comparison PeptideIndexer.xml @ 7:96dcf92f992d draft

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

6:cb86883cc573

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

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

#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 idXML file containing the identifications" help="(-in) "/>
    <param name="param_fasta" type="data" format="fasta" optional="False" label="Input sequence database in FASTA format" help="(-fasta) Non-existing relative filenames are looked up via 'OpenMS.ini:id_db_dir'"/>
    <param name="param_decoy_string" type="text" size="30" value="DECOY_" label="String that was appended (or prefixed - see 'decoy_string_position' flag below) to the accessions in the protein database to indicate decoy proteins" help="(-decoy_string) ">
      <sanitizer>

    <data name="param_out" format="idxml"/>
  </outputs>
  <help>Refreshes the protein references for all peptide hits.


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

7:96dcf92f992d

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

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

#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
#end if
-threads "\${GALAXY_SLOTS:-1}"
]]></command>
  <inputs>
    <param name="param_in" type="data" format="idxml" optional="False" label="Input idXML file containing the identifications" help="(-in) "/>
    <param name="param_fasta" type="data" format="fasta" optional="False" label="Input sequence database in FASTA format" help="(-fasta) Non-existing relative filenames are looked up via 'OpenMS.ini:id_db_dir'"/>
    <param name="param_decoy_string" type="text" size="30" value="DECOY_" label="String that was appended (or prefixed - see 'decoy_string_position' flag below) to the accessions in the protein database to indicate decoy proteins" help="(-decoy_string) ">
      <sanitizer>

    <data name="param_out" format="idxml"/>
  </outputs>
  <help>Refreshes the protein references for all peptide hits.


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