annotate MzTabExporter.xml @ 13:2735db4dd8d9 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3

<?xml version='1.0' encoding='UTF-8'?>
<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
<!--Proposed Tool Section: [File Handling]-->
<tool id="MzTabExporter" name="MzTabExporter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
  <description>Exports various XML formats to an mzTab file.</description>
  <macros>
    <token name="@EXECUTABLE@">MzTabExporter</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
@EXT_FOO@
#import re

## Preprocessing
#if $in:
  mkdir in &&
  ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
#end if
mkdir out &&

## Main program call

set -o pipefail &&
@EXECUTABLE@ -write_ctd ./ &&
python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
@EXECUTABLE@ -ini @EXECUTABLE@.ctd
#if $in:
  -in
  'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
#end if
-out
'out/output.${gxy2omsext("mztab")}'

## Postprocessing
&& mv 'out/output.${gxy2omsext("mztab")}' '$out'
#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
  && mv '@EXECUTABLE@.ctd' '$ctd_out'
#end if]]></command>
  <configfiles>
    <inputs name="args_json" data_style="paths"/>
    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
  </configfiles>
  <inputs>
    <param argument="-in" type="data" format="consensusxml,featurexml,idxml,mzid" optional="true" label="Input files used to generate the mzTab file" help=" select consensusxml,featurexml,idxml,mzid data sets(s)"/>
    <param argument="-opt_columns" display="checkboxes" multiple="true" type="select" optional="true" label="Add optional columns which are not part of the mzTab standard" help="">
      <option value="subfeatures" selected="true">subfeatures</option>
      <expand macro="list_string_san" name="opt_columns"/>
    </param>
    <expand macro="adv_opts_macro">
      <param argument="-first_run_inference_only" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Does the first IdentificationRun in the file only represent (protein) inference results" help="If so, read peptide information only from second to last runs"/>
      <param argument="-export_all_psms" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Export all PSMs instead of only the best per spectrum" help=""/>
      <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
        <expand macro="list_string_san" name="test"/>
      </param>
    </expand>
    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
    </param>
  </inputs>
  <outputs>
    <data name="out" label="${tool.name} on ${on_string}: out" format="mztab"/>
    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
  </outputs>
  <tests><!-- TOPP_MzTabExporter_1 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="first_run_inference_only" value="false"/>
        <param name="export_all_psms" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="MzTabExporter_1_input.consensusXML"/>
      <output name="out" file="MzTabExporter_1_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
      <param name="opt_columns" value="subfeatures"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <!-- TOPP_MzTabExporter_2 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="first_run_inference_only" value="false"/>
        <param name="export_all_psms" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="MzTabExporter_2_input.idXML"/>
      <output name="out" file="MzTabExporter_2_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
      <param name="opt_columns" value="subfeatures"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <!-- TOPP_MzTabExporter_3 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="first_run_inference_only" value="false"/>
        <param name="export_all_psms" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="MzTabExporter_3_input.featureXML"/>
      <output name="out" file="MzTabExporter_3_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
      <param name="opt_columns" value="subfeatures"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <!-- TOPP_MzTabExporter_4 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="first_run_inference_only" value="false"/>
        <param name="export_all_psms" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="Epifany_2_out.consensusXML"/>
      <output name="out" file="MzTabExporter_4_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
      <param name="opt_columns" value="subfeatures"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <!-- TOPP_MzTabExporter_5 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="first_run_inference_only" value="true"/>
        <param name="export_all_psms" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="MzTabExporter_5_in.consensusXML"/>
      <output name="out" file="MzTabExporter_5_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
      <param name="opt_columns" value="subfeatures"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <!-- TOPP_MzTabExporter_6 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="first_run_inference_only" value="false"/>
        <param name="export_all_psms" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="MzTabExporter_6_input.idXML"/>
      <output name="out" file="MzTabExporter_6_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
      <param name="opt_columns" value="subfeatures"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <!-- TOPP_MzTabExporter_7 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="first_run_inference_only" value="false"/>
        <param name="export_all_psms" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="MzTabExporter_7_input.consensusXML"/>
      <output name="out" file="MzTabExporter_7_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
      <param name="opt_columns" value="subfeatures"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <!-- TOPP_MzTabExporter_8 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="first_run_inference_only" value="false"/>
        <param name="export_all_psms" value="true"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="MzTabExporter_6_input.idXML"/>
      <output name="out" file="MzTabExporter_8_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
      <param name="opt_columns" value="subfeatures"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
  </tests>
  <help><![CDATA[Exports various XML formats to an mzTab file.


For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MzTabExporter.html]]></help>
  <expand macro="references"/>
</tool>