comparison ProteinInference.xml @ 7:4a39dd3bbe69 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5

6:bfba20e0425e

    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>ProteinInference

#if $param_in:
  -in $param_in
#end if
#if $param_out:

#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="idxml" optional="False" label="input file" help="(-in) "/>
    <param name="param_min_peptides_per_protein" type="integer" min="1" optional="True" value="2" label="Minimal number of peptides needed for a protein identification" help="(-min_peptides_per_protein) "/>
    <param name="param_treat_charge_variants_separately" display="radio" type="boolean" truevalue="-treat_charge_variants_separately" falsevalue="" checked="false" optional="True" label="If this flag is set, different charge variants of the same peptide sequence count as inidividual evidences" help="(-treat_charge_variants_separately) "/>
    <param name="param_treat_modification_variants_separately" display="radio" type="boolean" truevalue="-treat_modification_variants_separately" falsevalue="" checked="false" optional="True" label="If this flag is set, different modification variants of the same peptide sequence count as individual evidences" help="(-treat_modification_variants_separately) "/>

    <data name="param_out" format="idxml"/>
  </outputs>
  <help>Protein inference based on the number of identified peptides.


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ProteinInference.html</help>
</tool>

7:4a39dd3bbe69

    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command detect_errors="aggressive"><![CDATA[ProteinInference

#if $param_in:
  -in $param_in
#end if
#if $param_out:

#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
#end if
]]></command>
  <inputs>
    <param name="param_in" type="data" format="idxml" optional="False" label="input file" help="(-in) "/>
    <param name="param_min_peptides_per_protein" type="integer" min="1" optional="True" value="2" label="Minimal number of peptides needed for a protein identification" help="(-min_peptides_per_protein) "/>
    <param name="param_treat_charge_variants_separately" display="radio" type="boolean" truevalue="-treat_charge_variants_separately" falsevalue="" checked="false" optional="True" label="If this flag is set, different charge variants of the same peptide sequence count as inidividual evidences" help="(-treat_charge_variants_separately) "/>
    <param name="param_treat_modification_variants_separately" display="radio" type="boolean" truevalue="-treat_modification_variants_separately" falsevalue="" checked="false" optional="True" label="If this flag is set, different modification variants of the same peptide sequence count as individual evidences" help="(-treat_modification_variants_separately) "/>

    <data name="param_out" format="idxml"/>
  </outputs>
  <help>Protein inference based on the number of identified peptides.


For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_ProteinInference.html</help>
</tool>