Mercurial > repos > galaxyp > openms_idextractor

annotate IDExtractor.xml @ 16:a6124b08daff draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:28:53 +0000
parents 589bf635f424
children
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1 <!--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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2 <!--Proposed Tool Section: [Identification Processing]-->
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3 <tool id="IDExtractor" name="IDExtractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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4 <description>Extracts 'n' peptides randomly or best 'n' from idXML files</description>
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5 <macros>
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6 <token name="@EXECUTABLE@">IDExtractor</token>
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7 <import>macros.xml</import>
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8 </macros>
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9 <expand macro="requirements"/>
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10 <expand macro="stdio"/>
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11 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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12 @EXT_FOO@
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13 #import re
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15 ## Preprocessing
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16 mkdir in &&
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17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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18 mkdir out &&
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20 ## Main program call
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21
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22 set -o pipefail &&
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23 @EXECUTABLE@ -write_ctd ./ &&
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24 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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25 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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26 -in
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27 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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28 -out
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29 'out/output.${gxy2omsext("idxml")}'
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31 ## Postprocessing
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32 && mv 'out/output.${gxy2omsext("idxml")}' '$out'
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33 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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34 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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35 #end if]]></command>
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36 <configfiles>
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37 <inputs name="args_json" data_style="paths"/>
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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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39 </configfiles>
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40 <inputs>
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41 <param argument="-in" type="data" format="idxml" label="input file" help=" select idxml data sets(s)"/>
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42 <param argument="-number_of_peptides" type="integer" min="1" value="10" label="Number of randomly chosen peptides" help=""/>
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43 <param argument="-number_of_rand_invokations" type="integer" min="0" value="0" label="Number of rand invocations before random draw (basically a seed)" help=""/>
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44 <param argument="-best_hits" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this flag is set the best n peptides are chosen" help=""/>
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45 <expand macro="adv_opts_macro">
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46 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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47 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
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48 <expand macro="list_string_san" name="test"/>
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49 </param>
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50 </expand>
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51 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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52 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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53 </param>
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54 </inputs>
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55 <outputs>
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56 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
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57 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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58 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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59 </data>
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60 </outputs>
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61 <tests>
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62 <test expect_num_outputs="1">
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63 <!-- -->
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64 <param name="adv_opts|test" value="true"/>
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65 <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML"/>
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66 <param name="best_hits" value="true"/>
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67 <param name="number_of_peptides" value="1"/>
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68 <output name="out" value="IDExtractor.idXML" compare="sim_size"/>
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69 </test>
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70 </tests>
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71 <help><![CDATA[Extracts 'n' peptides randomly or best 'n' from idXML files.
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73
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74 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_IDExtractor.html]]></help>
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75 <expand macro="references"/>
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76 </tool>