comparison ProteinInference.xml @ 11:7951e3db2efd draft

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

10:e80e453c3b04

      <expand macro="list_string_san"/>
    </param>
    <param name="annotate_indist_groups" argument="-annotate_indist_groups" type="boolean" truevalue="true" falsevalue="false" checked="true" label="If you want to annotate indistinguishable protein groups, either for reporting or for group based quant" help="later. Only works with a single ID run in the file"/>
    <section name="Merging" title="" help="" expanded="false">
      <param name="annotate_origin" argument="-Merging:annotate_origin" type="boolean" truevalue="true" falsevalue="false" checked="true" label="If true, adds a map_index MetaValue to the PeptideIDs to annotate the IDRun they came from" help=""/>
    </section>
    <section name="Algorithm" title="" help="" expanded="false">
      <param name="min_peptides_per_protein" argument="-Algorithm:min_peptides_per_protein" type="integer" optional="true" min="0" value="1" label="Minimal number of peptides needed for a protein identification" help="If set to zero, unmatched proteins get a score of -Infinity. If bigger than zero, proteins with less peptides are filtered and evidences removed from the PSMs. PSMs that do not reference any proteins anymore are removed but the spectrum info is kept"/>
      <param name="score_aggregation_method" argument="-Algorithm:score_aggregation_method" display="radio" type="select" optional="false" label="How to aggregate scores of peptides matching to the same protein?" help="">
        <option value="maximum" selected="true">maximum</option>

      <param name="skip_count_annotation" argument="-Algorithm:skip_count_annotation" type="text" optional="true" value="false" label="If this is true, peptide counts won't be annotated at the proteins" help="">
        <expand macro="list_string_san"/>
      </param>
    </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="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"/>

    <expand macro="manutest_ProteinInference"/>
  </tests>
  <help><![CDATA[Protein inference based on an aggregation of the scores of the identified peptides.


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

11:7951e3db2efd

      <expand macro="list_string_san"/>
    </param>
    <param name="annotate_indist_groups" argument="-annotate_indist_groups" type="boolean" truevalue="true" falsevalue="false" checked="true" label="If you want to annotate indistinguishable protein groups, either for reporting or for group based quant" help="later. Only works with a single ID run in the file"/>
    <section name="Merging" title="" help="" expanded="false">
      <param name="annotate_origin" argument="-Merging:annotate_origin" type="boolean" truevalue="true" falsevalue="false" checked="true" label="If true, adds a map_index MetaValue to the PeptideIDs to annotate the IDRun they came from" help=""/>
      <param name="allow_disagreeing_settings" argument="-Merging:allow_disagreeing_settings" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Force merging of disagreeing runs" help="Use at your own risk"/>
    </section>
    <section name="Algorithm" title="" help="" expanded="false">
      <param name="min_peptides_per_protein" argument="-Algorithm:min_peptides_per_protein" type="integer" optional="true" min="0" value="1" label="Minimal number of peptides needed for a protein identification" help="If set to zero, unmatched proteins get a score of -Infinity. If bigger than zero, proteins with less peptides are filtered and evidences removed from the PSMs. PSMs that do not reference any proteins anymore are removed but the spectrum info is kept"/>
      <param name="score_aggregation_method" argument="-Algorithm:score_aggregation_method" display="radio" type="select" optional="false" label="How to aggregate scores of peptides matching to the same protein?" help="">
        <option value="maximum" selected="true">maximum</option>

      <param name="skip_count_annotation" argument="-Algorithm:skip_count_annotation" type="text" optional="true" value="false" label="If this is true, peptide counts won't be annotated at the proteins" help="">
        <expand macro="list_string_san"/>
      </param>
    </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="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"/>

    <expand macro="manutest_ProteinInference"/>
  </tests>
  <help><![CDATA[Protein inference based on an aggregation of the scores of the identified peptides.


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