annotate Digestor.xml @ 15:74db964d4818 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: [Identification Processing]-->
<tool id="Digestor" name="Digestor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
  <description>Digests a protein database in-silico</description>
  <macros>
    <token name="@EXECUTABLE@">Digestor</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 &&

## 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($in.ext)'
-out
'out/output.${out_type}'

## Postprocessing
&& mv 'out/output.${out_type}' '$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="fasta" label="input file" help=" select fasta data sets(s)"/>
    <param argument="-out_type" type="select" label="Set this if you cannot control the filename of 'out'" help="e.g., in TOPPAS">
      <option value="fasta">fasta</option>
      <option value="idXML">idxml</option>
      <validator type="expression" message="A value needs to be selected">value != "select a value"</validator>
      <expand macro="list_string_san" name="out_type"/>
    </param>
    <param argument="-missed_cleavages" type="integer" min="0" value="1" label="The number of allowed missed cleavages" help=""/>
    <param argument="-min_length" type="integer" value="6" label="Minimum length of peptide" help=""/>
    <param argument="-max_length" type="integer" value="40" label="Maximum length of peptide" help=""/>
    <param argument="-enzyme" type="select" label="The type of digestion enzyme" help="">
      <option value="no cleavage">no cleavage</option>
      <option value="unspecific cleavage">unspecific cleavage</option>
      <option value="V8-DE">V8-DE</option>
      <option value="V8-E">V8-E</option>
      <option value="leukocyte elastase">leukocyte elastase</option>
      <option value="proline endopeptidase">proline endopeptidase</option>
      <option value="staphylococcal protease/D">staphylococcal protease/D</option>
      <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
      <option value="Glu-C+P">Glu-C+P</option>
      <option value="PepsinA + P">PepsinA + P</option>
      <option value="cyanogen-bromide">cyanogen-bromide</option>
      <option value="Clostripain/P">Clostripain/P</option>
      <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
      <option value="TrypChymo">TrypChymo</option>
      <option value="Trypsin/P">Trypsin/P</option>
      <option value="Trypsin" selected="true">Trypsin</option>
      <option value="Arg-C">Arg-C</option>
      <option value="Arg-C/P">Arg-C/P</option>
      <option value="Asp-N">Asp-N</option>
      <option value="Asp-N/B">Asp-N/B</option>
      <option value="Asp-N_ambic">Asp-N_ambic</option>
      <option value="Chymotrypsin">Chymotrypsin</option>
      <option value="Chymotrypsin/P">Chymotrypsin/P</option>
      <option value="CNBr">CNBr</option>
      <option value="Formic_acid">Formic_acid</option>
      <option value="Lys-C">Lys-C</option>
      <option value="Lys-N">Lys-N</option>
      <option value="Lys-C/P">Lys-C/P</option>
      <option value="PepsinA">PepsinA</option>
      <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
      <option value="Alpha-lytic protease">Alpha-lytic protease</option>
      <option value="2-iodobenzoate">2-iodobenzoate</option>
      <option value="iodosobenzoate">iodosobenzoate</option>
      <expand macro="list_string_san" name="enzyme"/>
    </param>
    <section name="FASTA" title="Options for FASTA output files" help="" expanded="false">
      <param name="ID" argument="-FASTA:ID" type="select" label="Identifier to use for each peptide: copy from parent protein (parent); a consecutive number (number); parent ID + consecutive number (both)" help="">
        <option value="parent" selected="true">parent</option>
        <option value="number">number</option>
        <option value="both">both</option>
        <expand macro="list_string_san" name="ID"/>
      </param>
      <param name="description" argument="-FASTA:description" type="select" label="Keep or remove the (possibly lengthy) FASTA header description" help="Keeping it can increase resulting FASTA file significantly">
        <option value="remove" selected="true">remove</option>
        <option value="keep">keep</option>
        <expand macro="list_string_san" name="description"/>
      </param>
    </section>
    <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="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
    </param>
  </inputs>
  <outputs>
    <data name="out" label="${tool.name} on ${on_string}: out" format="fasta">
      <change_format>
        <when input="out_type" value="idXML" format="idxml"/>
      </change_format>
    </data>
    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
  </outputs>
  <tests>
    <test expect_num_outputs="1">
      <!-- just using some random fasta, in contrast to DigestorMotif idXML/fasta output possible, testing for the non-default fasta option -->
      <param name="adv_opts|test" value="true"/>
      <param name="in" ftype="fasta" value="random.fa"/>
      <output name="out" ftype="fasta" value="Digestor.fasta"/>
      <param name="out_type" value="fasta"/>
    </test>
  </tests>
  <help><![CDATA[Digests a protein database in-silico.


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