comparison MascotAdapter.xml @ 11:57fb2083a8cb draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"

10:6ff54b799207

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("idxml")}'

## Postprocessing
&& mv 'out/output.${gxy2omsext("idxml")}' '$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[{"mascot_directory": "TODO", "temp_data_directory": "\$TMP_DIR", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
  </configfiles>
  <inputs>
    <param name="in" argument="-in" type="data" format="txt" optional="false" label="input file in mzData format" help="Note: In mode 'mascot_out' a Mascot results file (.mascotXML) is read select txt data sets(s)"/>
    <param name="mascot_in" argument="-mascot_in" type="boolean" truevalue="true" falsevalue="false" checked="false" label="if this flag is set the MascotAdapter will read in mzData and write Mascot generic format" help=""/>
    <param name="mascot_out" argument="-mascot_out" type="boolean" truevalue="true" falsevalue="false" checked="false" label="if this flag is set the MascotAdapter will read in a Mascot results file (.mascotXML) and write idXML" help=""/>
    <param name="instrument" argument="-instrument" type="text" optional="true" value="Default" label="the instrument that was used to measure the spectra" help="">
      <expand macro="list_string_san"/>
    </param>
    <param name="precursor_mass_tolerance" argument="-precursor_mass_tolerance" type="float" optional="true" value="2.0" label="the precursor mass tolerance" help=""/>
    <param name="peak_mass_tolerance" argument="-peak_mass_tolerance" type="float" optional="true" value="1.0" label="the peak mass tolerance" help=""/>

      <option value="Monoisotopic" selected="true">Monoisotopic</option>
      <option value="Average">Average</option>
      <expand macro="list_string_san"/>
    </param>
    <expand macro="adv_opts_macro">
      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
      <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
        <expand macro="list_string_san"/>
      </param>
    </expand>
    <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
    </param>
  </inputs>
  <outputs>
    <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
  </outputs>
  <tests>

    <expand macro="manutest_MascotAdapter"/>
  </tests>
  <help><![CDATA[Annotates MS/MS spectra using Mascot.


For more information, visit http://www.openms.de/documentation/TOPP_MascotAdapter.html]]></help>
  <expand macro="references"/>
</tool>

11:57fb2083a8cb

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[{"mascot_directory": "TODO", "temp_data_directory": "\$TMP_DIR", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
  </configfiles>
  <inputs>
    <param name="in" argument="-in" type="data" format="mascotxml,mzdata" optional="false" label="input file in mzData format" help="Note: In mode 'mascot_out' a Mascot results file (.mascotXML) is read select mascotxml,mzdata data sets(s)"/>
    <param name="out_type" argument="-out_type" display="radio" type="select" optional="false" label="output file type (for TOPPAS)" help="">
      <option value="idXML">idxml</option>
      <option value="mgf">mgf</option>
      <expand macro="list_string_san"/>
    </param>
    <param name="instrument" argument="-instrument" type="text" optional="true" value="Default" label="the instrument that was used to measure the spectra" help="">
      <expand macro="list_string_san"/>
    </param>
    <param name="precursor_mass_tolerance" argument="-precursor_mass_tolerance" type="float" optional="true" value="2.0" label="the precursor mass tolerance" help=""/>
    <param name="peak_mass_tolerance" argument="-peak_mass_tolerance" type="float" optional="true" value="1.0" label="the peak mass tolerance" help=""/>

      <option value="Monoisotopic" selected="true">Monoisotopic</option>
      <option value="Average">Average</option>
      <expand macro="list_string_san"/>
    </param>
    <expand macro="adv_opts_macro">
      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
      <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
        <expand macro="list_string_san"/>
      </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 ${on_string}: out">
      <change_format>
        <when input="out_type" value="idXML" format="idxml"/>
        <when input="out_type" value="mgf" format="mgf"/>
      </change_format>
    </data>
    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
  </outputs>
  <tests>

    <expand macro="manutest_MascotAdapter"/>
  </tests>
  <help><![CDATA[Annotates MS/MS spectra using Mascot.


For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_MascotAdapter.html]]></help>
  <expand macro="references"/>
</tool>