comparison IDMapper.xml @ 9:d29bb4c9831e draft

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

8:a3960e7c2d1d

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

#if $param_id:
  -id $param_id
#end if
#if $param_in:

#end if
    #if $adv_opts.param_consensus_annotate_ids_with_subelements:
  -consensus:annotate_ids_with_subelements
#end if
#end if
</command>
  <inputs>
    <param name="param_id" type="data" format="mzid,idxml" optional="False" label="Protein/peptide identifications file" help="(-id) "/>
    <param name="param_in" type="data" format="featurexml,consensusxml,mzq" optional="False" label="Feature map/consensus map file" help="(-in) "/>
    <param name="param_rt_tolerance" type="float" min="0.0" optional="True" value="5.0" label="RT tolerance (in seconds) for the matching of peptide identifications and (consensus) features" help="(-rt_tolerance) &lt;br&gt;Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value"/>
    <param name="param_mz_tolerance" type="float" min="0.0" optional="True" value="20.0" label="m/z tolerance (in ppm or Da) for the matching of peptide identifications and (consensus) features" help="(-mz_tolerance) &lt;br&gt;Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value"/>

    <data name="param_out" metadata_source="param_in" format_source="param_in" />
  </outputs>
  <help>Assigns protein/peptide identifications to features or consensus features.


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

9:d29bb4c9831e

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

#if $param_id:
  -id $param_id
#end if
#if $param_in:

#end if
    #if $adv_opts.param_consensus_annotate_ids_with_subelements:
  -consensus:annotate_ids_with_subelements
#end if
#end if
]]></command>
  <inputs>
    <param name="param_id" type="data" format="mzid,idxml" optional="False" label="Protein/peptide identifications file" help="(-id) "/>
    <param name="param_in" type="data" format="featurexml,consensusxml,mzq" optional="False" label="Feature map/consensus map file" help="(-in) "/>
    <param name="param_rt_tolerance" type="float" min="0.0" optional="True" value="5.0" label="RT tolerance (in seconds) for the matching of peptide identifications and (consensus) features" help="(-rt_tolerance) &lt;br&gt;Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value"/>
    <param name="param_mz_tolerance" type="float" min="0.0" optional="True" value="20.0" label="m/z tolerance (in ppm or Da) for the matching of peptide identifications and (consensus) features" help="(-mz_tolerance) &lt;br&gt;Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value"/>

    <data name="param_out" metadata_source="param_in" format_source="param_in" />
  </outputs>
  <help>Assigns protein/peptide identifications to features or consensus features.


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