Mercurial > repos > galaxyp > openms_idripper
annotate IDRipper.xml @ 13:7960e660446e draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
| author | galaxyp |
|---|---|
| date | Thu, 01 Dec 2022 19:15:32 +0000 |
| parents | b017e7bd2316 |
| children | e64214bd2f6e |
| rev | line source |
|---|---|
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0
9af6146f168b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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1 <?xml version='1.0' encoding='UTF-8'?> |
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5
2b74ab49b619
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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9af6146f168b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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3 <!--Proposed Tool Section: [File Handling]--> |
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13
7960e660446e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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4 <tool id="IDRipper" name="IDRipper" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> |
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7960e660446e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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5 <description>Split protein/peptide identification file into several files according to identification run and annotated file origin.</description> |
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0
9af6146f168b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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6 <macros> |
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9af6146f168b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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7 <token name="@EXECUTABLE@">IDRipper</token> |
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9af6146f168b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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8 <import>macros.xml</import> |
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9af6146f168b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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9 </macros> |
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9
b50cc9d1d1a9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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10 <expand macro="requirements"/> |
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0
9af6146f168b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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11 <expand macro="stdio"/> |
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b50cc9d1d1a9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ |
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b50cc9d1d1a9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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13 @EXT_FOO@ |
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b50cc9d1d1a9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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14 #import re |
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b50cc9d1d1a9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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15 |
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b50cc9d1d1a9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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16 ## Preprocessing |
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b50cc9d1d1a9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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17 mkdir in && |
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b50cc9d1d1a9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && |
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7960e660446e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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19 mkdir out && |
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9
b50cc9d1d1a9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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20 |
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b50cc9d1d1a9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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21 ## Main program call |
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0
9af6146f168b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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22 |
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b50cc9d1d1a9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
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23 set -o pipefail && |
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b50cc9d1d1a9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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24 @EXECUTABLE@ -write_ctd ./ && |
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b50cc9d1d1a9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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25 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && |
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b50cc9d1d1a9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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26 @EXECUTABLE@ -ini @EXECUTABLE@.ctd |
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b50cc9d1d1a9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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27 -in |
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b50cc9d1d1a9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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28 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' |
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7960e660446e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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29 -out |
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7960e660446e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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30 out/ |
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b50cc9d1d1a9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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31 |
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b50cc9d1d1a9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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32 ## Postprocessing |
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b50cc9d1d1a9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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33 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS |
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b50cc9d1d1a9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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34 && mv '@EXECUTABLE@.ctd' '$ctd_out' |
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b50cc9d1d1a9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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35 #end if]]></command> |
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b50cc9d1d1a9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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36 <configfiles> |
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b50cc9d1d1a9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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37 <inputs name="args_json" data_style="paths"/> |
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b50cc9d1d1a9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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38 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
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b50cc9d1d1a9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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39 </configfiles> |
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0
9af6146f168b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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40 <inputs> |
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7960e660446e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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41 <param argument="-in" type="data" format="idxml" optional="false" label="Input file, in which the protein/peptide identifications must be tagged with 'file_origin'" help=" select idxml data sets(s)"/> |
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7960e660446e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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42 <param argument="-numeric_filenames" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not infer output filenames from spectra_data or file_origin but use the input filename with numeric suffixes" help=""/> |
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7960e660446e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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43 <param argument="-split_ident_runs" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Split different identification runs into separate files" help=""/> |
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b50cc9d1d1a9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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44 <expand macro="adv_opts_macro"> |
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7960e660446e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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45 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> |
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7960e660446e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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46 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> |
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7960e660446e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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47 <expand macro="list_string_san" name="test"/> |
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b50cc9d1d1a9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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48 </param> |
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b50cc9d1d1a9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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49 </expand> |
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11
b017e7bd2316
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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50 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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51 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> |
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9af6146f168b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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52 </param> |
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9af6146f168b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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53 </inputs> |
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9af6146f168b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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54 <outputs> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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55 <collection type="list" name="out" label="${tool.name} on ${on_string}: out"> |
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7960e660446e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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56 <discover_datasets directory="out" recurse="true" format="idxml" pattern="_?(?P<designation>.*)\.[^.]*"/> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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57 </collection> |
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b50cc9d1d1a9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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58 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> |
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b50cc9d1d1a9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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59 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> |
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b50cc9d1d1a9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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60 </data> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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61 </outputs> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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62 <tests><!-- TOPP_IDRipper_1 --> |
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7960e660446e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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63 <!-- TOPP_IDRipper_2 --> |
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7960e660446e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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64 <!-- TOPP_IDRipper_2a --> |
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7960e660446e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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65 <!-- TOPP_IDRipper_3 --> |
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7960e660446e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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66 <test expect_num_outputs="2"> |
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7960e660446e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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67 <section name="adv_opts"> |
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7960e660446e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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68 <param name="test" value="true"/> |
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7960e660446e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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69 </section> |
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7960e660446e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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70 <param name="in" value="IDRipper_1_input.idXML"/> |
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7960e660446e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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71 <output_collection name="out" count="2"> |
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72 <element name="IDRipper_1_output_1" file="IDRipper_1_output1.idXML" ftype="idxml" compare="sim_size" delta="5700"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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73 <element name="IDRipper_1_output_2" file="IDRipper_1_output2.idXML" ftype="idxml" compare="sim_size" delta="5700"/> |
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7960e660446e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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74 </output_collection> |
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7960e660446e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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75 <param name="numeric_filenames" value="false"/> |
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7960e660446e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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76 <param name="split_ident_runs" value="false"/> |
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7960e660446e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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77 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
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7960e660446e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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78 <output name="ctd_out" ftype="xml"> |
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7960e660446e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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79 <assert_contents> |
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7960e660446e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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80 <is_valid_xml/> |
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7960e660446e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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81 </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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82 </output> |
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83 </test><test expect_num_outputs="2"> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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84 <section name="adv_opts"> |
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7960e660446e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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85 <param name="test" value="true"/> |
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7960e660446e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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86 </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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87 <param name="in" value="IDRipper_2_input.idXML"/> |
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7960e660446e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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88 <output_collection name="out" count="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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89 <element name="IDRipper_2_input_idXML_0_0" file="IDRipper_2_input_0_0.idXML" ftype="idxml"/> |
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7960e660446e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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90 <element name="IDRipper_2_input_idXML_1_0" file="IDRipper_2_input_1_0.idXML" ftype="idxml"/> |
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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 <element name="IDRipper_2_input_idXML_2_1" file="IDRipper_2_input_2_1.idXML" ftype="idxml"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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92 </output_collection> |
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93 <param name="numeric_filenames" value="true"/> |
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94 <param name="split_ident_runs" value="true"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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95 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
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7960e660446e
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96 <output name="ctd_out" ftype="xml"> |
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97 <assert_contents> |
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98 <is_valid_xml/> |
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99 </assert_contents> |
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100 </output> |
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101 </test><test expect_num_outputs="2"> |
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102 <section name="adv_opts"> |
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103 <param name="test" value="true"/> |
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104 </section> |
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105 <param name="in" value="IDRipper_2_input.idXML"/> |
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106 <output_collection name="out" count="2"> |
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107 <element name="IDRipper_2_input_idXML_0" file="IDRipper_2a_output_0.idXML" ftype="idxml"/> |
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108 <element name="IDRipper_2_input_idXML_1" file="IDRipper_2a_output_1.idXML" ftype="idxml"/> |
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109 </output_collection> |
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110 <param name="numeric_filenames" value="true"/> |
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111 <param name="split_ident_runs" value="false"/> |
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112 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
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113 <output name="ctd_out" ftype="xml"> |
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114 <assert_contents> |
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115 <is_valid_xml/> |
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116 </assert_contents> |
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117 </output> |
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118 </test><test expect_num_outputs="2"> |
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119 <section name="adv_opts"> |
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120 <param name="test" value="true"/> |
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121 </section> |
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122 <param name="in" value="IDRipper_3_output.idXML"/> |
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123 <output_collection name="out" count="2"> |
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124 <element name="IDRipper_3_input1" file="IDRipper_3_input1.idXML" ftype="idxml"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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125 <element name="IDRipper_3_input2" file="IDRipper_3_input2.idXML" ftype="idxml"/> |
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126 </output_collection> |
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127 <param name="numeric_filenames" value="false"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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128 <param name="split_ident_runs" value="false"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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129 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
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130 <output name="ctd_out" ftype="xml"> |
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131 <assert_contents> |
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132 <is_valid_xml/> |
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133 </assert_contents> |
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134 </output> |
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135 </test> |
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136 </tests> |
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137 <help><![CDATA[Split protein/peptide identification file into several files according to identification run and annotated file origin. |
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0
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138 |
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139 |
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13
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140 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_IDRipper.html]]></help> |
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9
b50cc9d1d1a9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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141 <expand macro="references"/> |
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0
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142 </tool> |