comparison FileMerger.xml @ 7:3d5cda05df45 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b

6:27cba4c5fc42

<?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: [File Handling]-->
<tool id="FileMerger" name="FileMerger" version="2.2.0">
  <description>Merges several MS files into one file.</description>
  <macros>
    <token name="@EXECUTABLE@">FileMerger</token>
    <import>macros.xml</import>
  </macros>

#end if
#if $param_rt_concat_gap:
  -rt_concat:gap $param_rt_concat_gap
#end if

#if $param_raw_rt_auto:
  -raw:rt_auto
#end if

#if $rep_param_raw_rt_custom:

  -force
#end if
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="mzData,mzxml,mzml,dta,dta2d,mgf,featurexml,consensusxml,fid,traml" multiple="true" optional="False" size="30" label="Input files separated by blank" help="(-in) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>

    </param>
    <param name="param_annotate_file_origin" display="radio" type="boolean" truevalue="-annotate_file_origin" falsevalue="" checked="false" optional="True" label="Store the original filename in each feature using meta value &quot;file_origin&quot; (for featureXML and consensusXML only)" help="(-annotate_file_origin) "/>
    <param name="param_rt_concat_gap" type="float" value="0.0" label="The amount of gap (in seconds) to insert between the RT ranges of different input files" help="(-gap) RT concatenation is enabled if a value &gt; 0 is set"/>
    <param name="param_raw_rt_auto" display="radio" type="boolean" truevalue="-raw:rt_auto" falsevalue="" checked="false" optional="True" label="Assign retention times automatically (integers starting at 1)" help="(-rt_auto) "/>
    <repeat name="rep_param_raw_rt_custom" min="0" title="param_raw_rt_custom">
      <param name="param_raw_rt_custom" type="text" size="30" value="0" label="Custom retention times that are assigned to the files" help="(-rt_custom) The number of given retention times must be equal to the number of input files">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>

    <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="mzml"/>
  </outputs>
  <help>Merges several MS files into one file.


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

7:3d5cda05df45

<?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 CTDConverter.-->
<!--Proposed Tool Section: [File Handling]-->
<tool id="FileMerger" name="FileMerger" version="2.3.0">
  <description>Merges several MS files into one file.</description>
  <macros>
    <token name="@EXECUTABLE@">FileMerger</token>
    <import>macros.xml</import>
  </macros>

#end if
#if $param_rt_concat_gap:
  -rt_concat:gap $param_rt_concat_gap
#end if

#if $rep_param_rt_concat_trafo_out:
-rt_concat:trafo_out
  #for token in $rep_param_rt_concat_trafo_out:
    #if " " in str(token):
      "$token.param_rt_concat_trafo_out"
    #else
      $token.param_rt_concat_trafo_out
    #end if
  #end for
#end if
#if $param_raw_rt_auto:
  -raw:rt_auto
#end if

#if $rep_param_raw_rt_custom:

  -force
#end if
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="mzData,mzxml,mzml,dta,dta2d,mgf,featurexml,consensusxml,fid,traml,fasta" multiple="true" optional="False" size="30" label="Input files separated by blank" help="(-in) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>

    </param>
    <param name="param_annotate_file_origin" display="radio" type="boolean" truevalue="-annotate_file_origin" falsevalue="" checked="false" optional="True" label="Store the original filename in each feature using meta value &quot;file_origin&quot; (for featureXML and consensusXML only)" help="(-annotate_file_origin) "/>
    <param name="param_rt_concat_gap" type="float" value="0.0" label="The amount of gap (in seconds) to insert between the RT ranges of different input files" help="(-gap) RT concatenation is enabled if a value &gt; 0 is set"/>
    <param name="param_raw_rt_auto" display="radio" type="boolean" truevalue="-raw:rt_auto" falsevalue="" checked="false" optional="True" label="Assign retention times automatically (integers starting at 1)" help="(-rt_auto) "/>
    <repeat name="rep_param_raw_rt_custom" min="0" title="param_raw_rt_custom">
      <param name="param_raw_rt_custom" type="text" size="30" value="0" label="List of custom retention times that are assigned to the files" help="(-rt_custom) The number of given retention times must be equal to the number of input files">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>

    <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="featurexml"/>
    <data name="param_rt_concat_trafo_out" format="trafoxml"/>
  </outputs>
  <help>Merges several MS files into one file.


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