comparison SpecLibCreator.xml @ 4:6ead64a594bd draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty

3:ec62782f6c68

<?xml version='1.0' encoding='UTF-8'?>
<tool id="SpecLibCreator" name="SpecLibCreator" version="1.12.0">
  <description>Creates an MSP formatted spectral library.</description>
  <macros>
    <token name="@EXECUTABLE@">SpecLibCreator</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>SpecLibCreator

-info ${param_info}
-itemseperator ${param_itemseperator}
${param_itemenclosed}
-spec ${param_spec}
-out ${param_out}
-threads \${GALAXY_SLOTS:-24} 
</command>
  <inputs>
    <param name="param_info" type="data" format="tabular" optional="False" label="Holds id, peptide, retention time etc." help="(-info)"/>
    <param name="param_itemseperator" type="text" size="20" value="," label=" Seperator between items. e.g. ," help="(-itemseperator)"/>
    <param name="param_itemenclosed" type="boolean" truevalue="-itemenclosed true" falsevalue="-itemenclosed false" checked="false" optional="True" label="'true' or 'false' if true every item is enclosed e.g. '$peptide$,$run$..." help="(-itemenclosed)"/>
    <param name="param_spec" type="data" format="mzXML" optional="False" label="spectra" help="(-spec)"/>
  </inputs>
  <outputs>
    <data name="param_out" label="output MSP formated spectra library" format="data"/>
  </outputs>
  <help>**What it does**

Creates an MSP formatted spectral library.


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

@REFERENCES@
</help>
</tool>

4:6ead64a594bd

<?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="2.0.0">
    <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 $param_itemseperator:
  -itemseperator     &quot;$param_itemseperator&quot;
#end if
#if $param_itemenclosed:
  -itemenclosed
#end if
#if $param_spec:
  -spec $param_spec
#end if
#if $param_out:
  -out $param_out
#end if
-threads \${GALAXY_SLOTS:-24}
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
    <inputs>
      <param format="tabular" help="(-info) " label="Holds id, peptide, retention time etc" name="param_info" optional="False" type="data"/>
      <param help="(-itemseperator) " label=" Seperator between items. e.g. ," name="param_itemseperator" size="30" type="text" value=",">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
      <param checked="false" falsevalue="" help="(-itemenclosed) e.g. '$peptide$,$run$" label="'true' or 'false' if true every item is enclosed" name="param_itemenclosed" optional="True" truevalue="-itemenclosed" type="boolean"/>
      <param format="xml,mzxml" help="(-spec) " label="spectra" name="param_spec" optional="False" type="data"/>
      <expand macro="advanced_options">
        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
      </expand>
    </inputs>
    <outputs>
      <data format="txt" name="param_out"/>
    </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>