param name="x_intensity" argument="-fasta_to_mzml:x_intensity" type="float" optional="true" min="0.0" value="1.0" label="Intensity of the x-ions" help=""/> |
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99 <param name="z_intensity" argument="-fasta_to_mzml:z_intensity" type="float" optional="true" min="0.0" value="1.0" label="Intensity of the z-ions" help=""/> |
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100 <param name="relative_loss_intensity" argument="-fasta_to_mzml:relative_loss_intensity" type="float" optional="true" min="0.0" max="1.0" value="0.1" label="Intensity of loss ions, in relation to the intact ion intensity" help=""/> |
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101 <param name="precursor_intensity" argument="-fasta_to_mzml:precursor_intensity" type="float" optional="true" min="0.0" value="1.0" label="Intensity of the precursor peak" help=""/> |
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102 <param name="precursor_H2O_intensity" argument="-fasta_to_mzml:precursor_H2O_intensity" type="float" optional="true" min="0.0" value="1.0" label="Intensity of the H2O loss peak of the precurso" help=""/> |
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103 <param name="precursor_NH3_intensity" argument="-fasta_to_mzml:precursor_NH3_intensity" type="float" optional="true" min="0.0" value="1.0" label="Intensity of the NH3 loss peak of the precurso" help=""/> |
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104 <param name="enzyme" argument="-fasta_to_mzml:enzyme" type="select" optional="true" label="Enzym used to digest the fasta proteins" help=""> |
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105 <option value="Trypsin" selected="true">Trypsin</option> |
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106 <option value="Chymotrypsin">Chymotrypsin</option> |
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107 <option value="Chymotrypsin/P">Chymotrypsin/P</option> |
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108 <option value="CNBr">CNBr</option> |
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109 <option value="Formic_acid">Formic_acid</option> |
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110 <option value="leukocyte elastase">leukocyte elastase</option> |
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111 <option value="proline endopeptidase">proline endopeptidase</option> |
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112 <option value="Arg-C/P">Arg-C/P</option> |
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113 <option value="Asp-N">Asp-N</option> |
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114 <option value="Asp-N/B">Asp-N/B</option> |
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115 <option value="Asp-N_ambic">Asp-N_ambic</option> |
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116 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> |
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117 <option value="Alpha-lytic protease">Alpha-lytic protease</option> |
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118 <option value="2-iodobenzoate">2-iodobenzoate</option> |
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119 <option value="iodosobenzoate">iodosobenzoate</option> |
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120 <option value="cyanogen-bromide">cyanogen-bromide</option> |
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121 <option value="Clostripain/P">Clostripain/P</option> |
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122 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option> |
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123 <option value="no cleavage">no cleavage</option> |
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124 <option value="unspecific cleavage">unspecific cleavage</option> |
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125 <option value="Lys-C">Lys-C</option> |
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126 <option value="Lys-N">Lys-N</option> |
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127 <option value="Lys-C/P">Lys-C/P</option> |
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128 <option value="PepsinA">PepsinA</option> |
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129 <option value="TrypChymo">TrypChymo</option> |
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130 <option value="Trypsin/P">Trypsin/P</option> |
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131 <option value="V8-DE">V8-DE</option> |
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132 <option value="V8-E">V8-E</option> |
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133 <option value="staphylococcal protease/D">staphylococcal protease/D</option> |
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134 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option> |
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135 <option value="Glu-C+P">Glu-C+P</option> |
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136 <option value="PepsinA + P">PepsinA + P</option> |
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137 <option value="Arg-C">Arg-C</option> |
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138 <expand macro="list_string_san" name="enzyme"/> |
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139 </param> |
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140 <param name="missed_cleavages" argument="-fasta_to_mzml:missed_cleavages" type="integer" optional="true" value="0" label="Number of allowed missed cleavages while digesting the fasta proteins" help=""/> |
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141 <param name="min_charge" argument="-fasta_to_mzml:min_charge" type="integer" optional="true" value="1" label="Minimum charge" help=""/> |
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142 <param name="max_charge" argument="-fasta_to_mzml:max_charge" type="integer" optional="true" value="1" label="Maximum charge" help=""/> |
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143 <param name="precursor_charge" argument="-fasta_to_mzml:precursor_charge" type="integer" optional="true" value="0" label="Manually set precursor charge" help="(default: 0, meaning max_charge + 1 will be used as precursor charge)"/> |
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144 </section> |
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145 <expand macro="adv_opts_macro"> |
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146 <param argument="-ignore_proteins_per_peptide" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[Sequest only] Workaround to deal with .out files that contain" help="e.g. "+1" in references column,. but do not list extra references in subsequent lines (try -debug 3 or 4)"/> |
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147 <param argument="-scan_regex" type="text" optional="true" value="" label="[Mascot, pepXML, Percolator only] Regular expression used to extract the scan number or retention time" help="See documentation for details"> |
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148 <expand macro="list_string_san" name="scan_regex"/> |
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149 </param> |
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150 <param argument="-no_spectra_data_override" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[+mz_file only] Avoid overriding 'spectra_data' in protein identifications if 'mz_file' is given and 'spectrum_reference's are added/updated" help="Use only if you are sure it is absolutely the same 'mz_file' as used for identification"/> |
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151 <param argument="-no_spectra_references_override" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[+mz_file only] Avoid overriding 'spectrum_reference' in peptide identifications if 'mz_file' is given and a 'spectrum_reference' is already present" help=""/> |
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152 <param argument="-add_ionmatch_annotation" type="float" optional="true" value="0.0" label="[+mz_file only] Annotate the identifications with ion matches from spectra in 'mz_file' using the given tolerance (in Da)" help="This will take quite some time"/> |
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153 <param argument="-concatenate_peptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[FASTA output only] Will concatenate the top peptide hits to one peptide sequence, rather than write a new peptide for each hit" help=""/> |
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154 <param argument="-number_of_hits" type="integer" optional="true" value="1" label="[FASTA output only] Controls how many peptide hits will be exported" help="A value of 0 or less exports all hits"/> |
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155 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> |
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156 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> |
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157 <expand macro="list_string_san" name="test"/> |
11
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158 </param> |
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159 </expand> |
13
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160 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> |
11
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161 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> |
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162 </param> |
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163 </inputs> |
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164 <outputs> |
15
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165 <data name="out" label="${tool.name} on ${on_string}: out" format="fasta"> |
11
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166 <change_format> |
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167 <when input="out_type" value="idXML" format="idxml"/> |
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168 <when input="out_type" value="mzML" format="mzml"/> |
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169 <when input="out_type" value="mzid" format="mzid"/> |
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170 <when input="out_type" value="oms" format="sqlite"/> |
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171 <when input="out_type" value="pepXML" format="pepxml"/> |
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172 <when input="out_type" value="xquest.xml" format="xquest.xml"/> |
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173 </change_format> |
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174 </data> |
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175 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> |
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176 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> |
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177 </data> |
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178 </outputs> |
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179 <tests><!-- TOPP_IDFileConverter_1 --> |
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180 <test expect_num_outputs="2"> |
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181 <section name="adv_opts"> |
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182 <param name="ignore_proteins_per_peptide" value="false"/> |
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183 <param name="scan_regex" value=""/> |
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184 <param name="no_spectra_data_override" value="false"/> |
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185 <param name="no_spectra_references_override" value="false"/> |
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186 <param name="add_ionmatch_annotation" value="0.0"/> |
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187 <param name="concatenate_peptides" value="false"/> |
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188 <param name="number_of_hits" value="1"/> |
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189 <param name="force" value="false"/> |
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190 <param name="test" value="true"/> |
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191 </section> |
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192 <param name="in" value="IDFileConverter_1_input1.mascotXML"/> |
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193 <output name="out" file="IDFileConverter_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> |
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194 <param name="out_type" value="idXML"/> |
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195 <param name="mz_file" value="IDFileConverter_1_input2.mzML"/> |
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196 <param name="mz_name" value=""/> |
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197 <param name="peptideprophet_analyzed" value="false"/> |
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198 <param name="score_type" value="qvalue"/> |
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199 <section name="fasta_to_mzml"> |
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200 <param name="isotope_model" value="none"/> |
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201 <param name="max_isotope" value="2"/> |
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202 <param name="max_isotope_probability" value="0.05"/> |
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203 <param name="add_metainfo" value="false"/> |
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204 <param name="add_losses" value="false"/> |
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205 <param name="sort_by_position" value="true"/> |
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206 <param name="add_precursor_peaks" value="false"/> |
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207 <param name="add_all_precursor_charges" value="false"/> |
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208 <param name="add_abundant_immonium_ions" value="false"/> |
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209 <param name="add_first_prefix_ion" value="false"/> |
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210 <param name="add_y_ions" value="true"/> |
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211 <param name="add_b_ions" value="true"/> |
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212 <param name="add_a_ions" value="false"/> |
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213 <param name="add_c_ions" value="false"/> |
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214 <param name="add_x_ions" value="false"/> |
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215 <param name="add_z_ions" value="false"/> |
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216 <param name="y_intensity" value="1.0"/> |
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217 <param name="b_intensity" value="1.0"/> |
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218 <param name="a_intensity" value="1.0"/> |
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219 <param name="c_intensity" value="1.0"/> |
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220 <param name="x_intensity" value="1.0"/> |
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221 <param name="z_intensity" value="1.0"/> |
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222 <param name="relative_loss_intensity" value="0.1"/> |
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223 <param name="precursor_intensity" value="1.0"/> |
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224 <param name="precursor_H2O_intensity" value="1.0"/> |
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225 <param name="precursor_NH3_intensity" value="1.0"/> |
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226 <param name="enzyme" value="Trypsin"/> |
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227 <param name="missed_cleavages" value="0"/> |
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228 <param name="min_charge" value="1"/> |
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229 <param name="max_charge" value="1"/> |
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230 <param name="precursor_charge" value="0"/> |
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231 </section> |
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232 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
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233 <output name="ctd_out" ftype="xml"> |
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234 <assert_contents> |
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235 <is_valid_xml/> |
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236 </assert_contents> |
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237 </output> |
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238 </test> |
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239 <!-- TOPP_IDFileConverter_2 --> |
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240 <test expect_num_outputs="2"> |
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241 <section name="adv_opts"> |
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242 <param name="ignore_proteins_per_peptide" value="false"/> |
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243 <param name="scan_regex" value=""/> |
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244 <param name="no_spectra_data_override" value="false"/> |
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245 <param name="no_spectra_references_override" value="false"/> |
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246 <param name="add_ionmatch_annotation" value="0.0"/> |
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247 <param name="concatenate_peptides" value="false"/> |
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248 <param name="number_of_hits" value="1"/> |
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249 <param name="force" value="false"/> |
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250 <param name="test" value="true"/> |
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251 </section> |
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252 <param name="in" value="PepXMLFile_test.pepxml"/> |
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253 <output name="out" file="IDFileConverter_2_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> |
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254 <param name="out_type" value="idXML"/> |
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255 <param name="mz_file" value="PepXMLFile_test.mzML"/> |
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256 <param name="mz_name" value="PepXMLFile_test"/> |
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257 <param name="peptideprophet_analyzed" value="false"/> |
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258 <param name="score_type" value="qvalue"/> |
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259 <section name="fasta_to_mzml"> |
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260 <param name="isotope_model" value="none"/> |
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261 <param name="max_isotope" value="2"/> |
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262 <param name="max_isotope_probability" value="0.05"/> |
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263 <param name="add_metainfo" value="false"/> |
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264 <param name="add_losses" value="false"/> |
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265 <param name="sort_by_position" value="true"/> |
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266 <param name="add_precursor_peaks" value="false"/> |
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267 <param name="add_all_precursor_charges" value="false"/> |
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268 <param name="add_abundant_immonium_ions" value="false"/> |
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269 <param name="add_first_prefix_ion" value="false"/> |
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270 <param name="add_y_ions" value="true"/> |
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271 <param name="add_b_ions" value="true"/> |
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272 <param name="add_a_ions" value="false"/> |
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273 <param name="add_c_ions" value="false"/> |
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274 <param name="add_x_ions" value="false"/> |
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275 <param name="add_z_ions" value="false"/> |
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276 <param name="y_intensity" value="1.0"/> |
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277 <param name="b_intensity" value="1.0"/> |
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278 <param name="a_intensity" value="1.0"/> |
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279 <param name="c_intensity" value="1.0"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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280 <param name="x_intensity" value="1.0"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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281 <param name="z_intensity" value="1.0"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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282 <param name="relative_loss_intensity" value="0.1"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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283 <param name="precursor_intensity" value="1.0"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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284 <param name="precursor_H2O_intensity" value="1.0"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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285 <param name="precursor_NH3_intensity" value="1.0"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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286 <param name="enzyme" value="Trypsin"/> |
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287 <param name="missed_cleavages" value="0"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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288 <param name="min_charge" value="1"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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289 <param name="max_charge" value="1"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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290 <param name="precursor_charge" value="0"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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291 </section> |
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292 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
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293 <output name="ctd_out" ftype="xml"> |
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294 <assert_contents> |
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295 <is_valid_xml/> |
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296 </assert_contents> |
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297 </output> |
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298 </test> |
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299 <!-- TOPP_IDFileConverter_3 --> |
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300 <test expect_num_outputs="2"> |
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301 <section name="adv_opts"> |
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302 <param name="ignore_proteins_per_peptide" value="false"/> |
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303 <param name="scan_regex" value=""/> |
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304 <param name="no_spectra_data_override" value="false"/> |
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305 <param name="no_spectra_references_override" value="false"/> |
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306 <param name="add_ionmatch_annotation" value="0.0"/> |
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307 <param name="concatenate_peptides" value="false"/> |
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308 <param name="number_of_hits" value="1"/> |
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309 <param name="force" value="false"/> |
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310 <param name="test" value="true"/> |
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311 </section> |
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312 <param name="in" value="IDFileConverter_3_input.protXML"/> |
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313 <output name="out" file="IDFileConverter_3_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> |
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314 <param name="out_type" value="idXML"/> |
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315 <param name="mz_name" value=""/> |
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316 <param name="peptideprophet_analyzed" value="false"/> |
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317 <param name="score_type" value="qvalue"/> |
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318 <section name="fasta_to_mzml"> |
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319 <param name="isotope_model" value="none"/> |
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320 <param name="max_isotope" value="2"/> |
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321 <param name="max_isotope_probability" value="0.05"/> |
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322 <param name="add_metainfo" value="false"/> |
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323 <param name="add_losses" value="false"/> |
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324 <param name="sort_by_position" value="true"/> |
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325 <param name="add_precursor_peaks" value="false"/> |
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326 <param name="add_all_precursor_charges" value="false"/> |
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327 <param name="add_abundant_immonium_ions" value="false"/> |
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328 <param name="add_first_prefix_ion" value="false"/> |
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329 <param name="add_y_ions" value="true"/> |
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330 <param name="add_b_ions" value="true"/> |
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331 <param name="add_a_ions" value="false"/> |
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332 <param name="add_c_ions" value="false"/> |
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333 <param name="add_x_ions" value="false"/> |
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334 <param name="add_z_ions" value="false"/> |
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335 <param name="y_intensity" value="1.0"/> |
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336 <param name="b_intensity" value="1.0"/> |
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337 <param name="a_intensity" value="1.0"/> |
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338 <param name="c_intensity" value="1.0"/> |
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339 <param name="x_intensity" value="1.0"/> |
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340 <param name="z_intensity" value="1.0"/> |
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341 <param name="relative_loss_intensity" value="0.1"/> |
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342 <param name="precursor_intensity" value="1.0"/> |
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343 <param name="precursor_H2O_intensity" value="1.0"/> |
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344 <param name="precursor_NH3_intensity" value="1.0"/> |
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345 <param name="enzyme" value="Trypsin"/> |
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346 <param name="missed_cleavages" value="0"/> |
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347 <param name="min_charge" value="1"/> |
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348 <param name="max_charge" value="1"/> |
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349 <param name="precursor_charge" value="0"/> |
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350 </section> |
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351 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
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352 <output name="ctd_out" ftype="xml"> |
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353 <assert_contents> |
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354 <is_valid_xml/> |
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355 </assert_contents> |
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356 </output> |
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357 </test> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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358 <!-- TOPP_IDFileConverter_5 --> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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359 <test expect_num_outputs="2"> |
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360 <section name="adv_opts"> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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361 <param name="ignore_proteins_per_peptide" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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362 <param name="scan_regex" value="scan=(?<SCAN>\d+)"/> |
7d0eb300f360
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363 <param name="no_spectra_data_override" value="false"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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364 <param name="no_spectra_references_override" value="false"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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365 <param name="add_ionmatch_annotation" value="0.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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366 <param name="concatenate_peptides" value="false"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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367 <param name="number_of_hits" value="1"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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368 <param name="force" value="false"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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369 <param name="test" value="true"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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370 </section> |
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371 <param name="in" value="IDFileConverter_1_input1.mascotXML"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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372 <output name="out" file="IDFileConverter_5_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> |
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373 <param name="out_type" value="idXML"/> |
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374 <param name="mz_file" value="IDFileConverter_1_input2.mzML"/> |
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375 <param name="mz_name" value=""/> |
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376 <param name="peptideprophet_analyzed" value="false"/> |
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377 <param name="score_type" value="qvalue"/> |
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378 <section name="fasta_to_mzml"> |
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379 <param name="isotope_model" value="none"/> |
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380 <param name="max_isotope" value="2"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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381 <param name="max_isotope_probability" value="0.05"/> |
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382 <param name="add_metainfo" value="false"/> |
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383 <param name="add_losses" value="false"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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384 <param name="sort_by_position" value="true"/> |
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385 <param name="add_precursor_peaks" value="false"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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386 <param name="add_all_precursor_charges" value="false"/> |
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387 <param name="add_abundant_immonium_ions" value="false"/> |
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388 <param name="add_first_prefix_ion" value="false"/> |
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389 <param name="add_y_ions" value="true"/> |
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390 <param name="add_b_ions" value="true"/> |
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391 <param name="add_a_ions" value="false"/> |
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392 <param name="add_c_ions" value="false"/> |
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393 <param name="add_x_ions" value="false"/> |
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394 <param name="add_z_ions" value="false"/> |
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395 <param name="y_intensity" value="1.0"/> |
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396 <param name="b_intensity" value="1.0"/> |
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397 <param name="a_intensity" value="1.0"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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398 <param name="c_intensity" value="1.0"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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399 <param name="x_intensity" value="1.0"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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400 <param name="z_intensity" value="1.0"/> |
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401 <param name="relative_loss_intensity" value="0.1"/> |
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402 <param name="precursor_intensity" value="1.0"/> |
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403 <param name="precursor_H2O_intensity" value="1.0"/> |
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404 <param name="precursor_NH3_intensity" value="1.0"/> |
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405 <param name="enzyme" value="Trypsin"/> |
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406 <param name="missed_cleavages" value="0"/> |
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407 <param name="min_charge" value="1"/> |
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408 <param name="max_charge" value="1"/> |
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409 <param name="precursor_charge" value="0"/> |
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410 </section> |
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411 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
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412 <output name="ctd_out" ftype="xml"> |
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413 <assert_contents> |
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414 <is_valid_xml/> |
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415 </assert_contents> |
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416 </output> |
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417 </test> |
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418 <!-- TOPP_IDFileConverter_6 --> |
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419 <test expect_num_outputs="2"> |
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420 <section name="adv_opts"> |
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421 <param name="ignore_proteins_per_peptide" value="false"/> |
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422 <param name="scan_regex" value=""/> |
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423 <param name="no_spectra_data_override" value="false"/> |
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424 <param name="no_spectra_references_override" value="false"/> |
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425 <param name="add_ionmatch_annotation" value="0.0"/> |
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426 <param name="concatenate_peptides" value="false"/> |
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427 <param name="number_of_hits" value="1"/> |
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428 <param name="force" value="false"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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429 <param name="test" value="true"/> |
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430 </section> |
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galaxyp
parents:
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changeset
|
431 <param name="in" value="IDFileConverter_6_input1.pepXML"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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432 <output name="out" file="IDFileConverter_6_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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433 <param name="out_type" value="idXML"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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434 <param name="mz_file" value="IDFileConverter_1_input2.mzML"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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435 <param name="mz_name" value="F025589.dat.mzML"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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436 <param name="peptideprophet_analyzed" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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437 <param name="score_type" value="qvalue"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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changeset
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438 <section name="fasta_to_mzml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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439 <param name="isotope_model" value="none"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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440 <param name="max_isotope" value="2"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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441 <param name="max_isotope_probability" value="0.05"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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442 <param name="add_metainfo" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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changeset
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443 <param name="add_losses" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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444 <param name="sort_by_position" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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445 <param name="add_precursor_peaks" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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446 <param name="add_all_precursor_charges" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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447 <param name="add_abundant_immonium_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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448 <param name="add_first_prefix_ion" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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449 <param name="add_y_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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450 <param name="add_b_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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451 <param name="add_a_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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452 <param name="add_c_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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453 <param name="add_x_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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454 <param name="add_z_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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455 <param name="y_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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456 <param name="b_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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457 <param name="a_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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458 <param name="c_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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459 <param name="x_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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460 <param name="z_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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461 <param name="relative_loss_intensity" value="0.1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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462 <param name="precursor_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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463 <param name="precursor_H2O_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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464 <param name="precursor_NH3_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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465 <param name="enzyme" value="Trypsin"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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466 <param name="missed_cleavages" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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467 <param name="min_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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468 <param name="max_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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469 <param name="precursor_charge" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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470 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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471 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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472 <output name="ctd_out" ftype="xml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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473 <assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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474 <is_valid_xml/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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475 </assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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476 </output> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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477 </test> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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478 <!-- TOPP_IDFileConverter_7 --> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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479 <test expect_num_outputs="2"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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480 <section name="adv_opts"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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481 <param name="ignore_proteins_per_peptide" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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482 <param name="scan_regex" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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483 <param name="no_spectra_data_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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484 <param name="no_spectra_references_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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485 <param name="add_ionmatch_annotation" value="0.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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486 <param name="concatenate_peptides" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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487 <param name="number_of_hits" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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488 <param name="force" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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489 <param name="test" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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490 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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491 <param name="in" value="IDFileConverter_7_input1.xml"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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492 <output name="out" file="IDFileConverter_7_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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493 <param name="out_type" value="idXML"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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494 <param name="mz_name" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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changeset
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495 <param name="peptideprophet_analyzed" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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496 <param name="score_type" value="qvalue"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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497 <section name="fasta_to_mzml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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changeset
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498 <param name="isotope_model" value="none"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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changeset
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499 <param name="max_isotope" value="2"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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500 <param name="max_isotope_probability" value="0.05"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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501 <param name="add_metainfo" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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changeset
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502 <param name="add_losses" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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changeset
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503 <param name="sort_by_position" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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504 <param name="add_precursor_peaks" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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505 <param name="add_all_precursor_charges" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
506 <param name="add_abundant_immonium_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
507 <param name="add_first_prefix_ion" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
508 <param name="add_y_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
509 <param name="add_b_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
510 <param name="add_a_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
511 <param name="add_c_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
512 <param name="add_x_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
513 <param name="add_z_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
514 <param name="y_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
515 <param name="b_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
516 <param name="a_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
517 <param name="c_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
518 <param name="x_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
519 <param name="z_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
520 <param name="relative_loss_intensity" value="0.1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
521 <param name="precursor_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
522 <param name="precursor_H2O_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
523 <param name="precursor_NH3_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
524 <param name="enzyme" value="Trypsin"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
525 <param name="missed_cleavages" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
526 <param name="min_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
527 <param name="max_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
528 <param name="precursor_charge" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
529 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
530 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
531 <output name="ctd_out" ftype="xml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
532 <assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
533 <is_valid_xml/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
534 </assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
535 </output> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
536 </test> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
537 <!-- TOPP_IDFileConverter_8 --> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
538 <test expect_num_outputs="2"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
539 <section name="adv_opts"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
540 <param name="ignore_proteins_per_peptide" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
541 <param name="scan_regex" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
542 <param name="no_spectra_data_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
543 <param name="no_spectra_references_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
544 <param name="add_ionmatch_annotation" value="0.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
545 <param name="concatenate_peptides" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
546 <param name="number_of_hits" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
547 <param name="force" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
548 <param name="test" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
549 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
550 <param name="in" value="IDFileConverter_8_input.mzid"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
551 <output name="out" file="IDFileConverter_8_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
552 <param name="out_type" value="idXML"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
553 <param name="mz_name" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
554 <param name="peptideprophet_analyzed" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
555 <param name="score_type" value="qvalue"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
556 <section name="fasta_to_mzml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
557 <param name="isotope_model" value="none"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
558 <param name="max_isotope" value="2"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
559 <param name="max_isotope_probability" value="0.05"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
560 <param name="add_metainfo" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
561 <param name="add_losses" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
562 <param name="sort_by_position" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
563 <param name="add_precursor_peaks" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
564 <param name="add_all_precursor_charges" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
565 <param name="add_abundant_immonium_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
566 <param name="add_first_prefix_ion" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
567 <param name="add_y_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
568 <param name="add_b_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
569 <param name="add_a_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
570 <param name="add_c_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
571 <param name="add_x_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
572 <param name="add_z_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
573 <param name="y_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
574 <param name="b_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
575 <param name="a_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
576 <param name="c_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
577 <param name="x_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
578 <param name="z_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
579 <param name="relative_loss_intensity" value="0.1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
580 <param name="precursor_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
581 <param name="precursor_H2O_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
582 <param name="precursor_NH3_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
583 <param name="enzyme" value="Trypsin"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
584 <param name="missed_cleavages" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
585 <param name="min_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
586 <param name="max_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
587 <param name="precursor_charge" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
588 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
589 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
590 <output name="ctd_out" ftype="xml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
591 <assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
592 <is_valid_xml/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
593 </assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
594 </output> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
595 </test> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
596 <!-- TOPP_IDFileConverter_9 --> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
597 <test expect_num_outputs="2"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
598 <section name="adv_opts"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
599 <param name="ignore_proteins_per_peptide" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
600 <param name="scan_regex" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
601 <param name="no_spectra_data_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
602 <param name="no_spectra_references_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
603 <param name="add_ionmatch_annotation" value="0.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
604 <param name="concatenate_peptides" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
605 <param name="number_of_hits" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
606 <param name="force" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
607 <param name="test" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
608 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
609 <param name="in" value="IDFileConverter_9_input.idXML"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
610 <output name="out" file="IDFileConverter_9_output.mzid" compare="sim_size" delta_frac="0.7" ftype="mzid"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
611 <param name="out_type" value="mzid"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
612 <param name="mz_name" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
613 <param name="peptideprophet_analyzed" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
614 <param name="score_type" value="qvalue"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
615 <section name="fasta_to_mzml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
616 <param name="isotope_model" value="none"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
617 <param name="max_isotope" value="2"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
618 <param name="max_isotope_probability" value="0.05"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
619 <param name="add_metainfo" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
620 <param name="add_losses" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
621 <param name="sort_by_position" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
622 <param name="add_precursor_peaks" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
623 <param name="add_all_precursor_charges" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
624 <param name="add_abundant_immonium_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
625 <param name="add_first_prefix_ion" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
626 <param name="add_y_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
627 <param name="add_b_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
628 <param name="add_a_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
629 <param name="add_c_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
630 <param name="add_x_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
631 <param name="add_z_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
632 <param name="y_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
633 <param name="b_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
634 <param name="a_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
635 <param name="c_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
636 <param name="x_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
637 <param name="z_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
638 <param name="relative_loss_intensity" value="0.1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
639 <param name="precursor_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
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640 <param name="precursor_H2O_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
641 <param name="precursor_NH3_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
642 <param name="enzyme" value="Trypsin"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
643 <param name="missed_cleavages" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
644 <param name="min_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
645 <param name="max_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
646 <param name="precursor_charge" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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647 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
648 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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649 <output name="ctd_out" ftype="xml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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650 <assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
651 <is_valid_xml/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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652 </assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
653 </output> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
654 </test> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
655 <!-- TOPP_IDFileConverter_10 --> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
656 <test expect_num_outputs="2"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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657 <section name="adv_opts"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
658 <param name="ignore_proteins_per_peptide" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
659 <param name="scan_regex" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
660 <param name="no_spectra_data_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
661 <param name="no_spectra_references_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
662 <param name="add_ionmatch_annotation" value="0.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
663 <param name="concatenate_peptides" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
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664 <param name="number_of_hits" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
665 <param name="force" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
666 <param name="test" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
667 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
668 <param name="in" value="IDFileConverter_10_input.pepXML"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
669 <output name="out" file="IDFileConverter_10_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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670 <param name="out_type" value="idXML"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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671 <param name="mz_name" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
672 <param name="peptideprophet_analyzed" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
673 <param name="score_type" value="qvalue"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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674 <section name="fasta_to_mzml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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675 <param name="isotope_model" value="none"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
676 <param name="max_isotope" value="2"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
677 <param name="max_isotope_probability" value="0.05"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
678 <param name="add_metainfo" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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679 <param name="add_losses" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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680 <param name="sort_by_position" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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681 <param name="add_precursor_peaks" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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682 <param name="add_all_precursor_charges" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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683 <param name="add_abundant_immonium_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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684 <param name="add_first_prefix_ion" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
685 <param name="add_y_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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686 <param name="add_b_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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687 <param name="add_a_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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688 <param name="add_c_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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689 <param name="add_x_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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690 <param name="add_z_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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691 <param name="y_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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692 <param name="b_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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693 <param name="a_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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694 <param name="c_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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695 <param name="x_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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696 <param name="z_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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697 <param name="relative_loss_intensity" value="0.1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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698 <param name="precursor_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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699 <param name="precursor_H2O_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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700 <param name="precursor_NH3_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
701 <param name="enzyme" value="Trypsin"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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702 <param name="missed_cleavages" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
703 <param name="min_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
704 <param name="max_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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705 <param name="precursor_charge" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
706 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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707 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
708 <output name="ctd_out" ftype="xml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
709 <assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
710 <is_valid_xml/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
711 </assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
712 </output> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
713 </test> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
714 <!-- TOPP_IDFileConverter_11 --> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
715 <test expect_num_outputs="2"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
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716 <section name="adv_opts"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
717 <param name="ignore_proteins_per_peptide" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
718 <param name="scan_regex" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
719 <param name="no_spectra_data_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
720 <param name="no_spectra_references_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
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721 <param name="add_ionmatch_annotation" value="0.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
722 <param name="concatenate_peptides" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
723 <param name="number_of_hits" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
724 <param name="force" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
725 <param name="test" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
726 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
727 <param name="in" value="IDFileConverter_11_input.tsv" ftype="tabular"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
728 <output name="out" file="IDFileConverter_11_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
729 <param name="out_type" value="idXML"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
730 <param name="mz_name" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
731 <param name="peptideprophet_analyzed" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
732 <param name="score_type" value="qvalue"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
733 <section name="fasta_to_mzml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
734 <param name="isotope_model" value="none"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
735 <param name="max_isotope" value="2"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
736 <param name="max_isotope_probability" value="0.05"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
737 <param name="add_metainfo" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
738 <param name="add_losses" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
739 <param name="sort_by_position" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
740 <param name="add_precursor_peaks" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
741 <param name="add_all_precursor_charges" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
742 <param name="add_abundant_immonium_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
743 <param name="add_first_prefix_ion" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
744 <param name="add_y_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
745 <param name="add_b_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
746 <param name="add_a_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
747 <param name="add_c_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
748 <param name="add_x_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
749 <param name="add_z_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
750 <param name="y_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
751 <param name="b_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
752 <param name="a_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
753 <param name="c_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
754 <param name="x_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
755 <param name="z_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
756 <param name="relative_loss_intensity" value="0.1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
757 <param name="precursor_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
758 <param name="precursor_H2O_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
759 <param name="precursor_NH3_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
760 <param name="enzyme" value="Trypsin"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
761 <param name="missed_cleavages" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
762 <param name="min_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
763 <param name="max_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
764 <param name="precursor_charge" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
765 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
766 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
767 <output name="ctd_out" ftype="xml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
768 <assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
769 <is_valid_xml/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
770 </assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
771 </output> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
772 </test> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
773 <!-- TOPP_IDFileConverter_12 --> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
774 <test expect_num_outputs="2"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
775 <section name="adv_opts"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
776 <param name="ignore_proteins_per_peptide" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
777 <param name="scan_regex" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
778 <param name="no_spectra_data_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
779 <param name="no_spectra_references_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
780 <param name="add_ionmatch_annotation" value="0.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
781 <param name="concatenate_peptides" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
782 <param name="number_of_hits" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
783 <param name="force" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
784 <param name="test" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
785 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
786 <param name="in" value="IDFileConverter_12_input.psms"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
787 <output name="out" file="IDFileConverter_12_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
788 <param name="out_type" value="idXML"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
789 <param name="mz_name" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
790 <param name="peptideprophet_analyzed" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
791 <param name="score_type" value="qvalue"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
792 <section name="fasta_to_mzml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
793 <param name="isotope_model" value="none"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
794 <param name="max_isotope" value="2"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
795 <param name="max_isotope_probability" value="0.05"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
796 <param name="add_metainfo" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
797 <param name="add_losses" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
798 <param name="sort_by_position" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
799 <param name="add_precursor_peaks" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
800 <param name="add_all_precursor_charges" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
801 <param name="add_abundant_immonium_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
802 <param name="add_first_prefix_ion" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
803 <param name="add_y_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
804 <param name="add_b_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
805 <param name="add_a_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
806 <param name="add_c_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
807 <param name="add_x_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
808 <param name="add_z_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
809 <param name="y_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
810 <param name="b_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
811 <param name="a_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
812 <param name="c_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
813 <param name="x_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
814 <param name="z_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
815 <param name="relative_loss_intensity" value="0.1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
816 <param name="precursor_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
817 <param name="precursor_H2O_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
818 <param name="precursor_NH3_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
819 <param name="enzyme" value="Trypsin"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
820 <param name="missed_cleavages" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
821 <param name="min_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
822 <param name="max_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
823 <param name="precursor_charge" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
824 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
825 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
826 <output name="ctd_out" ftype="xml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
827 <assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
828 <is_valid_xml/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
829 </assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
830 </output> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
831 </test> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
832 <!-- TOPP_IDFileConverter_13 --> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
833 <test expect_num_outputs="2"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
834 <section name="adv_opts"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
835 <param name="ignore_proteins_per_peptide" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
836 <param name="scan_regex" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
837 <param name="no_spectra_data_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
838 <param name="no_spectra_references_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
839 <param name="add_ionmatch_annotation" value="0.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
840 <param name="concatenate_peptides" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
841 <param name="number_of_hits" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
842 <param name="force" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
843 <param name="test" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
844 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
845 <param name="in" value="IDFileConverter_12_input.psms"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
846 <output name="out" file="IDFileConverter_13_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
847 <param name="out_type" value="idXML"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
848 <param name="mz_name" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
849 <param name="peptideprophet_analyzed" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
850 <param name="score_type" value="PEP"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
851 <section name="fasta_to_mzml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
852 <param name="isotope_model" value="none"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
853 <param name="max_isotope" value="2"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
854 <param name="max_isotope_probability" value="0.05"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
855 <param name="add_metainfo" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
856 <param name="add_losses" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
857 <param name="sort_by_position" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
858 <param name="add_precursor_peaks" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
859 <param name="add_all_precursor_charges" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
860 <param name="add_abundant_immonium_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
861 <param name="add_first_prefix_ion" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
862 <param name="add_y_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
863 <param name="add_b_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
864 <param name="add_a_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
865 <param name="add_c_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
866 <param name="add_x_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
867 <param name="add_z_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
868 <param name="y_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
869 <param name="b_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
870 <param name="a_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
871 <param name="c_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
872 <param name="x_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
873 <param name="z_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
874 <param name="relative_loss_intensity" value="0.1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
875 <param name="precursor_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
876 <param name="precursor_H2O_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
877 <param name="precursor_NH3_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
878 <param name="enzyme" value="Trypsin"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
879 <param name="missed_cleavages" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
880 <param name="min_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
881 <param name="max_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
882 <param name="precursor_charge" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
883 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
884 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
885 <output name="ctd_out" ftype="xml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
886 <assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
887 <is_valid_xml/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
888 </assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
889 </output> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
890 </test> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
891 <!-- TOPP_IDFileConverter_14 --> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
892 <test expect_num_outputs="2"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
893 <section name="adv_opts"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
894 <param name="ignore_proteins_per_peptide" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
895 <param name="scan_regex" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
896 <param name="no_spectra_data_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
897 <param name="no_spectra_references_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
898 <param name="add_ionmatch_annotation" value="0.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
899 <param name="concatenate_peptides" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
900 <param name="number_of_hits" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
901 <param name="force" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
902 <param name="test" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
903 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
904 <param name="in" value="IDFileConverter_12_input.psms"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
905 <output name="out" file="IDFileConverter_14_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
906 <param name="out_type" value="idXML"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
907 <param name="mz_name" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
908 <param name="peptideprophet_analyzed" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
909 <param name="score_type" value="score"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
910 <section name="fasta_to_mzml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
911 <param name="isotope_model" value="none"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
912 <param name="max_isotope" value="2"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
913 <param name="max_isotope_probability" value="0.05"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
914 <param name="add_metainfo" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
915 <param name="add_losses" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
916 <param name="sort_by_position" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
917 <param name="add_precursor_peaks" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
918 <param name="add_all_precursor_charges" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
919 <param name="add_abundant_immonium_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
920 <param name="add_first_prefix_ion" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
921 <param name="add_y_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
922 <param name="add_b_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
923 <param name="add_a_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
924 <param name="add_c_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
925 <param name="add_x_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
926 <param name="add_z_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
927 <param name="y_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
928 <param name="b_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
929 <param name="a_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
930 <param name="c_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
931 <param name="x_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
932 <param name="z_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
933 <param name="relative_loss_intensity" value="0.1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
934 <param name="precursor_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
935 <param name="precursor_H2O_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
936 <param name="precursor_NH3_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
937 <param name="enzyme" value="Trypsin"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
938 <param name="missed_cleavages" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
939 <param name="min_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
940 <param name="max_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
941 <param name="precursor_charge" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
942 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
943 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
944 <output name="ctd_out" ftype="xml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
945 <assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
946 <is_valid_xml/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
947 </assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
948 </output> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
949 </test> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
950 <!-- TOPP_IDFileConverter_15 --> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
951 <test expect_num_outputs="2"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
952 <section name="adv_opts"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
953 <param name="ignore_proteins_per_peptide" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
954 <param name="scan_regex" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
955 <param name="no_spectra_data_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
956 <param name="no_spectra_references_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
957 <param name="add_ionmatch_annotation" value="0.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
958 <param name="concatenate_peptides" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
959 <param name="number_of_hits" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
960 <param name="force" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
961 <param name="test" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
962 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
963 <param name="in" value="MSGFPlusAdapter_1_out.mzid"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
964 <output name="out" file="IDFileConverter_15_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
965 <param name="out_type" value="idXML"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
966 <param name="mz_file" value="spectra.mzML"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
967 <param name="mz_name" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
968 <param name="peptideprophet_analyzed" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
969 <param name="score_type" value="qvalue"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
970 <section name="fasta_to_mzml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
971 <param name="isotope_model" value="none"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
972 <param name="max_isotope" value="2"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
973 <param name="max_isotope_probability" value="0.05"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
974 <param name="add_metainfo" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
975 <param name="add_losses" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
976 <param name="sort_by_position" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
977 <param name="add_precursor_peaks" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
978 <param name="add_all_precursor_charges" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
979 <param name="add_abundant_immonium_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
980 <param name="add_first_prefix_ion" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
981 <param name="add_y_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
982 <param name="add_b_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
983 <param name="add_a_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
984 <param name="add_c_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
985 <param name="add_x_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
986 <param name="add_z_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
987 <param name="y_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
988 <param name="b_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
989 <param name="a_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
990 <param name="c_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
991 <param name="x_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
992 <param name="z_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
993 <param name="relative_loss_intensity" value="0.1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
994 <param name="precursor_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
995 <param name="precursor_H2O_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
996 <param name="precursor_NH3_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
997 <param name="enzyme" value="Trypsin"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
998 <param name="missed_cleavages" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
999 <param name="min_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1000 <param name="max_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1001 <param name="precursor_charge" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents:
13
diff
changeset
|
1002 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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changeset
|
1003 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
1004 <output name="ctd_out" ftype="xml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents:
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changeset
|
1005 <assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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|
1006 <is_valid_xml/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
1007 </assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
1008 </output> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents:
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diff
changeset
|
1009 </test> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
1010 <!-- TOPP_IDFileConverter_16 --> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
1011 <test expect_num_outputs="2"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
1012 <section name="adv_opts"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
1013 <param name="ignore_proteins_per_peptide" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
1014 <param name="scan_regex" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
1015 <param name="no_spectra_data_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
1016 <param name="no_spectra_references_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1017 <param name="add_ionmatch_annotation" value="0.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1018 <param name="concatenate_peptides" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
1019 <param name="number_of_hits" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
1020 <param name="force" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
1021 <param name="test" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
1022 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
1023 <param name="in" value="IDFileConverter_16_input.pepXML"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
1024 <output name="out" file="IDFileConverter_16_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
1025 <param name="out_type" value="idXML"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
1026 <param name="mz_name" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
1027 <param name="peptideprophet_analyzed" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1028 <param name="score_type" value="qvalue"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
1029 <section name="fasta_to_mzml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
1030 <param name="isotope_model" value="none"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
1031 <param name="max_isotope" value="2"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1032 <param name="max_isotope_probability" value="0.05"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1033 <param name="add_metainfo" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
1034 <param name="add_losses" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1035 <param name="sort_by_position" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1036 <param name="add_precursor_peaks" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1037 <param name="add_all_precursor_charges" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1038 <param name="add_abundant_immonium_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1039 <param name="add_first_prefix_ion" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1040 <param name="add_y_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1041 <param name="add_b_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1042 <param name="add_a_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1043 <param name="add_c_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1044 <param name="add_x_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1045 <param name="add_z_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1046 <param name="y_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1047 <param name="b_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1048 <param name="a_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1049 <param name="c_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1050 <param name="x_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1051 <param name="z_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1052 <param name="relative_loss_intensity" value="0.1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1053 <param name="precursor_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1054 <param name="precursor_H2O_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1055 <param name="precursor_NH3_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1056 <param name="enzyme" value="Trypsin"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1057 <param name="missed_cleavages" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1058 <param name="min_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1059 <param name="max_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1060 <param name="precursor_charge" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1061 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1062 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1063 <output name="ctd_out" ftype="xml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1064 <assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1065 <is_valid_xml/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1066 </assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1067 </output> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1068 </test> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1069 <!-- TOPP_IDFileConverter_17 --> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1070 <test expect_num_outputs="2"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1071 <section name="adv_opts"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1072 <param name="ignore_proteins_per_peptide" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1073 <param name="scan_regex" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1074 <param name="no_spectra_data_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1075 <param name="no_spectra_references_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1076 <param name="add_ionmatch_annotation" value="0.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1077 <param name="concatenate_peptides" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1078 <param name="number_of_hits" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1079 <param name="force" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1080 <param name="test" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1081 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1082 <param name="in" value="IDFileConverter_17_input.idXML"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1083 <output name="out" file="IDFileConverter_17_output.pepXML" compare="sim_size" delta_frac="0.7" ftype="pepxml"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1084 <param name="out_type" value="pepXML"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1085 <param name="mz_name" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1086 <param name="peptideprophet_analyzed" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1087 <param name="score_type" value="qvalue"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1088 <section name="fasta_to_mzml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1089 <param name="isotope_model" value="none"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1090 <param name="max_isotope" value="2"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1091 <param name="max_isotope_probability" value="0.05"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1092 <param name="add_metainfo" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1093 <param name="add_losses" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1094 <param name="sort_by_position" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1095 <param name="add_precursor_peaks" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1096 <param name="add_all_precursor_charges" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1097 <param name="add_abundant_immonium_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1098 <param name="add_first_prefix_ion" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1099 <param name="add_y_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1100 <param name="add_b_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1101 <param name="add_a_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1102 <param name="add_c_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1103 <param name="add_x_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1104 <param name="add_z_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1105 <param name="y_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1106 <param name="b_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1107 <param name="a_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1108 <param name="c_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1109 <param name="x_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1110 <param name="z_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1111 <param name="relative_loss_intensity" value="0.1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1112 <param name="precursor_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1113 <param name="precursor_H2O_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1114 <param name="precursor_NH3_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1115 <param name="enzyme" value="Trypsin"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1116 <param name="missed_cleavages" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1117 <param name="min_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1118 <param name="max_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1119 <param name="precursor_charge" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1120 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1121 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1122 <output name="ctd_out" ftype="xml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1123 <assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1124 <is_valid_xml/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1125 </assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1126 </output> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1127 </test> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1128 <!-- TOPP_IDFileConverter_18 --> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1129 <test expect_num_outputs="2"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1130 <section name="adv_opts"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1131 <param name="ignore_proteins_per_peptide" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1132 <param name="scan_regex" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1133 <param name="no_spectra_data_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1134 <param name="no_spectra_references_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1135 <param name="add_ionmatch_annotation" value="0.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1136 <param name="concatenate_peptides" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1137 <param name="number_of_hits" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1138 <param name="force" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1139 <param name="test" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1140 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1141 <param name="in" value="IDFileConverter_18_input.idXML"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1142 <output name="out" file="IDFileConverter_18_output.pepXML" compare="sim_size" delta_frac="0.7" ftype="pepxml"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1143 <param name="out_type" value="pepXML"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1144 <param name="mz_name" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1145 <param name="peptideprophet_analyzed" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1146 <param name="score_type" value="qvalue"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1147 <section name="fasta_to_mzml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1148 <param name="isotope_model" value="none"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1149 <param name="max_isotope" value="2"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1150 <param name="max_isotope_probability" value="0.05"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1151 <param name="add_metainfo" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1152 <param name="add_losses" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1153 <param name="sort_by_position" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1154 <param name="add_precursor_peaks" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1155 <param name="add_all_precursor_charges" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1156 <param name="add_abundant_immonium_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1157 <param name="add_first_prefix_ion" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1158 <param name="add_y_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1159 <param name="add_b_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1160 <param name="add_a_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1161 <param name="add_c_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1162 <param name="add_x_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1163 <param name="add_z_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1164 <param name="y_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1165 <param name="b_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1166 <param name="a_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1167 <param name="c_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1168 <param name="x_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1169 <param name="z_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1170 <param name="relative_loss_intensity" value="0.1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1171 <param name="precursor_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1172 <param name="precursor_H2O_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1173 <param name="precursor_NH3_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1174 <param name="enzyme" value="Trypsin"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1175 <param name="missed_cleavages" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1176 <param name="min_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1177 <param name="max_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1178 <param name="precursor_charge" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1179 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1180 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1181 <output name="ctd_out" ftype="xml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1182 <assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1183 <is_valid_xml/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1184 </assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1185 </output> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1186 </test> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1187 <!-- TOPP_IDFileConverter_19 --> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1188 <test expect_num_outputs="2"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1189 <section name="adv_opts"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1190 <param name="ignore_proteins_per_peptide" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1191 <param name="scan_regex" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1192 <param name="no_spectra_data_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1193 <param name="no_spectra_references_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1194 <param name="add_ionmatch_annotation" value="0.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1195 <param name="concatenate_peptides" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1196 <param name="number_of_hits" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1197 <param name="force" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1198 <param name="test" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1199 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1200 <param name="in" value="IDFileConverter_19_input.idXML"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1201 <output name="out" file="IDFileConverter_19_output.pepXML" compare="sim_size" delta_frac="0.7" ftype="pepxml"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1202 <param name="out_type" value="pepXML"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1203 <param name="mz_name" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1204 <param name="peptideprophet_analyzed" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1205 <param name="score_type" value="qvalue"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1206 <section name="fasta_to_mzml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1207 <param name="isotope_model" value="none"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1208 <param name="max_isotope" value="2"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1209 <param name="max_isotope_probability" value="0.05"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1210 <param name="add_metainfo" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1211 <param name="add_losses" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1212 <param name="sort_by_position" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1213 <param name="add_precursor_peaks" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1214 <param name="add_all_precursor_charges" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1215 <param name="add_abundant_immonium_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1216 <param name="add_first_prefix_ion" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1217 <param name="add_y_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1218 <param name="add_b_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1219 <param name="add_a_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1220 <param name="add_c_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1221 <param name="add_x_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1222 <param name="add_z_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1223 <param name="y_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1224 <param name="b_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1225 <param name="a_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1226 <param name="c_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1227 <param name="x_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1228 <param name="z_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1229 <param name="relative_loss_intensity" value="0.1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1230 <param name="precursor_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1231 <param name="precursor_H2O_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1232 <param name="precursor_NH3_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1233 <param name="enzyme" value="Trypsin"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1234 <param name="missed_cleavages" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1235 <param name="min_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1236 <param name="max_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1237 <param name="precursor_charge" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1238 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1239 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1240 <output name="ctd_out" ftype="xml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1241 <assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1242 <is_valid_xml/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1243 </assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1244 </output> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1245 </test> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1246 <!-- TOPP_IDFileConverter_20 --> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1247 <test expect_num_outputs="2"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1248 <section name="adv_opts"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1249 <param name="ignore_proteins_per_peptide" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1250 <param name="scan_regex" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1251 <param name="no_spectra_data_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1252 <param name="no_spectra_references_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1253 <param name="add_ionmatch_annotation" value="0.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1254 <param name="concatenate_peptides" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1255 <param name="number_of_hits" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1256 <param name="force" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1257 <param name="test" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1258 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1259 <param name="in" value="IDFileConverter_20_input.idXML"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1260 <output name="out" file="IDFileConverter_20_output.pepXML" compare="sim_size" delta_frac="0.7" ftype="pepxml"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1261 <param name="out_type" value="pepXML"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1262 <param name="mz_name" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1263 <param name="peptideprophet_analyzed" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1264 <param name="score_type" value="qvalue"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1265 <section name="fasta_to_mzml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1266 <param name="isotope_model" value="none"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1267 <param name="max_isotope" value="2"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1268 <param name="max_isotope_probability" value="0.05"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1269 <param name="add_metainfo" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1270 <param name="add_losses" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1271 <param name="sort_by_position" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1272 <param name="add_precursor_peaks" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1273 <param name="add_all_precursor_charges" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1274 <param name="add_abundant_immonium_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1275 <param name="add_first_prefix_ion" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1276 <param name="add_y_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1277 <param name="add_b_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1278 <param name="add_a_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1279 <param name="add_c_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1280 <param name="add_x_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1281 <param name="add_z_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1282 <param name="y_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1283 <param name="b_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1284 <param name="a_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1285 <param name="c_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1286 <param name="x_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1287 <param name="z_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1288 <param name="relative_loss_intensity" value="0.1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1289 <param name="precursor_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1290 <param name="precursor_H2O_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1291 <param name="precursor_NH3_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1292 <param name="enzyme" value="Trypsin"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1293 <param name="missed_cleavages" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1294 <param name="min_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1295 <param name="max_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1296 <param name="precursor_charge" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1297 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1298 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1299 <output name="ctd_out" ftype="xml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1300 <assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1301 <is_valid_xml/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1302 </assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1303 </output> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1304 </test> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1305 <!-- TOPP_IDFileConverter_21 --> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1306 <test expect_num_outputs="2"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1307 <section name="adv_opts"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1308 <param name="ignore_proteins_per_peptide" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1309 <param name="scan_regex" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1310 <param name="no_spectra_data_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1311 <param name="no_spectra_references_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1312 <param name="add_ionmatch_annotation" value="0.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1313 <param name="concatenate_peptides" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1314 <param name="number_of_hits" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1315 <param name="force" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1316 <param name="test" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1317 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1318 <param name="in" value="IDFileConverter_21_input.idXML"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1319 <output name="out" file="IDFileConverter_21_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1320 <param name="out_type" value="idXML"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1321 <param name="mz_file" value="IDMapper_4_input.mzML"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
1322 <param name="mz_name" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1323 <param name="peptideprophet_analyzed" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1324 <param name="score_type" value="qvalue"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1325 <section name="fasta_to_mzml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1326 <param name="isotope_model" value="none"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1327 <param name="max_isotope" value="2"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1328 <param name="max_isotope_probability" value="0.05"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1329 <param name="add_metainfo" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1330 <param name="add_losses" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1331 <param name="sort_by_position" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1332 <param name="add_precursor_peaks" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1333 <param name="add_all_precursor_charges" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1334 <param name="add_abundant_immonium_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1335 <param name="add_first_prefix_ion" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1336 <param name="add_y_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1337 <param name="add_b_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1338 <param name="add_a_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1339 <param name="add_c_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1340 <param name="add_x_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1341 <param name="add_z_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1342 <param name="y_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1343 <param name="b_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1344 <param name="a_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1345 <param name="c_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1346 <param name="x_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1347 <param name="z_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1348 <param name="relative_loss_intensity" value="0.1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1349 <param name="precursor_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1350 <param name="precursor_H2O_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1351 <param name="precursor_NH3_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1352 <param name="enzyme" value="Trypsin"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1353 <param name="missed_cleavages" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1354 <param name="min_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1355 <param name="max_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1356 <param name="precursor_charge" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1357 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1358 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1359 <output name="ctd_out" ftype="xml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1360 <assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1361 <is_valid_xml/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1362 </assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1363 </output> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1364 </test> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1365 <!-- TOPP_IDFileConverter_22 --> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1366 <test expect_num_outputs="2"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1367 <section name="adv_opts"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1368 <param name="ignore_proteins_per_peptide" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1369 <param name="scan_regex" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1370 <param name="no_spectra_data_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1371 <param name="no_spectra_references_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1372 <param name="add_ionmatch_annotation" value="0.01"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1373 <param name="concatenate_peptides" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1374 <param name="number_of_hits" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1375 <param name="force" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1376 <param name="test" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1377 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1378 <param name="in" value="MSGFPlusAdapter_1_out.mzid"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1379 <output name="out" file="IDFileConverter_22_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1380 <param name="out_type" value="idXML"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1381 <param name="mz_file" value="spectra.mzML"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1382 <param name="mz_name" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1383 <param name="peptideprophet_analyzed" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1384 <param name="score_type" value="qvalue"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1385 <section name="fasta_to_mzml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1386 <param name="isotope_model" value="none"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1387 <param name="max_isotope" value="2"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1388 <param name="max_isotope_probability" value="0.05"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1389 <param name="add_metainfo" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1390 <param name="add_losses" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1391 <param name="sort_by_position" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1392 <param name="add_precursor_peaks" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1393 <param name="add_all_precursor_charges" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1394 <param name="add_abundant_immonium_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1395 <param name="add_first_prefix_ion" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1396 <param name="add_y_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1397 <param name="add_b_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1398 <param name="add_a_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1399 <param name="add_c_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1400 <param name="add_x_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1401 <param name="add_z_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1402 <param name="y_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1403 <param name="b_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1404 <param name="a_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1405 <param name="c_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1406 <param name="x_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1407 <param name="z_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1408 <param name="relative_loss_intensity" value="0.1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1409 <param name="precursor_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1410 <param name="precursor_H2O_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1411 <param name="precursor_NH3_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1412 <param name="enzyme" value="Trypsin"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1413 <param name="missed_cleavages" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1414 <param name="min_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1415 <param name="max_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1416 <param name="precursor_charge" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1417 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1418 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1419 <output name="ctd_out" ftype="xml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1420 <assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1421 <is_valid_xml/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1422 </assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1423 </output> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1424 </test> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1425 <!-- TOPP_IDFileConverter_23 --> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1426 <test expect_num_outputs="2"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1427 <section name="adv_opts"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1428 <param name="ignore_proteins_per_peptide" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1429 <param name="scan_regex" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1430 <param name="no_spectra_data_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1431 <param name="no_spectra_references_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1432 <param name="add_ionmatch_annotation" value="0.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1433 <param name="concatenate_peptides" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1434 <param name="number_of_hits" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1435 <param name="force" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1436 <param name="test" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1437 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1438 <param name="in" value="IDFileConverter_23_input.mzid"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1439 <output name="out" file="IDFileConverter_23_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1440 <param name="out_type" value="idXML"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1441 <param name="mz_name" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1442 <param name="peptideprophet_analyzed" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1443 <param name="score_type" value="qvalue"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1444 <section name="fasta_to_mzml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1445 <param name="isotope_model" value="none"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1446 <param name="max_isotope" value="2"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1447 <param name="max_isotope_probability" value="0.05"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1448 <param name="add_metainfo" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1449 <param name="add_losses" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1450 <param name="sort_by_position" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1451 <param name="add_precursor_peaks" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1452 <param name="add_all_precursor_charges" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1453 <param name="add_abundant_immonium_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1454 <param name="add_first_prefix_ion" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1455 <param name="add_y_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1456 <param name="add_b_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1457 <param name="add_a_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1458 <param name="add_c_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1459 <param name="add_x_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1460 <param name="add_z_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1461 <param name="y_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1462 <param name="b_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1463 <param name="a_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1464 <param name="c_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1465 <param name="x_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1466 <param name="z_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1467 <param name="relative_loss_intensity" value="0.1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1468 <param name="precursor_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1469 <param name="precursor_H2O_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1470 <param name="precursor_NH3_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1471 <param name="enzyme" value="Trypsin"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1472 <param name="missed_cleavages" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1473 <param name="min_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1474 <param name="max_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1475 <param name="precursor_charge" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1476 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1477 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1478 <output name="ctd_out" ftype="xml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1479 <assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1480 <is_valid_xml/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1481 </assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1482 </output> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1483 </test> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1484 <!-- TOPP_IDFileConverter_24 --> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1485 <test expect_num_outputs="2"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1486 <section name="adv_opts"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1487 <param name="ignore_proteins_per_peptide" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1488 <param name="scan_regex" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1489 <param name="no_spectra_data_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1490 <param name="no_spectra_references_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1491 <param name="add_ionmatch_annotation" value="0.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1492 <param name="concatenate_peptides" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1493 <param name="number_of_hits" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1494 <param name="force" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1495 <param name="test" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1496 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1497 <param name="in" value="IDFileConverter_24_input.pep.xml"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1498 <output name="out" file="IDFileConverter_24_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1499 <param name="out_type" value="idXML"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1500 <param name="mz_name" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1501 <param name="peptideprophet_analyzed" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1502 <param name="score_type" value="qvalue"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1503 <section name="fasta_to_mzml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1504 <param name="isotope_model" value="none"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1505 <param name="max_isotope" value="2"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1506 <param name="max_isotope_probability" value="0.05"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1507 <param name="add_metainfo" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1508 <param name="add_losses" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1509 <param name="sort_by_position" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1510 <param name="add_precursor_peaks" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1511 <param name="add_all_precursor_charges" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1512 <param name="add_abundant_immonium_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1513 <param name="add_first_prefix_ion" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1514 <param name="add_y_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1515 <param name="add_b_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1516 <param name="add_a_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1517 <param name="add_c_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1518 <param name="add_x_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1519 <param name="add_z_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1520 <param name="y_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1521 <param name="b_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1522 <param name="a_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1523 <param name="c_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1524 <param name="x_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1525 <param name="z_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1526 <param name="relative_loss_intensity" value="0.1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1527 <param name="precursor_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1528 <param name="precursor_H2O_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1529 <param name="precursor_NH3_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1530 <param name="enzyme" value="Trypsin"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1531 <param name="missed_cleavages" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1532 <param name="min_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1533 <param name="max_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1534 <param name="precursor_charge" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1535 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1536 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1537 <output name="ctd_out" ftype="xml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1538 <assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1539 <is_valid_xml/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1540 </assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1541 </output> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1542 </test> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1543 <!-- TOPP_IDFileConverter_25 --> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1544 <test expect_num_outputs="2"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1545 <section name="adv_opts"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1546 <param name="ignore_proteins_per_peptide" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1547 <param name="scan_regex" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1548 <param name="no_spectra_data_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1549 <param name="no_spectra_references_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1550 <param name="add_ionmatch_annotation" value="0.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1551 <param name="concatenate_peptides" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1552 <param name="number_of_hits" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1553 <param name="force" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1554 <param name="test" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1555 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1556 <param name="in" value="IDFileConverter_25_input.idXML"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1557 <output name="out" file="IDFileConverter_25_output.pep.xml" compare="sim_size" delta_frac="0.7" ftype="pepxml"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1558 <param name="out_type" value="pepXML"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1559 <param name="mz_name" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1560 <param name="peptideprophet_analyzed" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1561 <param name="score_type" value="qvalue"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1562 <section name="fasta_to_mzml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1563 <param name="isotope_model" value="none"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1564 <param name="max_isotope" value="2"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1565 <param name="max_isotope_probability" value="0.05"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1566 <param name="add_metainfo" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1567 <param name="add_losses" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1568 <param name="sort_by_position" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1569 <param name="add_precursor_peaks" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1570 <param name="add_all_precursor_charges" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1571 <param name="add_abundant_immonium_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1572 <param name="add_first_prefix_ion" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1573 <param name="add_y_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1574 <param name="add_b_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1575 <param name="add_a_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1576 <param name="add_c_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1577 <param name="add_x_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1578 <param name="add_z_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1579 <param name="y_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1580 <param name="b_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1581 <param name="a_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1582 <param name="c_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1583 <param name="x_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1584 <param name="z_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1585 <param name="relative_loss_intensity" value="0.1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1586 <param name="precursor_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1587 <param name="precursor_H2O_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1588 <param name="precursor_NH3_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1589 <param name="enzyme" value="Trypsin"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1590 <param name="missed_cleavages" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1591 <param name="min_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1592 <param name="max_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1593 <param name="precursor_charge" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1594 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1595 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1596 <output name="ctd_out" ftype="xml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1597 <assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1598 <is_valid_xml/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1599 </assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1600 </output> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1601 </test> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1602 <!-- TOPP_IDFileConverter_26 --> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1603 <test expect_num_outputs="2"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1604 <section name="adv_opts"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1605 <param name="ignore_proteins_per_peptide" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1606 <param name="scan_regex" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1607 <param name="no_spectra_data_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1608 <param name="no_spectra_references_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1609 <param name="add_ionmatch_annotation" value="0.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1610 <param name="concatenate_peptides" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1611 <param name="number_of_hits" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1612 <param name="force" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1613 <param name="test" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1614 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1615 <param name="in" value="IDFileConverter_26_input.mzid"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1616 <output name="out" file="IDFileConverter_26_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1617 <param name="out_type" value="idXML"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1618 <param name="mz_name" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1619 <param name="peptideprophet_analyzed" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1620 <param name="score_type" value="qvalue"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1621 <section name="fasta_to_mzml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1622 <param name="isotope_model" value="none"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1623 <param name="max_isotope" value="2"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1624 <param name="max_isotope_probability" value="0.05"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1625 <param name="add_metainfo" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1626 <param name="add_losses" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1627 <param name="sort_by_position" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1628 <param name="add_precursor_peaks" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1629 <param name="add_all_precursor_charges" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1630 <param name="add_abundant_immonium_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1631 <param name="add_first_prefix_ion" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1632 <param name="add_y_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1633 <param name="add_b_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1634 <param name="add_a_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1635 <param name="add_c_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1636 <param name="add_x_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1637 <param name="add_z_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1638 <param name="y_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1639 <param name="b_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1640 <param name="a_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1641 <param name="c_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1642 <param name="x_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1643 <param name="z_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1644 <param name="relative_loss_intensity" value="0.1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1645 <param name="precursor_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1646 <param name="precursor_H2O_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1647 <param name="precursor_NH3_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1648 <param name="enzyme" value="Trypsin"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1649 <param name="missed_cleavages" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1650 <param name="min_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1651 <param name="max_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1652 <param name="precursor_charge" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1653 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1654 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1655 <output name="ctd_out" ftype="xml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1656 <assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1657 <is_valid_xml/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1658 </assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1659 </output> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1660 </test> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1661 <!-- TOPP_IDFileConverter_27 --> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1662 <test expect_num_outputs="2"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1663 <section name="adv_opts"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1664 <param name="ignore_proteins_per_peptide" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1665 <param name="scan_regex" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1666 <param name="no_spectra_data_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1667 <param name="no_spectra_references_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1668 <param name="add_ionmatch_annotation" value="0.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1669 <param name="concatenate_peptides" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1670 <param name="number_of_hits" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1671 <param name="force" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1672 <param name="test" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1673 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1674 <param name="in" value="IDFileConverter_27_input.idXML"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1675 <output name="out" file="IDFileConverter_27_output.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1676 <param name="out_type" value="fasta"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1677 <param name="mz_name" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1678 <param name="peptideprophet_analyzed" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1679 <param name="score_type" value="qvalue"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1680 <section name="fasta_to_mzml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1681 <param name="isotope_model" value="none"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1682 <param name="max_isotope" value="2"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1683 <param name="max_isotope_probability" value="0.05"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1684 <param name="add_metainfo" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1685 <param name="add_losses" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1686 <param name="sort_by_position" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1687 <param name="add_precursor_peaks" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1688 <param name="add_all_precursor_charges" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1689 <param name="add_abundant_immonium_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1690 <param name="add_first_prefix_ion" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1691 <param name="add_y_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1692 <param name="add_b_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1693 <param name="add_a_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1694 <param name="add_c_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1695 <param name="add_x_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1696 <param name="add_z_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1697 <param name="y_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1698 <param name="b_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1699 <param name="a_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1700 <param name="c_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1701 <param name="x_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1702 <param name="z_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1703 <param name="relative_loss_intensity" value="0.1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1704 <param name="precursor_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1705 <param name="precursor_H2O_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1706 <param name="precursor_NH3_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1707 <param name="enzyme" value="Trypsin"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1708 <param name="missed_cleavages" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1709 <param name="min_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1710 <param name="max_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1711 <param name="precursor_charge" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1712 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1713 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1714 <output name="ctd_out" ftype="xml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1715 <assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1716 <is_valid_xml/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1717 </assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1718 </output> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1719 </test> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1720 <!-- TOPP_IDFileConverter_28 --> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1721 <test expect_num_outputs="2"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1722 <section name="adv_opts"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1723 <param name="ignore_proteins_per_peptide" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1724 <param name="scan_regex" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1725 <param name="no_spectra_data_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1726 <param name="no_spectra_references_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1727 <param name="add_ionmatch_annotation" value="0.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1728 <param name="concatenate_peptides" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1729 <param name="number_of_hits" value="-1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1730 <param name="force" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1731 <param name="test" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1732 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1733 <param name="in" value="IDFileConverter_27_input.idXML"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1734 <output name="out" file="IDFileConverter_28_output.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1735 <param name="out_type" value="fasta"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1736 <param name="mz_name" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1737 <param name="peptideprophet_analyzed" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1738 <param name="score_type" value="qvalue"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1739 <section name="fasta_to_mzml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1740 <param name="isotope_model" value="none"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1741 <param name="max_isotope" value="2"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1742 <param name="max_isotope_probability" value="0.05"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1743 <param name="add_metainfo" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1744 <param name="add_losses" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1745 <param name="sort_by_position" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1746 <param name="add_precursor_peaks" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1747 <param name="add_all_precursor_charges" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1748 <param name="add_abundant_immonium_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1749 <param name="add_first_prefix_ion" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1750 <param name="add_y_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1751 <param name="add_b_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1752 <param name="add_a_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1753 <param name="add_c_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1754 <param name="add_x_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1755 <param name="add_z_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1756 <param name="y_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1757 <param name="b_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1758 <param name="a_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1759 <param name="c_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1760 <param name="x_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1761 <param name="z_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1762 <param name="relative_loss_intensity" value="0.1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1763 <param name="precursor_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1764 <param name="precursor_H2O_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1765 <param name="precursor_NH3_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1766 <param name="enzyme" value="Trypsin"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1767 <param name="missed_cleavages" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1768 <param name="min_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1769 <param name="max_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1770 <param name="precursor_charge" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1771 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1772 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1773 <output name="ctd_out" ftype="xml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1774 <assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1775 <is_valid_xml/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1776 </assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1777 </output> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1778 </test> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1779 <!-- TOPP_IDFileConverter_29 --> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1780 <test expect_num_outputs="2"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1781 <section name="adv_opts"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1782 <param name="ignore_proteins_per_peptide" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1783 <param name="scan_regex" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1784 <param name="no_spectra_data_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1785 <param name="no_spectra_references_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1786 <param name="add_ionmatch_annotation" value="0.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1787 <param name="concatenate_peptides" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1788 <param name="number_of_hits" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1789 <param name="force" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1790 <param name="test" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1791 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1792 <param name="in" value="IDFileConverter_27_input.idXML"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1793 <output name="out" file="IDFileConverter_29_output.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1794 <param name="out_type" value="fasta"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1795 <param name="mz_name" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1796 <param name="peptideprophet_analyzed" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1797 <param name="score_type" value="qvalue"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1798 <section name="fasta_to_mzml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1799 <param name="isotope_model" value="none"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1800 <param name="max_isotope" value="2"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1801 <param name="max_isotope_probability" value="0.05"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1802 <param name="add_metainfo" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1803 <param name="add_losses" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1804 <param name="sort_by_position" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1805 <param name="add_precursor_peaks" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1806 <param name="add_all_precursor_charges" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1807 <param name="add_abundant_immonium_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1808 <param name="add_first_prefix_ion" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1809 <param name="add_y_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1810 <param name="add_b_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1811 <param name="add_a_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1812 <param name="add_c_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1813 <param name="add_x_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1814 <param name="add_z_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1815 <param name="y_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1816 <param name="b_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1817 <param name="a_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1818 <param name="c_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1819 <param name="x_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1820 <param name="z_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1821 <param name="relative_loss_intensity" value="0.1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1822 <param name="precursor_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1823 <param name="precursor_H2O_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1824 <param name="precursor_NH3_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1825 <param name="enzyme" value="Trypsin"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1826 <param name="missed_cleavages" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1827 <param name="min_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1828 <param name="max_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1829 <param name="precursor_charge" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1830 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1831 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1832 <output name="ctd_out" ftype="xml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1833 <assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1834 <is_valid_xml/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1835 </assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1836 </output> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1837 </test> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1838 <!-- TOPP_IDFileConverter_30 --> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1839 <test expect_num_outputs="2"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1840 <section name="adv_opts"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1841 <param name="ignore_proteins_per_peptide" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1842 <param name="scan_regex" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1843 <param name="no_spectra_data_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1844 <param name="no_spectra_references_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1845 <param name="add_ionmatch_annotation" value="0.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1846 <param name="concatenate_peptides" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1847 <param name="number_of_hits" value="2"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1848 <param name="force" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1849 <param name="test" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1850 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1851 <param name="in" value="IDFileConverter_27_input.idXML"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1852 <output name="out" file="IDFileConverter_30_output.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1853 <param name="out_type" value="fasta"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1854 <param name="mz_name" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1855 <param name="peptideprophet_analyzed" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1856 <param name="score_type" value="qvalue"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1857 <section name="fasta_to_mzml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1858 <param name="isotope_model" value="none"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1859 <param name="max_isotope" value="2"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
1860 <param name="max_isotope_probability" value="0.05"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1861 <param name="add_metainfo" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1862 <param name="add_losses" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1863 <param name="sort_by_position" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1864 <param name="add_precursor_peaks" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1865 <param name="add_all_precursor_charges" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1866 <param name="add_abundant_immonium_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1867 <param name="add_first_prefix_ion" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1868 <param name="add_y_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1869 <param name="add_b_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1870 <param name="add_a_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1871 <param name="add_c_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1872 <param name="add_x_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1873 <param name="add_z_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1874 <param name="y_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1875 <param name="b_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1876 <param name="a_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1877 <param name="c_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1878 <param name="x_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1879 <param name="z_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1880 <param name="relative_loss_intensity" value="0.1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1881 <param name="precursor_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1882 <param name="precursor_H2O_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1883 <param name="precursor_NH3_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1884 <param name="enzyme" value="Trypsin"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1885 <param name="missed_cleavages" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1886 <param name="min_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1887 <param name="max_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1888 <param name="precursor_charge" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1889 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1890 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1891 <output name="ctd_out" ftype="xml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1892 <assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1893 <is_valid_xml/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1894 </assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1895 </output> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1896 </test> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1897 <!-- TOPP_IDFileConverter_31 --> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1898 <test expect_num_outputs="2"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1899 <section name="adv_opts"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1900 <param name="ignore_proteins_per_peptide" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1901 <param name="scan_regex" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1902 <param name="no_spectra_data_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1903 <param name="no_spectra_references_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1904 <param name="add_ionmatch_annotation" value="0.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1905 <param name="concatenate_peptides" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1906 <param name="number_of_hits" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1907 <param name="force" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1908 <param name="test" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1909 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1910 <param name="in" value="IDFileConverter_31_input.mzid"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1911 <output name="out" file="IDFileConverter_31_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1912 <param name="out_type" value="idXML"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1913 <param name="mz_name" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1914 <param name="peptideprophet_analyzed" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1915 <param name="score_type" value="qvalue"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1916 <section name="fasta_to_mzml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1917 <param name="isotope_model" value="none"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1918 <param name="max_isotope" value="2"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1919 <param name="max_isotope_probability" value="0.05"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1920 <param name="add_metainfo" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1921 <param name="add_losses" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1922 <param name="sort_by_position" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1923 <param name="add_precursor_peaks" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1924 <param name="add_all_precursor_charges" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1925 <param name="add_abundant_immonium_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1926 <param name="add_first_prefix_ion" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1927 <param name="add_y_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1928 <param name="add_b_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1929 <param name="add_a_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1930 <param name="add_c_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1931 <param name="add_x_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1932 <param name="add_z_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1933 <param name="y_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
1934 <param name="b_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
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1935 <param name="a_intensity" value="1.0"/> |
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1936 <param name="c_intensity" value="1.0"/> |
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1937 <param name="x_intensity" value="1.0"/> |
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1938 <param name="z_intensity" value="1.0"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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1939 <param name="relative_loss_intensity" value="0.1"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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1940 <param name="precursor_intensity" value="1.0"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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1941 <param name="precursor_H2O_intensity" value="1.0"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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1942 <param name="precursor_NH3_intensity" value="1.0"/> |
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1943 <param name="enzyme" value="Trypsin"/> |
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1944 <param name="missed_cleavages" value="0"/> |
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1945 <param name="min_charge" value="1"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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1946 <param name="max_charge" value="1"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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1947 <param name="precursor_charge" value="0"/> |
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1948 </section> |
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1949 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
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1950 <output name="ctd_out" ftype="xml"> |
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1951 <assert_contents> |
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1952 <is_valid_xml/> |
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1953 </assert_contents> |
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1954 </output> |
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1955 </test> |
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1956 <!-- TOPP_IDFileConverter_32 --> |
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1957 <test expect_num_outputs="2"> |
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1958 <section name="adv_opts"> |
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1959 <param name="ignore_proteins_per_peptide" value="false"/> |
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1960 <param name="scan_regex" value=""/> |
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1961 <param name="no_spectra_data_override" value="false"/> |
7d0eb300f360
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1962 <param name="no_spectra_references_override" value="false"/> |
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1963 <param name="add_ionmatch_annotation" value="0.0"/> |
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1964 <param name="concatenate_peptides" value="false"/> |
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1965 <param name="number_of_hits" value="1"/> |
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1966 <param name="force" value="false"/> |
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1967 <param name="test" value="true"/> |
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1968 </section> |
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1969 <param name="in" value="IDFileConverter_32_input.FASTA"/> |
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1970 <output name="out" file="IDFileConverter_32_output.tmp" compare="sim_size" delta_frac="0.7"/> |
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1971 <param name="out_type" value="mzML"/> |
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1972 <param name="mz_name" value=""/> |
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1973 <param name="peptideprophet_analyzed" value="false"/> |
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1974 <param name="score_type" value="qvalue"/> |
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1975 <section name="fasta_to_mzml"> |
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1976 <param name="isotope_model" value="none"/> |
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1977 <param name="max_isotope" value="2"/> |
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1978 <param name="max_isotope_probability" value="0.05"/> |
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1979 <param name="add_metainfo" value="false"/> |
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1980 <param name="add_losses" value="false"/> |
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1981 <param name="sort_by_position" value="true"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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1982 <param name="add_precursor_peaks" value="false"/> |
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1983 <param name="add_all_precursor_charges" value="false"/> |
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1984 <param name="add_abundant_immonium_ions" value="false"/> |
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1985 <param name="add_first_prefix_ion" value="false"/> |
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1986 <param name="add_y_ions" value="true"/> |
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1987 <param name="add_b_ions" value="true"/> |
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1988 <param name="add_a_ions" value="false"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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1989 <param name="add_c_ions" value="false"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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1990 <param name="add_x_ions" value="false"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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1991 <param name="add_z_ions" value="false"/> |
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1992 <param name="y_intensity" value="1.0"/> |
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1993 <param name="b_intensity" value="1.0"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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1994 <param name="a_intensity" value="1.0"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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1995 <param name="c_intensity" value="1.0"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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1996 <param name="x_intensity" value="1.0"/> |
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1997 <param name="z_intensity" value="1.0"/> |
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1998 <param name="relative_loss_intensity" value="0.1"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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1999 <param name="precursor_intensity" value="1.0"/> |
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galaxyp
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2000 <param name="precursor_H2O_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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2001 <param name="precursor_NH3_intensity" value="1.0"/> |
7d0eb300f360
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galaxyp
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changeset
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2002 <param name="enzyme" value="Trypsin"/> |
7d0eb300f360
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galaxyp
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changeset
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2003 <param name="missed_cleavages" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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changeset
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2004 <param name="min_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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changeset
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2005 <param name="max_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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changeset
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2006 <param name="precursor_charge" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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changeset
|
2007 </section> |
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galaxyp
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changeset
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2008 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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changeset
|
2009 <output name="ctd_out" ftype="xml"> |
7d0eb300f360
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changeset
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2010 <assert_contents> |
7d0eb300f360
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2011 <is_valid_xml/> |
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galaxyp
parents:
13
diff
changeset
|
2012 </assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2013 </output> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2014 </test> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2015 <!-- TOPP_IDFileConverter_33 --> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2016 <test expect_num_outputs="2"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2017 <section name="adv_opts"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2018 <param name="ignore_proteins_per_peptide" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2019 <param name="scan_regex" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2020 <param name="no_spectra_data_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2021 <param name="no_spectra_references_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2022 <param name="add_ionmatch_annotation" value="0.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2023 <param name="concatenate_peptides" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2024 <param name="number_of_hits" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2025 <param name="force" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2026 <param name="test" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2027 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2028 <param name="in" value="IDFileConverter_32_input.FASTA"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2029 <output name="out" file="IDFileConverter_33_output.tmp" compare="sim_size" delta_frac="0.7"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2030 <param name="out_type" value="mzML"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2031 <param name="mz_name" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2032 <param name="peptideprophet_analyzed" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2033 <param name="score_type" value="qvalue"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2034 <section name="fasta_to_mzml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2035 <param name="isotope_model" value="none"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2036 <param name="max_isotope" value="2"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2037 <param name="max_isotope_probability" value="0.05"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2038 <param name="add_metainfo" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2039 <param name="add_losses" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2040 <param name="sort_by_position" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2041 <param name="add_precursor_peaks" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2042 <param name="add_all_precursor_charges" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2043 <param name="add_abundant_immonium_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2044 <param name="add_first_prefix_ion" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2045 <param name="add_y_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2046 <param name="add_b_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2047 <param name="add_a_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2048 <param name="add_c_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2049 <param name="add_x_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2050 <param name="add_z_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2051 <param name="y_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2052 <param name="b_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2053 <param name="a_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2054 <param name="c_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2055 <param name="x_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2056 <param name="z_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2057 <param name="relative_loss_intensity" value="0.1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2058 <param name="precursor_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2059 <param name="precursor_H2O_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2060 <param name="precursor_NH3_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2061 <param name="enzyme" value="Trypsin"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2062 <param name="missed_cleavages" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2063 <param name="min_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2064 <param name="max_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2065 <param name="precursor_charge" value="3"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2066 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2067 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2068 <output name="ctd_out" ftype="xml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2069 <assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2070 <is_valid_xml/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2071 </assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2072 </output> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2073 </test> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2074 <!-- TOPP_IDFileConverter_34_1 --> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2075 <test expect_num_outputs="2"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2076 <section name="adv_opts"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2077 <param name="ignore_proteins_per_peptide" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2078 <param name="scan_regex" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2079 <param name="no_spectra_data_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2080 <param name="no_spectra_references_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2081 <param name="add_ionmatch_annotation" value="0.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2082 <param name="concatenate_peptides" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2083 <param name="number_of_hits" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2084 <param name="force" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2085 <param name="test" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2086 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
changeset
|
2087 <param name="in" value="IDFileConverter_34_input.idXML"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2088 <output name="out" file="IDFileConverter_34_output1.oms" compare="sim_size" delta_frac="0.7" ftype="sqlite"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2089 <param name="out_type" value="oms"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2090 <param name="mz_name" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2091 <param name="peptideprophet_analyzed" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2092 <param name="score_type" value="qvalue"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2093 <section name="fasta_to_mzml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2094 <param name="isotope_model" value="none"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2095 <param name="max_isotope" value="2"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2096 <param name="max_isotope_probability" value="0.05"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2097 <param name="add_metainfo" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2098 <param name="add_losses" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2099 <param name="sort_by_position" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2100 <param name="add_precursor_peaks" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2101 <param name="add_all_precursor_charges" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2102 <param name="add_abundant_immonium_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2103 <param name="add_first_prefix_ion" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2104 <param name="add_y_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2105 <param name="add_b_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2106 <param name="add_a_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2107 <param name="add_c_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2108 <param name="add_x_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2109 <param name="add_z_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2110 <param name="y_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2111 <param name="b_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2112 <param name="a_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2113 <param name="c_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2114 <param name="x_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2115 <param name="z_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2116 <param name="relative_loss_intensity" value="0.1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2117 <param name="precursor_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2118 <param name="precursor_H2O_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2119 <param name="precursor_NH3_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2120 <param name="enzyme" value="Trypsin"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2121 <param name="missed_cleavages" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2122 <param name="min_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2123 <param name="max_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2124 <param name="precursor_charge" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2125 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2126 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2127 <output name="ctd_out" ftype="xml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2128 <assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2129 <is_valid_xml/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2130 </assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2131 </output> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2132 </test> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2133 <!-- TOPP_IDFileConverter_34_2 --> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2134 <test expect_num_outputs="2"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2135 <section name="adv_opts"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2136 <param name="ignore_proteins_per_peptide" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2137 <param name="scan_regex" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2138 <param name="no_spectra_data_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2139 <param name="no_spectra_references_override" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2140 <param name="add_ionmatch_annotation" value="0.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2141 <param name="concatenate_peptides" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2142 <param name="number_of_hits" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2143 <param name="force" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2144 <param name="test" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2145 </section> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2146 <param name="in" value="IDFileConverter_34_output1.oms"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2147 <output name="out" file="IDFileConverter_34_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2148 <param name="out_type" value="idXML"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2149 <param name="mz_name" value=""/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2150 <param name="peptideprophet_analyzed" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2151 <param name="score_type" value="qvalue"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2152 <section name="fasta_to_mzml"> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2153 <param name="isotope_model" value="none"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2154 <param name="max_isotope" value="2"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2155 <param name="max_isotope_probability" value="0.05"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2156 <param name="add_metainfo" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2157 <param name="add_losses" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2158 <param name="sort_by_position" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2159 <param name="add_precursor_peaks" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2160 <param name="add_all_precursor_charges" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
2161 <param name="add_abundant_immonium_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
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2162 <param name="add_first_prefix_ion" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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|
2163 <param name="add_y_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff
changeset
|
2164 <param name="add_b_ions" value="true"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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|
2165 <param name="add_a_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff
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|
2166 <param name="add_c_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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|
2167 <param name="add_x_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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diff
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|
2168 <param name="add_z_ions" value="false"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff
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|
2169 <param name="y_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
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|
2170 <param name="b_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
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|
2171 <param name="a_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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13
diff
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|
2172 <param name="c_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
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|
2173 <param name="x_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff
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2174 <param name="z_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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|
2175 <param name="relative_loss_intensity" value="0.1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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|
2176 <param name="precursor_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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2177 <param name="precursor_H2O_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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2178 <param name="precursor_NH3_intensity" value="1.0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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2179 <param name="enzyme" value="Trypsin"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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2180 <param name="missed_cleavages" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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2181 <param name="min_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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2182 <param name="max_charge" value="1"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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2183 <param name="precursor_charge" value="0"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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2184 </section> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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2185 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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2186 <output name="ctd_out" ftype="xml"> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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2187 <assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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2188 <is_valid_xml/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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2189 </assert_contents> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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2190 </output> |
7d0eb300f360
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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2191 </test> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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2192 </tests> |
43a1db77b7a6
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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2193 <help><![CDATA[Converts identification engine file formats. |
0
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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2194 |
bea4646ed591
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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2195 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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2196 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_IDFileConverter.html]]></help> |
11
43a1db77b7a6
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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2197 <expand macro="references"/> |
0
bea4646ed591
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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2198 </tool> |