view SpecLibCreator.xml @ 7:b854c87823d3 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 26556c08813e892b4d1eed0e98012601870cae5f

<?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: [Utilities]-->
<tool id="SpecLibCreator" name="SpecLibCreator" version="2.2.0">
  <description>Creates an MSP formatted spectral library.</description>
  <macros>
    <token name="@EXECUTABLE@">SpecLibCreator</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>SpecLibCreator

#if $param_info:
  -info $param_info
#end if
#if $param_itemseperator:
  -itemseperator     "$param_itemseperator"
#end if
#if $param_itemenclosed:
  -itemenclosed
#end if
#if $param_spec:
  -spec $param_spec
#end if
#if $param_out:
  -out $param_out
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
  <inputs>
    <param name="param_info" type="data" format="tabular" optional="False" label="Holds id, peptide, retention time etc" help="(-info) "/>
    <param name="param_itemseperator" type="text" size="30" value="," label=" Separator between items. e.g. ," help="(-itemseperator) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_itemenclosed" display="radio" type="boolean" truevalue="-itemenclosed" falsevalue="" checked="false" optional="True" label="'true' or 'false' if true every item is enclosed" help="(-itemenclosed) e.g. '$peptide$,$run$"/>
    <param name="param_spec" type="data" format="mzData,mzxml" optional="False" label="spectra" help="(-spec) "/>
    <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="msp"/>
  </outputs>
  <help>Creates an MSP formatted spectral library.


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