comparison OpenPepXL.xml @ 2:ec2524b5a07a draft

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

1:dde913004c8a

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

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

#end if
    #if $adv_opts.param_precursor_max_charge:
  -precursor:max_charge $adv_opts.param_precursor_max_charge
#end if
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="mzml" optional="False" label="Input file containing the spectra" help="(-in) "/>
    <param name="param_consensus" type="data" format="consensusxml" optional="False" label="Input file containing the linked mass peaks" help="(-consensus) "/>
    <param name="param_database" type="data" format="fasta" optional="False" label="Input file containing the protein database" help="(-database) "/>
    <param name="param_decoy_string" type="text" size="30" value="decoy" label="String that was appended (or prefixed - see 'prefix' flag below) to the accessions in the protein database to indicate decoy proteins" help="(-decoy_string) ">

    <data name="param_out_mzIdentML" format="mzid"/>
  </outputs>
  <help>Tool for protein-protein cross-linking identification using labeled linkers.


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

2:ec2524b5a07a

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

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

#end if
    #if $adv_opts.param_precursor_max_charge:
  -precursor:max_charge $adv_opts.param_precursor_max_charge
#end if
#end if
]]></command>
  <inputs>
    <param name="param_in" type="data" format="mzml" optional="False" label="Input file containing the spectra" help="(-in) "/>
    <param name="param_consensus" type="data" format="consensusxml" optional="False" label="Input file containing the linked mass peaks" help="(-consensus) "/>
    <param name="param_database" type="data" format="fasta" optional="False" label="Input file containing the protein database" help="(-database) "/>
    <param name="param_decoy_string" type="text" size="30" value="decoy" label="String that was appended (or prefixed - see 'prefix' flag below) to the accessions in the protein database to indicate decoy proteins" help="(-decoy_string) ">

    <data name="param_out_mzIdentML" format="mzid"/>
  </outputs>
  <help>Tool for protein-protein cross-linking identification using labeled linkers.


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