annotate FileMerger.xml @ 3:1dc8550349dd draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14

<?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>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>FileMerger

-in
  #for token in $param_in:
    $token
  #end for
#if $param_out:
  -out $param_out
#end if
#if $param_annotate_file_origin:
  -annotate_file_origin
#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:
-raw:rt_custom
  #for token in $rep_param_raw_rt_custom:
    #if " " in str(token):
      "$token.param_raw_rt_custom"
    #else
      $token.param_raw_rt_custom
    #end if
  #end for
#end if
#if $param_raw_rt_filename:
  -raw:rt_filename
#end if
#if $param_raw_ms_level:
  -raw:ms_level $param_raw_ms_level
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -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>
      </sanitizer>
    </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" max="1" 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>
        </sanitizer>
      </param>
    </repeat>
    <param name="param_raw_rt_filename" display="radio" type="boolean" truevalue="-raw:rt_filename" falsevalue="" checked="false" optional="True" label="Try to guess the retention time of a file based on the filename. This option is useful for merging DTA files, where filenames should contain the string 'rt' directly followed by a floating point number," help="(-rt_filename) e.g. 'my_spectrum_rt2795.15.dta'"/>
    <param name="param_raw_ms_level" type="integer" value="0" label="If 1 or higher, this number is assigned to spectra as the MS level" help="(-ms_level) This option is useful for DTA files which do not contain MS level information"/>
    <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>
</tool>