annotate FileInfo.xml @ 16:5a45e6ac9aae draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906

<!--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 Filtering / Extraction / Merging]-->
<tool id="FileInfo" name="FileInfo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
  <description>Shows basic information about the file, such as data ranges and file type</description>
  <macros>
    <token name="@EXECUTABLE@">FileInfo</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
mkdir in &&
cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
mkdir out &&
#if "out_tsv_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  mkdir out_tsv &&
#end if

## Main program call

set -o pipefail &&
@EXECUTABLE@ -write_ctd ./ &&
python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
@EXECUTABLE@ -ini @EXECUTABLE@.ctd
-in
'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
-out
'out/output.${gxy2omsext("txt")}'
#if "out_tsv_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  -out_tsv
  'out_tsv/output.${gxy2omsext("csv")}'
#end if
#if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
  | tee '$stdout'
#end if

## Postprocessing
&& mv 'out/output.${gxy2omsext("txt")}' '$out'
#if "out_tsv_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  && mv 'out_tsv/output.${gxy2omsext("csv")}' '$out_tsv'
#end if
#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,dta,dta2d,fasta,featurexml,idxml,mgf,mzdata,mzid,mzml,mzxml,pepxml,pqp,sqmass,trafoxml" label="input file" help=" select consensusxml,dta,dta2d,fasta,featurexml,idxml,mgf,mzdata,mzid,mzml,mzxml,pepxml,pqp,sqmass,trafoxml data sets(s)"/>
    <param argument="-m" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show meta information about the whole experiment" help=""/>
    <param argument="-p" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Shows data processing information" help=""/>
    <param argument="-s" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Computes a five-number statistics of intensities, qualities, and widths" help=""/>
    <param argument="-d" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show detailed listing of all spectra and chromatograms (peak files only)" help=""/>
    <param argument="-c" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Check for corrupt data in the file (peak files only)" help=""/>
    <param argument="-v" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Validate the file only (for mzML, mzData, mzXML, featureXML, idXML, consensusXML, pepXML)" help=""/>
    <param argument="-i" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Check whether a given mzML file contains valid indices (conforming to the indexedmzML standard)" help=""/>
    <expand macro="adv_opts_macro">
      <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
        <expand macro="list_string_san" name="test"/>
      </param>
    </expand>
    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
      <option value="out_tsv_FLAG">out_tsv (Second optional output file)</option>
      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
    </param>
  </inputs>
  <outputs>
    <data name="out" label="${tool.name} on ${on_string}: out" format="txt"/>
    <data name="out_tsv" label="${tool.name} on ${on_string}: out_tsv" format="csv">
      <filter>OPTIONAL_OUTPUTS is not None and "out_tsv_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
  </outputs>
  <tests>
    <!-- TOPP_FileInfo_1 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FileInfo_1_input.dta" ftype="dta"/>
      <output name="out" value="FileInfo_1_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
      <param name="m" value="false"/>
      <param name="p" value="false"/>
      <param name="s" value="false"/>
      <param name="d" value="false"/>
      <param name="c" value="false"/>
      <param name="v" value="false"/>
      <param name="i" value="false"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_FileInfo_2 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FileInfo_2_input.dta2d" ftype="dta2d"/>
      <output name="out" value="FileInfo_2_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
      <param name="m" value="false"/>
      <param name="p" value="false"/>
      <param name="s" value="false"/>
      <param name="d" value="false"/>
      <param name="c" value="false"/>
      <param name="v" value="false"/>
      <param name="i" value="false"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_FileInfo_3 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FileInfo_3_input.featureXML"/>
      <output name="out" value="FileInfo_3_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
      <param name="m" value="true"/>
      <param name="p" value="true"/>
      <param name="s" value="true"/>
      <param name="d" value="false"/>
      <param name="c" value="false"/>
      <param name="v" value="false"/>
      <param name="i" value="false"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_FileInfo_4 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FileInfo_4_input.mzXML"/>
      <output name="out" value="FileInfo_4_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
      <param name="m" value="true"/>
      <param name="p" value="false"/>
      <param name="s" value="false"/>
      <param name="d" value="false"/>
      <param name="c" value="false"/>
      <param name="v" value="false"/>
      <param name="i" value="false"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_FileInfo_5 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FileInfo_5_input.mzDat"/>
      <output name="out" value="FileInfo_5_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
      <param name="m" value="true"/>
      <param name="p" value="false"/>
      <param name="s" value="true"/>
      <param name="d" value="false"/>
      <param name="c" value="false"/>
      <param name="v" value="false"/>
      <param name="i" value="false"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_FileInfo_6 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FileInfo_6_input.mzData"/>
      <output name="out" value="FileInfo_6_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
      <param name="m" value="false"/>
      <param name="p" value="false"/>
      <param name="s" value="true"/>
      <param name="d" value="true"/>
      <param name="c" value="false"/>
      <param name="v" value="false"/>
      <param name="i" value="false"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_FileInfo_7 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FileInfo_7_input.consensusXML"/>
      <output name="out" value="FileInfo_7_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
      <param name="m" value="true"/>
      <param name="p" value="true"/>
      <param name="s" value="true"/>
      <param name="d" value="false"/>
      <param name="c" value="false"/>
      <param name="v" value="false"/>
      <param name="i" value="false"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_FileInfo_9 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FileInfo_9_input.mzML"/>
      <output name="out" value="FileInfo_9_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
      <param name="m" value="true"/>
      <param name="p" value="true"/>
      <param name="s" value="true"/>
      <param name="d" value="false"/>
      <param name="c" value="false"/>
      <param name="v" value="false"/>
      <param name="i" value="false"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_FileInfo_10 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FileInfo_10_input.idXML"/>
      <output name="out" value="FileInfo_10_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
      <param name="m" value="false"/>
      <param name="p" value="false"/>
      <param name="s" value="false"/>
      <param name="d" value="false"/>
      <param name="c" value="false"/>
      <param name="v" value="false"/>
      <param name="i" value="false"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_FileInfo_12 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FileInfo_12_input.mzML"/>
      <param name="m" value="false"/>
      <param name="p" value="false"/>
      <param name="s" value="false"/>
      <param name="d" value="false"/>
      <param name="c" value="false"/>
      <param name="v" value="false"/>
      <param name="i" value="true"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_FileInfo_13 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FileInfo_13_input.consensusXML"/>
      <param name="m" value="false"/>
      <param name="p" value="false"/>
      <param name="s" value="false"/>
      <param name="d" value="false"/>
      <param name="c" value="false"/>
      <param name="v" value="false"/>
      <param name="i" value="false"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_FileInfo_14 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FileInfo_14_input.mzid"/>
      <output name="out" value="FileInfo_14_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
      <param name="m" value="false"/>
      <param name="p" value="false"/>
      <param name="s" value="false"/>
      <param name="d" value="false"/>
      <param name="c" value="false"/>
      <param name="v" value="true"/>
      <param name="i" value="false"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_FileInfo_15 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FileInfo_15_input.mzid"/>
      <output name="out" value="FileInfo_15_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
      <param name="m" value="false"/>
      <param name="p" value="false"/>
      <param name="s" value="false"/>
      <param name="d" value="false"/>
      <param name="c" value="false"/>
      <param name="v" value="true"/>
      <param name="i" value="false"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_FileInfo_16 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FileInfo_16_input.trafoXML"/>
      <output name="out" value="FileInfo_16_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
      <param name="m" value="false"/>
      <param name="p" value="false"/>
      <param name="s" value="false"/>
      <param name="d" value="false"/>
      <param name="c" value="false"/>
      <param name="v" value="false"/>
      <param name="i" value="false"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_FileInfo_17 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FileInfo_17_input.fasta"/>
      <output name="out" value="FileInfo_17_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
      <param name="m" value="false"/>
      <param name="p" value="false"/>
      <param name="s" value="false"/>
      <param name="d" value="false"/>
      <param name="c" value="false"/>
      <param name="v" value="false"/>
      <param name="i" value="false"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_FileInfo_18 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FileInfo_18_input.fasta"/>
      <output name="out" value="FileInfo_18_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
      <param name="m" value="false"/>
      <param name="p" value="false"/>
      <param name="s" value="false"/>
      <param name="d" value="false"/>
      <param name="c" value="false"/>
      <param name="v" value="false"/>
      <param name="i" value="false"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_FileInfo_19 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FAIMS_test_data.mzML"/>
      <output name="out" value="FileInfo_19_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
      <param name="m" value="false"/>
      <param name="p" value="false"/>
      <param name="s" value="false"/>
      <param name="d" value="true"/>
      <param name="c" value="false"/>
      <param name="v" value="false"/>
      <param name="i" value="false"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
  </tests>
  <help><![CDATA[Shows basic information about the file, such as data ranges and file type.


For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FileInfo.html]]></help>
  <expand macro="references"/>
</tool>