Mercurial > repos > galaxyp > openms_epifany
annotate Epifany.xml @ 4:f3096a586de8 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 19:13:55 +0000 |
parents | 16cdef222ea2 |
children | e8c52c1d6f98 |
rev | line source |
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0
03e13b23a78b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
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1 <?xml version='1.0' encoding='UTF-8'?> |
03e13b23a78b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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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.--> |
03e13b23a78b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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3 <!--Proposed Tool Section: [Utilities]--> |
4
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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4 <tool id="Epifany" name="Epifany" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> |
0
03e13b23a78b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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5 <description>Runs a Bayesian protein inference.</description> |
03e13b23a78b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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6 <macros> |
03e13b23a78b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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7 <token name="@EXECUTABLE@">Epifany</token> |
03e13b23a78b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
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8 <import>macros.xml</import> |
03e13b23a78b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
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9 </macros> |
03e13b23a78b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
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10 <expand macro="requirements"/> |
03e13b23a78b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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11 <expand macro="stdio"/> |
03e13b23a78b
"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@ |
03e13b23a78b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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13 @EXT_FOO@ |
03e13b23a78b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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14 #import re |
03e13b23a78b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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15 |
03e13b23a78b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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16 ## Preprocessing |
4
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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17 mkdir in_cond.in && |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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18 #if $in_cond.in_select == "no" |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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19 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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20 ${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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21 #else |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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22 ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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23 #end if |
2
16cdef222ea2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
galaxyp
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24 #if $exp_design: |
16cdef222ea2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
galaxyp
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25 mkdir exp_design && |
16cdef222ea2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
galaxyp
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26 ln -s '$exp_design' 'exp_design/${re.sub("[^\w\-_]", "_", $exp_design.element_identifier)}.$gxy2omsext($exp_design.ext)' && |
16cdef222ea2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
galaxyp
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27 #end if |
0
03e13b23a78b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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28 mkdir out && |
03e13b23a78b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
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29 |
03e13b23a78b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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30 ## Main program call |
03e13b23a78b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
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31 |
03e13b23a78b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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32 set -o pipefail && |
03e13b23a78b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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33 @EXECUTABLE@ -write_ctd ./ && |
03e13b23a78b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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34 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && |
03e13b23a78b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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35 @EXECUTABLE@ -ini @EXECUTABLE@.ctd |
03e13b23a78b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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36 -in |
4
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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37 #if $in_cond.in_select == "no" |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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38 ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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39 #else |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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40 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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41 #end if |
2
16cdef222ea2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
galaxyp
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42 #if $exp_design: |
16cdef222ea2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
galaxyp
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43 -exp_design |
16cdef222ea2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
galaxyp
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44 'exp_design/${re.sub("[^\w\-_]", "_", $exp_design.element_identifier)}.$gxy2omsext($exp_design.ext)' |
16cdef222ea2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
galaxyp
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45 #end if |
0
03e13b23a78b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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46 -out |
2
16cdef222ea2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
galaxyp
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47 'out/output.${out_type}' |
0
03e13b23a78b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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48 |
03e13b23a78b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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49 ## Postprocessing |
2
16cdef222ea2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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50 && mv 'out/output.${out_type}' '$out' |
0
03e13b23a78b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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51 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS |
03e13b23a78b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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52 && mv '@EXECUTABLE@.ctd' '$ctd_out' |
03e13b23a78b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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53 #end if]]></command> |
03e13b23a78b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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54 <configfiles> |
03e13b23a78b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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55 <inputs name="args_json" data_style="paths"/> |
03e13b23a78b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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56 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
03e13b23a78b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
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57 </configfiles> |
03e13b23a78b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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58 <inputs> |
4
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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59 <conditional name="in_cond"> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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60 <param name="in_select" type="select" label="Run tool in batch mode for -in"> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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61 <option value="no">No: process all datasets jointly</option> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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62 <option value="yes">Yes: process each dataset in an independent job</option> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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63 </param> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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64 <when value="no"> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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65 <param argument="-in" type="data" format="consensusxml,idxml" multiple="true" optional="false" label="Input: identification results" help=" select consensusxml,idxml data sets(s)"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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66 </when> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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67 <when value="yes"> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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68 <param argument="-in" type="data" format="consensusxml,idxml" multiple="false" optional="false" label="Input: identification results" help=" select consensusxml,idxml data sets(s)"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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69 </when> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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70 </conditional> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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71 <param argument="-exp_design" type="data" format="tabular" optional="true" label="(Currently unused) Input: experimental design" help=" select tabular data sets(s)"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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72 <param argument="-out_type" display="radio" type="select" optional="false" label="Output type: auto detected by file extension but can be overwritten here" help=""> |
2
16cdef222ea2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
galaxyp
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73 <option value="consensusXML">consensusxml</option> |
16cdef222ea2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
galaxyp
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74 <option value="idXML">idxml</option> |
4
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75 <expand macro="list_string_san" name="out_type"/> |
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76 </param> |
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77 <param argument="-protein_fdr" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Additionally calculate the target-decoy FDR on protein-level based on the posteriors" help=""/> |
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78 <param argument="-greedy_group_resolution" type="select" optional="true" label="Post-process inference output with greedy resolution of shared peptides based on the parent protein probabilities" help="Also adds the resolved ambiguity groups to output"> |
0
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79 <option value="none" selected="true">none</option> |
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80 <option value="remove_associations_only">remove_associations_only</option> |
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81 <option value="remove_proteins_wo_evidence">remove_proteins_wo_evidence</option> |
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82 <expand macro="list_string_san" name="greedy_group_resolution"/> |
0
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83 </param> |
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84 <param argument="-max_psms_extreme_probability" type="float" optional="true" value="1.0" label="Set PSMs with probability higher than this to this maximum probability" help=""/> |
0
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85 <section name="algorithm" title="Parameters for the Algorithm section" help="" expanded="false"> |
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86 <param name="psm_probability_cutoff" argument="-algorithm:psm_probability_cutoff" type="float" optional="true" min="0.0" max="1.0" value="0.001" label="Remove PSMs with probabilities less than this cutoff" help=""/> |
0
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87 <param name="top_PSMs" argument="-algorithm:top_PSMs" type="integer" optional="true" min="0" value="1" label="Consider only top X PSMs per spectrum" help="0 considers all"/> |
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88 <param name="keep_best_PSM_only" argument="-algorithm:keep_best_PSM_only" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Epifany uses the best PSM per peptide for inference" help="Discard the rest (true) or keepe.g. for quantification/reporting?"/> |
0
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89 <param name="update_PSM_probabilities" argument="-algorithm:update_PSM_probabilities" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(Experimental:) Update PSM probabilities with their posteriors under consideration of the protein probabilities" help=""/> |
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90 <param name="user_defined_priors" argument="-algorithm:user_defined_priors" type="boolean" truevalue="true" falsevalue="false" checked="false" label="(Experimental:) Uses the current protein scores as user-defined priors" help=""/> |
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91 <param name="annotate_group_probabilities" argument="-algorithm:annotate_group_probabilities" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Annotates group probabilities for indistinguishable protein groups (indistinguishable by experimentally observed PSMs)" help=""/> |
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92 <param name="use_ids_outside_features" argument="-algorithm:use_ids_outside_features" type="boolean" truevalue="true" falsevalue="false" checked="false" label="(Only consensusXML) Also use IDs without associated features for inference?" help=""/> |
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93 <section name="model_parameters" title="Model parameters for the Bayesian network" help="" expanded="false"> |
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94 <param name="prot_prior" argument="-algorithm:model_parameters:prot_prior" type="float" optional="true" min="-1.0" max="1.0" value="-1.0" label="Protein prior probability ('gamma' parameter)" help="Negative values enable grid search for this param"/> |
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95 <param name="pep_emission" argument="-algorithm:model_parameters:pep_emission" type="float" optional="true" min="-1.0" max="1.0" value="-1.0" label="Peptide emission probability ('alpha' parameter)" help="Negative values enable grid search for this param"/> |
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96 <param name="pep_spurious_emission" argument="-algorithm:model_parameters:pep_spurious_emission" type="float" optional="true" min="-1.0" max="1.0" value="-1.0" label="Spurious peptide identification probability ('beta' parameter)" help="Usually much smaller than emission from proteins. Negative values enable grid search for this param"/> |
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97 <param name="pep_prior" argument="-algorithm:model_parameters:pep_prior" type="float" optional="true" min="0.0" max="1.0" value="0.1" label="Peptide prior probability (experimental, should be covered by combinations of the other params)" help=""/> |
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98 <param name="regularize" argument="-algorithm:model_parameters:regularize" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Regularize the number of proteins that produce a peptide together (experimental, should be activated when using higher p-norms)" help=""/> |
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99 <param name="extended_model" argument="-algorithm:model_parameters:extended_model" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Uses information from different peptidoforms also across runs (automatically activated if an experimental design is given!)" help=""/> |
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100 </section> |
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101 <section name="loopy_belief_propagation" title="Settings for the loopy belief propagation algorithm" help="" expanded="false"> |
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102 <param name="scheduling_type" argument="-algorithm:loopy_belief_propagation:scheduling_type" type="select" optional="true" label="(Not used yet) How to pick the next message: priority = based on difference to last message (higher = more important)" help="fifo = first in first out. subtree = message passing follows a random spanning tree in each iteration"> |
0
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103 <option value="priority" selected="true">priority</option> |
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104 <option value="fifo">fifo</option> |
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105 <option value="subtree">subtree</option> |
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106 <expand macro="list_string_san" name="scheduling_type"/> |
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107 </param> |
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108 <param name="convergence_threshold" argument="-algorithm:loopy_belief_propagation:convergence_threshold" type="float" optional="true" min="0.0" max="1.0" value="1e-05" label="Initial threshold under which MSE difference a message is considered to be converged" help=""/> |
0
03e13b23a78b
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109 <param name="dampening_lambda" argument="-algorithm:loopy_belief_propagation:dampening_lambda" type="float" optional="true" min="0.0" max="0.49999" value="0.001" label="Initial value for how strongly should messages be updated in each step" help="0 = new message overwrites old completely (no dampening; only recommended for trees),0.5 = equal contribution of old and new message (stay below that),In-between it will be a convex combination of both. Prevents oscillations but hinders convergence"/> |
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110 <param name="max_nr_iterations" argument="-algorithm:loopy_belief_propagation:max_nr_iterations" type="integer" optional="true" value="2147483647" label="(Usually auto-determined by estimated but you can set a hard limit here)" help="If not all messages converge, how many iterations should be done at max per connected component?"/> |
0
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111 <param name="p_norm_inference" argument="-algorithm:loopy_belief_propagation:p_norm_inference" type="float" optional="true" value="1.0" label="P-norm used for marginalization of multidimensional factors" help="1 == sum-product inference (all configurations vote equally) (default),<= 0 == infinity = max-product inference (only best configurations propagate)The higher the value the more important high probability configurations get"/> |
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112 </section> |
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113 <section name="param_optimize" title="Settings for the parameter optimization" help="" expanded="false"> |
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114 <param name="aucweight" argument="-algorithm:param_optimize:aucweight" type="float" optional="true" min="0.0" max="1.0" value="0.3" label="How important is target decoy AUC vs calibration of the posteriors" help="0 = maximize calibration only, 1 = maximize AUC only, between = convex combination"/> |
0
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115 <param name="conservative_fdr" argument="-algorithm:param_optimize:conservative_fdr" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use (D+1)/(T) instead of (D+1)/(T+D) for parameter estimation" help=""/> |
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116 <param name="regularized_fdr" argument="-algorithm:param_optimize:regularized_fdr" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use a regularized FDR for proteins without unique peptides" help=""/> |
0
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117 </section> |
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118 </section> |
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119 <expand macro="adv_opts_macro"> |
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120 <param argument="-conservative_fdr" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use (D+1)/(T) instead of (D+1)/(T+D) for reporting protein FDRs" help=""/> |
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121 <param argument="-picked_fdr" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use picked protein FDRs" help=""/> |
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122 <param argument="-picked_decoy_string" type="text" optional="true" value="" label="If using picked protein FDRs, which decoy string was used" help="Leave blank for auto-detection"> |
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123 <expand macro="list_string_san" name="picked_decoy_string"/> |
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124 </param> |
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125 <param argument="-picked_decoy_prefix" type="select" optional="true" label="If using picked protein FDRs, was the decoy string a prefix or suffix" help="Ignored during auto-detection"> |
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126 <option value="prefix" selected="true">prefix</option> |
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127 <option value="suffix">suffix</option> |
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128 <expand macro="list_string_san" name="picked_decoy_prefix"/> |
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129 </param> |
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130 <param argument="-min_psms_extreme_probability" type="float" optional="true" value="0.0" label="Set PSMs with probability lower than this to this minimum probability" help=""/> |
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131 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> |
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132 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> |
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133 <expand macro="list_string_san" name="test"/> |
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134 </param> |
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135 </expand> |
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136 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> |
0
03e13b23a78b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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137 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> |
03e13b23a78b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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138 </param> |
03e13b23a78b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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139 </inputs> |
03e13b23a78b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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140 <outputs> |
4
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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141 <data name="out" label="${tool.name} on ${on_string}: out" format="consensusxml"> |
2
16cdef222ea2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
galaxyp
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142 <change_format> |
16cdef222ea2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
galaxyp
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143 <when input="out_type" value="idXML" format="idxml"/> |
16cdef222ea2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
galaxyp
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144 </change_format> |
16cdef222ea2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
galaxyp
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145 </data> |
0
03e13b23a78b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
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146 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> |
03e13b23a78b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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147 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> |
03e13b23a78b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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148 </data> |
03e13b23a78b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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149 </outputs> |
4
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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150 <tests><!-- UTILS_Epifany_1 --> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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151 <test expect_num_outputs="2"> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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152 <section name="adv_opts"> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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153 <param name="conservative_fdr" value="true"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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154 <param name="picked_fdr" value="true"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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155 <param name="picked_decoy_string" value=""/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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156 <param name="picked_decoy_prefix" value="prefix"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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157 <param name="min_psms_extreme_probability" value="0.0"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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158 <param name="force" value="false"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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159 <param name="test" value="true"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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160 </section> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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161 <conditional name="in_cond"> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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162 <param name="in" value="FidoAdapter_1_input.idXML"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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163 </conditional> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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164 <output name="out" file="Epifany_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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165 <param name="out_type" value="idXML"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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166 <param name="protein_fdr" value="false"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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167 <param name="greedy_group_resolution" value="none"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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168 <param name="max_psms_extreme_probability" value="1.0"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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169 <section name="algorithm"> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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170 <param name="psm_probability_cutoff" value="0.001"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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171 <param name="top_PSMs" value="1"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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172 <param name="keep_best_PSM_only" value="true"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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173 <param name="update_PSM_probabilities" value="true"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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174 <param name="user_defined_priors" value="false"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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175 <param name="annotate_group_probabilities" value="true"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
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176 <param name="use_ids_outside_features" value="false"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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177 <section name="model_parameters"> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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178 <param name="prot_prior" value="0.7"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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179 <param name="pep_emission" value="0.1"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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180 <param name="pep_spurious_emission" value="0.001"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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181 <param name="pep_prior" value="0.1"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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182 <param name="regularize" value="false"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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183 <param name="extended_model" value="false"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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184 </section> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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185 <section name="loopy_belief_propagation"> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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186 <param name="scheduling_type" value="priority"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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187 <param name="convergence_threshold" value="1e-05"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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188 <param name="dampening_lambda" value="0.001"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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189 <param name="max_nr_iterations" value="2147483647"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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190 <param name="p_norm_inference" value="1.0"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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191 </section> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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192 <section name="param_optimize"> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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193 <param name="aucweight" value="0.3"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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194 <param name="conservative_fdr" value="true"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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195 <param name="regularized_fdr" value="true"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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196 </section> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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197 </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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198 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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199 <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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200 <assert_contents> |
f3096a586de8
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201 <is_valid_xml/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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202 </assert_contents> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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203 </output> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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204 </test> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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205 <!-- UTILS_Epifany_2 --> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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206 <test expect_num_outputs="2"> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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207 <section name="adv_opts"> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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208 <param name="conservative_fdr" value="true"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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209 <param name="picked_fdr" value="true"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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210 <param name="picked_decoy_string" value=""/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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211 <param name="picked_decoy_prefix" value="prefix"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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212 <param name="min_psms_extreme_probability" value="0.0"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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213 <param name="force" value="false"/> |
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214 <param name="test" value="true"/> |
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215 </section> |
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216 <conditional name="in_cond"> |
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217 <param name="in" value="Epifany_2_input.consensusXML"/> |
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218 </conditional> |
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219 <output name="out" file="Epifany_2_out.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> |
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220 <param name="out_type" value="consensusXML"/> |
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221 <param name="protein_fdr" value="false"/> |
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222 <param name="greedy_group_resolution" value="none"/> |
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223 <param name="max_psms_extreme_probability" value="1.0"/> |
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224 <section name="algorithm"> |
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225 <param name="psm_probability_cutoff" value="0.001"/> |
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226 <param name="top_PSMs" value="1"/> |
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227 <param name="keep_best_PSM_only" value="true"/> |
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228 <param name="update_PSM_probabilities" value="true"/> |
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229 <param name="user_defined_priors" value="false"/> |
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230 <param name="annotate_group_probabilities" value="true"/> |
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231 <param name="use_ids_outside_features" value="false"/> |
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232 <section name="model_parameters"> |
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233 <param name="prot_prior" value="0.7"/> |
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234 <param name="pep_emission" value="0.1"/> |
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235 <param name="pep_spurious_emission" value="0.001"/> |
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236 <param name="pep_prior" value="0.1"/> |
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237 <param name="regularize" value="false"/> |
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238 <param name="extended_model" value="false"/> |
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239 </section> |
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240 <section name="loopy_belief_propagation"> |
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241 <param name="scheduling_type" value="priority"/> |
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242 <param name="convergence_threshold" value="1e-05"/> |
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243 <param name="dampening_lambda" value="0.001"/> |
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244 <param name="max_nr_iterations" value="2147483647"/> |
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245 <param name="p_norm_inference" value="1.0"/> |
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246 </section> |
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247 <section name="param_optimize"> |
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248 <param name="aucweight" value="0.3"/> |
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249 <param name="conservative_fdr" value="true"/> |
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250 <param name="regularized_fdr" value="true"/> |
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251 </section> |
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252 </section> |
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253 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
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254 <output name="ctd_out" ftype="xml"> |
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255 <assert_contents> |
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256 <is_valid_xml/> |
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257 </assert_contents> |
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258 </output> |
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259 </test> |
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260 <!-- UTILS_Epifany_3 --> |
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261 <test expect_num_outputs="2"> |
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262 <section name="adv_opts"> |
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263 <param name="conservative_fdr" value="true"/> |
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264 <param name="picked_fdr" value="true"/> |
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265 <param name="picked_decoy_string" value=""/> |
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266 <param name="picked_decoy_prefix" value="prefix"/> |
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267 <param name="min_psms_extreme_probability" value="0.0"/> |
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268 <param name="force" value="false"/> |
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269 <param name="test" value="true"/> |
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270 </section> |
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271 <conditional name="in_cond"> |
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272 <param name="in" value="Epifany_2_input.consensusXML"/> |
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273 </conditional> |
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274 <output name="out" file="Epifany_3_out.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> |
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275 <param name="out_type" value="consensusXML"/> |
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276 <param name="protein_fdr" value="false"/> |
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277 <param name="greedy_group_resolution" value="none"/> |
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278 <param name="max_psms_extreme_probability" value="1.0"/> |
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279 <section name="algorithm"> |
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280 <param name="psm_probability_cutoff" value="0.001"/> |
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281 <param name="top_PSMs" value="1"/> |
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282 <param name="keep_best_PSM_only" value="false"/> |
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283 <param name="update_PSM_probabilities" value="true"/> |
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284 <param name="user_defined_priors" value="false"/> |
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285 <param name="annotate_group_probabilities" value="true"/> |
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286 <param name="use_ids_outside_features" value="false"/> |
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287 <section name="model_parameters"> |
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288 <param name="prot_prior" value="0.7"/> |
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289 <param name="pep_emission" value="0.1"/> |
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290 <param name="pep_spurious_emission" value="0.001"/> |
f3096a586de8
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291 <param name="pep_prior" value="0.1"/> |
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292 <param name="regularize" value="false"/> |
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293 <param name="extended_model" value="false"/> |
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294 </section> |
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295 <section name="loopy_belief_propagation"> |
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296 <param name="scheduling_type" value="priority"/> |
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297 <param name="convergence_threshold" value="1e-05"/> |
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298 <param name="dampening_lambda" value="0.001"/> |
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299 <param name="max_nr_iterations" value="2147483647"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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300 <param name="p_norm_inference" value="1.0"/> |
f3096a586de8
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301 </section> |
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302 <section name="param_optimize"> |
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303 <param name="aucweight" value="0.3"/> |
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304 <param name="conservative_fdr" value="true"/> |
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305 <param name="regularized_fdr" value="true"/> |
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306 </section> |
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307 </section> |
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308 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
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309 <output name="ctd_out" ftype="xml"> |
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310 <assert_contents> |
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311 <is_valid_xml/> |
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312 </assert_contents> |
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313 </output> |
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314 </test> |
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315 <!-- UTILS_Epifany_4 --> |
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316 <test expect_num_outputs="2"> |
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317 <section name="adv_opts"> |
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318 <param name="conservative_fdr" value="true"/> |
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319 <param name="picked_fdr" value="true"/> |
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320 <param name="picked_decoy_string" value=""/> |
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321 <param name="picked_decoy_prefix" value="prefix"/> |
f3096a586de8
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322 <param name="min_psms_extreme_probability" value="0.0"/> |
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323 <param name="force" value="false"/> |
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324 <param name="test" value="true"/> |
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325 </section> |
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326 <conditional name="in_cond"> |
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327 <param name="in" value="FidoAdapter_1_input_singlerun.idXML"/> |
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328 </conditional> |
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329 <output name="out" file="Epifany_4_out_singlerun.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> |
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330 <param name="out_type" value="idXML"/> |
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331 <param name="protein_fdr" value="false"/> |
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332 <param name="greedy_group_resolution" value="remove_proteins_wo_evidence"/> |
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333 <param name="max_psms_extreme_probability" value="1.0"/> |
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334 <section name="algorithm"> |
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335 <param name="psm_probability_cutoff" value="0.001"/> |
f3096a586de8
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336 <param name="top_PSMs" value="1"/> |
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337 <param name="keep_best_PSM_only" value="true"/> |
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338 <param name="update_PSM_probabilities" value="true"/> |
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339 <param name="user_defined_priors" value="false"/> |
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340 <param name="annotate_group_probabilities" value="true"/> |
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341 <param name="use_ids_outside_features" value="false"/> |
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342 <section name="model_parameters"> |
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343 <param name="prot_prior" value="0.7"/> |
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344 <param name="pep_emission" value="0.1"/> |
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345 <param name="pep_spurious_emission" value="0.001"/> |
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346 <param name="pep_prior" value="0.1"/> |
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347 <param name="regularize" value="false"/> |
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348 <param name="extended_model" value="false"/> |
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349 </section> |
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350 <section name="loopy_belief_propagation"> |
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351 <param name="scheduling_type" value="priority"/> |
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352 <param name="convergence_threshold" value="1e-05"/> |
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353 <param name="dampening_lambda" value="0.001"/> |
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354 <param name="max_nr_iterations" value="2147483647"/> |
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355 <param name="p_norm_inference" value="1.0"/> |
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356 </section> |
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357 <section name="param_optimize"> |
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358 <param name="aucweight" value="0.3"/> |
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359 <param name="conservative_fdr" value="true"/> |
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360 <param name="regularized_fdr" value="true"/> |
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361 </section> |
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362 </section> |
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363 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
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364 <output name="ctd_out" ftype="xml"> |
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365 <assert_contents> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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366 <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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367 </assert_contents> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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368 </output> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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369 </test> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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370 <!-- UTILS_Epifany_5 --> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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371 <test expect_num_outputs="2"> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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372 <section name="adv_opts"> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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373 <param name="conservative_fdr" value="true"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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374 <param name="picked_fdr" value="false"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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375 <param name="picked_decoy_string" value=""/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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376 <param name="picked_decoy_prefix" value="prefix"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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377 <param name="min_psms_extreme_probability" value="0.0"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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378 <param name="force" value="false"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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379 <param name="test" value="true"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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380 </section> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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381 <conditional name="in_cond"> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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382 <param name="in" value="FidoAdapter_1_input_singlerun.idXML"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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383 </conditional> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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384 <output name="out" file="Epifany_4_out_singlerun_fdr.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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385 <param name="out_type" value="idXML"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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386 <param name="protein_fdr" value="true"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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387 <param name="greedy_group_resolution" value="remove_proteins_wo_evidence"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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388 <param name="max_psms_extreme_probability" value="1.0"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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389 <section name="algorithm"> |
f3096a586de8
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390 <param name="psm_probability_cutoff" value="0.001"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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391 <param name="top_PSMs" value="1"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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392 <param name="keep_best_PSM_only" value="true"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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393 <param name="update_PSM_probabilities" value="true"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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394 <param name="user_defined_priors" value="false"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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395 <param name="annotate_group_probabilities" value="true"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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396 <param name="use_ids_outside_features" value="false"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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397 <section name="model_parameters"> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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398 <param name="prot_prior" value="0.7"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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399 <param name="pep_emission" value="0.1"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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400 <param name="pep_spurious_emission" value="0.001"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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401 <param name="pep_prior" value="0.1"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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402 <param name="regularize" value="false"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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403 <param name="extended_model" value="false"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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404 </section> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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405 <section name="loopy_belief_propagation"> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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406 <param name="scheduling_type" value="priority"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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407 <param name="convergence_threshold" value="1e-05"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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408 <param name="dampening_lambda" value="0.001"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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409 <param name="max_nr_iterations" value="2147483647"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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410 <param name="p_norm_inference" value="1.0"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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411 </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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412 <section name="param_optimize"> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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413 <param name="aucweight" value="0.3"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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414 <param name="conservative_fdr" value="true"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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415 <param name="regularized_fdr" value="true"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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416 </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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417 </section> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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418 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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419 <output name="ctd_out" ftype="xml"> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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420 <assert_contents> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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421 <is_valid_xml/> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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422 </assert_contents> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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423 </output> |
f3096a586de8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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424 </test> |
0
03e13b23a78b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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425 </tests> |
03e13b23a78b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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426 <help><![CDATA[Runs a Bayesian protein inference. |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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427 |
03e13b23a78b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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428 |
4
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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 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_Epifany.html]]></help> |
0
03e13b23a78b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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430 <expand macro="references"/> |
03e13b23a78b
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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431 </tool> |