comparison MapAlignerTreeGuided.xml @ 2:25c08f95cdf4 draft

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

1:4bdaddb03b67

#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 name="in" argument="-in" type="data" format="featurexml" multiple="true" optional="false" label="Input files to align (all must have the same file type)" help=" select featurexml data sets(s)"/>
    <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
      <param name="model_type" argument="-algorithm:model_type" display="radio" type="select" optional="false" label="Options to control the modeling of retention time transformations from data" help="">

        <param name="use_unassigned_peptides" argument="-algorithm:align_algorithm:use_unassigned_peptides" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Should unassigned peptide identifications be used when computing an alignment of feature or consensus maps" help="If 'false', only peptide IDs assigned to features will be used"/>
        <param name="use_feature_rt" argument="-algorithm:align_algorithm:use_feature_rt" type="boolean" truevalue="true" falsevalue="false" checked="true" label="When aligning feature or consensus maps, don't use the retention time of a peptide identification directly; instead, use the retention time of the centroid of the feature (apex of the elution profile) that the peptide was matched to" help="If different identifications are matched to one feature, only the peptide closest to the centroid in RT is used.. Precludes 'use_unassigned_peptides'"/>
      </section>
    </section>
    <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="false">
      <option value="out_FLAG">out (When aligning feature or consensus maps, don't use the retention time of a peptide identification directly; instead, use the retention time of the centroid of the feature (apex of the elution profile) that the peptide was matched to)</option>
      <option value="trafo_out_FLAG">trafo_out (When aligning feature or consensus maps, don't use the retention time of a peptide identification directly; instead, use the retention time of the centroid of the feature (apex of the elution profile) that the peptide was matched to)</option>
      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
    </param>
  </inputs>
  <outputs>
    <collection type="list" name="out" label="${tool.name} on ${on_string}: out">

    <expand macro="manutest_MapAlignerTreeGuided"/>
  </tests>
  <help><![CDATA[Tree guided correction of retention time distortions between maps.


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

2:25c08f95cdf4

#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[{"copy_data": "false", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
  </configfiles>
  <inputs>
    <param name="in" argument="-in" type="data" format="featurexml" multiple="true" optional="false" label="Input files to align (all must have the same file type)" help=" select featurexml data sets(s)"/>
    <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
      <param name="model_type" argument="-algorithm:model_type" display="radio" type="select" optional="false" label="Options to control the modeling of retention time transformations from data" help="">

        <param name="use_unassigned_peptides" argument="-algorithm:align_algorithm:use_unassigned_peptides" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Should unassigned peptide identifications be used when computing an alignment of feature or consensus maps" help="If 'false', only peptide IDs assigned to features will be used"/>
        <param name="use_feature_rt" argument="-algorithm:align_algorithm:use_feature_rt" type="boolean" truevalue="true" falsevalue="false" checked="true" label="When aligning feature or consensus maps, don't use the retention time of a peptide identification directly; instead, use the retention time of the centroid of the feature (apex of the elution profile) that the peptide was matched to" help="If different identifications are matched to one feature, only the peptide closest to the centroid in RT is used.. Precludes 'use_unassigned_peptides'"/>
      </section>
    </section>
    <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="out_FLAG">out (Output files (same file type as 'in'))</option>
      <option value="trafo_out_FLAG">trafo_out (Transformation output files)</option>
      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
    </param>
  </inputs>
  <outputs>
    <collection type="list" name="out" label="${tool.name} on ${on_string}: out">

    <expand macro="manutest_MapAlignerTreeGuided"/>
  </tests>
  <help><![CDATA[Tree guided correction of retention time distortions between maps.


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