annotate OpenSwathDIAPreScoring.xml @ 2:579b44f7b552 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 1e51bed3a1c10c67ef0404216608e9333db04c64

<?xml version='1.0' encoding='UTF-8'?>
<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
<!--Proposed Tool Section: [Targeted Experiments]-->
<tool id="OpenSwathDIAPreScoring" name="OpenSwathDIAPreScoring" version="2.2.0">
  <description>Scoring spectra using the DIA scores.</description>
  <macros>
    <token name="@EXECUTABLE@">OpenSwathDIAPreScoring</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>OpenSwathDIAPreScoring

#if $param_tr:
  -tr $param_tr
#end if
#if $param_out:
  -out $param_out
#end if
-swath_files
  #for token in $param_swath_files:
    $token
  #end for
#if $param_min_upper_edge_dist:
  -min_upper_edge_dist $param_min_upper_edge_dist
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
  <inputs>
    <param name="param_tr" type="data" format="traml" optional="False" label="transition file" help="(-tr) "/>
    <param name="param_swath_files" type="data" format="mzml" multiple="true" optional="True" size="30" label="Swath files that were used to extract the transitions" help="(-swath_files) If present, SWATH specific scoring will be applied">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_min_upper_edge_dist" type="float" value="0.0" label="Minimal distance to the edge to still consider a precursor, in Thomson (only in SWATH)" help="(-min_upper_edge_dist) "/>
    <expand macro="advanced_options">
      <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" format="tabular"/>
  </outputs>
  <help>Scoring spectra using the DIA scores.


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