Mercurial > repos > galaxyp > openms_openswathfilesplitter

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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 21:45:22 +0000
parents 4bb198c0bd3e
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: [Targeted Experiments and OpenSWATH]-->
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3 <tool id="OpenSwathFileSplitter" name="OpenSwathFileSplitter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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4 <description>Splits SWATH files into n files, each containing one window</description>
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5 <macros>
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6 <token name="@EXECUTABLE@">OpenSwathFileSplitter</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($in.ext)' &&
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18 mkdir outputDirectory &&
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19 #if "out_qc_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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20 mkdir out_qc &&
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21 #end if
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23 ## Main program call
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25 set -o pipefail &&
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26 @EXECUTABLE@ -write_ctd ./ &&
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27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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29 -in
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30 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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31 -outputDirectory
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32 outputDirectory/
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33 #if "out_qc_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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34 -out_qc
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35 'out_qc/output.${gxy2omsext("json")}'
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36 #end if
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37 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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38 | tee '$stdout'
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39 #end if
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41 ## Postprocessing
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42 #if "out_qc_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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43 && mv 'out_qc/output.${gxy2omsext("json")}' '$out_qc'
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44 #end if
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45 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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46 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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47 #end if]]></command>
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48 <configfiles>
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49 <inputs name="args_json" data_style="paths"/>
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50 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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51 </configfiles>
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52 <inputs>
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53 <param argument="-in" type="data" format="mzml,mzxml" label="Input file (SWATH/DIA file)" help=" select mzml,mzxml data sets(s)"/>
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54 <expand macro="adv_opts_macro">
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55 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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56 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
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57 <expand macro="list_string_san" name="test"/>
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58 </param>
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59 </expand>
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60 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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61 <option value="out_qc_FLAG">out_qc (Optional QC meta data (charge distribution in MS1))</option>
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62 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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63 </param>
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64 </inputs>
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65 <outputs>
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66 <collection type="list" name="outputDirectory" label="${tool.name} on ${on_string}: outputDirectory">
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67 <discover_datasets directory="outputDirectory" recurse="true" format="mzml" pattern="_?(?P&lt;designation&gt;.*)\.[^.]*"/>
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68 </collection>
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69 <data name="out_qc" label="${tool.name} on ${on_string}: out_qc" format="json">
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70 <filter>OPTIONAL_OUTPUTS is not None and "out_qc_FLAG" in OPTIONAL_OUTPUTS</filter>
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71 </data>
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72 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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73 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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74 </data>
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75 </outputs>
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76 <tests>
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77 <!-- TOPP_OpenSwathFileSplitter_1 -->
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78 <test expect_num_outputs="3">
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79 <section name="adv_opts">
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80 <param name="test" value="true"/>
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81 </section>
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82 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
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83 <param name="OPTIONAL_OUTPUTS" value="out_qc_FLAG,ctd_out_FLAG"/>
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84 <output_collection name="outputDirectory" count="6">
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85 <element name="OpenSwathWorkflow_1_input_mzML_4" file="openswath_tmpfile_4.mzML" ftype="mzml"/>
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86 <element name="OpenSwathWorkflow_1_input_mzML_ms1" file="openswath_tmpfile_ms1.mzML" ftype="mzml"/>
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87 </output_collection>
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88 <output name="out_qc" file="OpenSwathFileSplitter_1.json" compare="sim_size" delta="5700" ftype="json"/>
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89 <output name="ctd_out" ftype="xml">
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90 <assert_contents>
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91 <is_valid_xml/>
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92 </assert_contents>
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93 </output>
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94 </test>
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95 </tests>
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96 <help><![CDATA[Splits SWATH files into n files, each containing one window.
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97
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98
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99 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_OpenSwathFileSplitter.html]]></help>
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100 <expand macro="references"/>
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101 </tool>