Mercurial > repos > galaxyp > openms_noisefiltersgolay
annotate NoiseFilterSGolay.xml @ 13:cf86c9091cb3 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 19:05:55 +0000 |
parents | 1312f9119f74 |
children | 35468667de97 |
rev | line source |
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2b7b288f2d2a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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1 <?xml version='1.0' encoding='UTF-8'?> |
5
39f42442e20d
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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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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3 <!--Proposed Tool Section: [Signal processing and preprocessing]--> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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4 <tool id="NoiseFilterSGolay" name="NoiseFilterSGolay" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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5 <description>Removes noise from profile spectra by using a Savitzky Golay filter. Requires uniform (equidistant) data.</description> |
2b7b288f2d2a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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6 <macros> |
2b7b288f2d2a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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7 <token name="@EXECUTABLE@">NoiseFilterSGolay</token> |
2b7b288f2d2a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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8 <import>macros.xml</import> |
2b7b288f2d2a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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9 </macros> |
9
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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10 <expand macro="requirements"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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11 <expand macro="stdio"/> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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13 @EXT_FOO@ |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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14 #import re |
f2834f001a80
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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15 |
f2834f001a80
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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16 ## Preprocessing |
f2834f001a80
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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17 mkdir in && |
f2834f001a80
"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($in.ext)' && |
f2834f001a80
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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19 mkdir out && |
f2834f001a80
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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20 |
f2834f001a80
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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21 ## Main program call |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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22 |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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23 set -o pipefail && |
f2834f001a80
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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24 @EXECUTABLE@ -write_ctd ./ && |
f2834f001a80
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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25 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && |
f2834f001a80
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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26 @EXECUTABLE@ -ini @EXECUTABLE@.ctd |
f2834f001a80
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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27 -in |
f2834f001a80
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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28 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' |
f2834f001a80
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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29 -out |
f2834f001a80
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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30 'out/output.${gxy2omsext("mzml")}' |
f2834f001a80
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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31 |
f2834f001a80
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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32 ## Postprocessing |
f2834f001a80
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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33 && mv 'out/output.${gxy2omsext("mzml")}' '$out' |
f2834f001a80
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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34 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS |
f2834f001a80
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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35 && mv '@EXECUTABLE@.ctd' '$ctd_out' |
f2834f001a80
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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36 #end if]]></command> |
f2834f001a80
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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37 <configfiles> |
f2834f001a80
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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38 <inputs name="args_json" data_style="paths"/> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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39 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
f2834f001a80
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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40 </configfiles> |
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2b7b288f2d2a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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41 <inputs> |
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42 <param argument="-in" type="data" format="mzml" optional="false" label="input raw data file" help=" select mzml data sets(s)"/> |
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43 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false"> |
f2834f001a80
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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44 <param name="frame_length" argument="-algorithm:frame_length" type="integer" optional="true" value="11" label="The number of subsequent data points used for smoothing" help="This number has to be uneven. If it is not, 1 will be added"/> |
f2834f001a80
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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45 <param name="polynomial_order" argument="-algorithm:polynomial_order" type="integer" optional="true" value="4" label="Order or the polynomial that is fitted" help=""/> |
f2834f001a80
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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46 </section> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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47 <expand macro="adv_opts_macro"> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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48 <param argument="-processOption" type="select" optional="true" label="Whether to load all data and process them in-memory or whether to process the data on the fly (lowmemory) without loading the whole file into memory first" help=""> |
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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 <option value="inmemory" selected="true">inmemory</option> |
2b7b288f2d2a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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50 <option value="lowmemory">lowmemory</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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51 <expand macro="list_string_san" name="processOption"/> |
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52 </param> |
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53 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> |
cf86c9091cb3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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54 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> |
cf86c9091cb3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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55 <expand macro="list_string_san" name="test"/> |
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56 </param> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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57 </expand> |
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58 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> |
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59 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> |
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60 </param> |
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61 </inputs> |
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62 <outputs> |
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63 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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64 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> |
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65 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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66 </data> |
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67 </outputs> |
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68 <tests><!-- TOPP_NoiseFilterSGolay_1 --> |
cf86c9091cb3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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69 <test expect_num_outputs="2"> |
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70 <section name="adv_opts"> |
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71 <param name="processOption" value="inmemory"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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72 <param name="force" value="false"/> |
cf86c9091cb3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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73 <param name="test" value="true"/> |
cf86c9091cb3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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74 </section> |
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75 <param name="in" value="NoiseFilterSGolay_1_input.mzML"/> |
cf86c9091cb3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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76 <output name="out" file="NoiseFilterSGolay_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
cf86c9091cb3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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77 <section name="algorithm"> |
cf86c9091cb3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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78 <param name="frame_length" value="9"/> |
cf86c9091cb3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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79 <param name="polynomial_order" value="4"/> |
cf86c9091cb3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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80 </section> |
cf86c9091cb3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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81 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
cf86c9091cb3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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82 <output name="ctd_out" ftype="xml"> |
cf86c9091cb3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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83 <assert_contents> |
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84 <is_valid_xml/> |
cf86c9091cb3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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85 </assert_contents> |
cf86c9091cb3
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86 </output> |
cf86c9091cb3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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87 </test> |
cf86c9091cb3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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88 <!-- TOPP_NoiseFilterSGolay_2 --> |
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89 <test expect_num_outputs="2"> |
cf86c9091cb3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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90 <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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91 <param name="processOption" value="inmemory"/> |
cf86c9091cb3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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92 <param name="force" value="false"/> |
cf86c9091cb3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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93 <param name="test" value="true"/> |
cf86c9091cb3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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94 </section> |
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95 <param name="in" value="NoiseFilterSGolay_2_input.chrom.mzML"/> |
cf86c9091cb3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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96 <output name="out" file="NoiseFilterSGolay_2_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
cf86c9091cb3
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97 <section name="algorithm"> |
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98 <param name="frame_length" value="11"/> |
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99 <param name="polynomial_order" value="4"/> |
cf86c9091cb3
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100 </section> |
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101 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
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102 <output name="ctd_out" ftype="xml"> |
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103 <assert_contents> |
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104 <is_valid_xml/> |
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105 </assert_contents> |
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106 </output> |
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107 </test> |
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108 <!-- TOPP_NoiseFilterSGolay_3 --> |
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109 <test expect_num_outputs="2"> |
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110 <section name="adv_opts"> |
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111 <param name="processOption" value="lowmemory"/> |
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112 <param name="force" value="false"/> |
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113 <param name="test" value="true"/> |
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114 </section> |
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115 <param name="in" value="NoiseFilterSGolay_1_input.mzML"/> |
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116 <output name="out" file="NoiseFilterSGolay_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
cf86c9091cb3
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117 <section name="algorithm"> |
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118 <param name="frame_length" value="9"/> |
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119 <param name="polynomial_order" value="4"/> |
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120 </section> |
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121 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
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122 <output name="ctd_out" ftype="xml"> |
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123 <assert_contents> |
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124 <is_valid_xml/> |
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125 </assert_contents> |
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126 </output> |
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127 </test> |
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128 <!-- TOPP_NoiseFilterSGolay_4 --> |
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129 <test expect_num_outputs="2"> |
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130 <section name="adv_opts"> |
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131 <param name="processOption" value="lowmemory"/> |
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132 <param name="force" value="false"/> |
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133 <param name="test" value="true"/> |
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134 </section> |
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135 <param name="in" value="NoiseFilterSGolay_2_input.chrom.mzML"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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136 <output name="out" file="NoiseFilterSGolay_2_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
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137 <section name="algorithm"> |
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138 <param name="frame_length" value="11"/> |
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139 <param name="polynomial_order" value="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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140 </section> |
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141 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
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142 <output name="ctd_out" ftype="xml"> |
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143 <assert_contents> |
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144 <is_valid_xml/> |
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145 </assert_contents> |
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146 </output> |
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147 </test> |
9
f2834f001a80
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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148 </tests> |
f2834f001a80
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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149 <help><![CDATA[Removes noise from profile spectra by using a Savitzky Golay filter. Requires uniform (equidistant) data. |
0
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150 |
2b7b288f2d2a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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151 |
13
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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152 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_NoiseFilterSGolay.html]]></help> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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153 <expand macro="references"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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154 </tool> |