comparison CometAdapter.xml @ 2:999615a63587 draft

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

1:475c4702fe58

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

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_database:
  -database $param_database
#end if
#if $param_comet_executable:
  -comet_executable $param_comet_executable
#end if
#if $param_comet_version:
  -comet_version
  #if " " in str($param_comet_version):
    "$param_comet_version"

#end if
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="mzml" optional="False" label="Input file" help="(-in) "/>
    <param name="param_database" type="data" format="fasta" optional="False" label="FASTA file" help="(-database) "/>
    <param name="param_comet_executable" type="data" format="txt" value="comet.exe" label="Comet executable of the installation" help="(-comet_executable) e.g. 'comet.exe'"/>
    <param name="param_comet_version" display="radio" type="select" optional="False" value="2016.01 rev. 2" label="comet version: (year,version,revision)" help="(-comet_version) ">
      <option value="2016.01 rev. 2" selected="true">2016.01 rev. 2</option>
      <option value="2016.01 rev. 3">2016.01 rev. 3</option>
      <option value="2017.01 rev. 0beta">2017.01 rev. 0beta</option>
    </param>

    <data name="param_pin_out" format="tabular"/>
  </outputs>
  <help>Annotates MS/MS spectra using Comet.


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

2:999615a63587

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

-comet_executable comet
#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_database:
  -database $param_database
#end if
#if $param_comet_version:
  -comet_version
  #if " " in str($param_comet_version):
    "$param_comet_version"

#end if
    #if $adv_opts.param_force:
  -force
#end if
#end if
-threads "\${GALAXY_SLOTS:-1}"
]]></command>
  <inputs>
    <param name="param_in" type="data" format="mzml" optional="False" label="Input file" help="(-in) "/>
    <param name="param_database" type="data" format="fasta" optional="False" label="FASTA file" help="(-database) "/>
    <param name="param_comet_version" display="radio" type="select" optional="False" value="2016.01 rev. 2" label="comet version: (year,version,revision)" help="(-comet_version) ">
      <option value="2016.01 rev. 2" selected="true">2016.01 rev. 2</option>
      <option value="2016.01 rev. 3">2016.01 rev. 3</option>
      <option value="2017.01 rev. 0beta">2017.01 rev. 0beta</option>
    </param>

    <data name="param_pin_out" format="tabular"/>
  </outputs>
  <help>Annotates MS/MS spectra using Comet.


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