annotate TextExporter.xml @ 5:33e848694dc1 draft

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

<?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="TextExporter" name="TextExporter" version="2.3.0">
  <description>Exports various XML formats to a text file.</description>
  <macros>
    <token name="@EXECUTABLE@">TextExporter</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>TextExporter

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_separator:
  -separator     "$param_separator"
#end if
#if $param_replacement:
  -replacement     "$param_replacement"
#end if
#if $param_quoting:
  -quoting
  #if " " in str($param_quoting):
    "$param_quoting"
  #else
    $param_quoting
  #end if
#end if
#if $param_no_ids:
  -no_ids
#end if
#if $param_feature_minimal:
  -feature:minimal
#end if
#if $param_feature_add_metavalues:
  -feature:add_metavalues $param_feature_add_metavalues
#end if
#if $param_id_proteins_only:
  -id:proteins_only
#end if
#if $param_id_peptides_only:
  -id:peptides_only
#end if
#if $param_id_first_dim_rt:
  -id:first_dim_rt
#end if
#if $param_id_add_metavalues:
  -id:add_metavalues $param_id_add_metavalues
#end if
#if $param_id_add_hit_metavalues:
  -id:add_hit_metavalues $param_id_add_hit_metavalues
#end if
#if $param_consensus_centroids:
  -consensus:centroids $param_consensus_centroids
#end if
#if $param_consensus_elements:
  -consensus:elements $param_consensus_elements
#end if
#if $param_consensus_features:
  -consensus:features $param_consensus_features
#end if
#if $param_consensus_sorting_method:
  -consensus:sorting_method
  #if " " in str($param_consensus_sorting_method):
    "$param_consensus_sorting_method"
  #else
    $param_consensus_sorting_method
  #end if
#end if
#if $param_consensus_sort_by_maps:
  -consensus:sort_by_maps
#end if
#if $param_consensus_sort_by_size:
  -consensus:sort_by_size
#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="featurexml,consensusxml,idxml,mzml" optional="False" label="Input file" help="(-in) "/>
    <param name="param_separator" type="text" size="30" label="The used separator character(s); if not set the 'tab' character is used" help="(-separator) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_replacement" type="text" size="30" value="_" label="Used to replace occurrences of the separator in strings before writing, if 'quoting' is 'none'" help="(-replacement) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_quoting" display="radio" type="select" optional="False" value="none" label="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes, &lt;br&gt;'escape' for quoting with backslash-escaping of embedded quotes" help="(-quoting) ">
      <option value="none" selected="true">none</option>
      <option value="double">double</option>
      <option value="escape">escape</option>
    </param>
    <param name="param_no_ids" display="radio" type="boolean" truevalue="-no_ids" falsevalue="" checked="false" optional="True" label="Suppresses output of identification data" help="(-no_ids) "/>
    <param name="param_feature_minimal" display="radio" type="boolean" truevalue="-feature:minimal" falsevalue="" checked="false" optional="True" label="Set this flag to write only three attributes: RT, m/z, and intensity" help="(-minimal) "/>
    <param name="param_feature_add_metavalues" type="integer" min="-1" max="100" optional="True" value="-1" label="Add columns for meta values which occur with a certain frequency (0-100%)" help="(-add_metavalues) Set to -1 to omit meta values (default)"/>
    <param name="param_id_proteins_only" display="radio" type="boolean" truevalue="-id:proteins_only" falsevalue="" checked="false" optional="True" label="Set this flag if you want only protein information from an idXML file" help="(-proteins_only) "/>
    <param name="param_id_peptides_only" display="radio" type="boolean" truevalue="-id:peptides_only" falsevalue="" checked="false" optional="True" label="Set this flag if you want only peptide information from an idXML file" help="(-peptides_only) "/>
    <param name="param_id_first_dim_rt" display="radio" type="boolean" truevalue="-id:first_dim_rt" falsevalue="" checked="false" optional="True" label="If this flag is set the first_dim RT of the peptide hits will also be printed (if present)" help="(-first_dim_rt) "/>
    <param name="param_id_add_metavalues" type="integer" min="-1" max="100" optional="True" value="-1" label="Add columns for meta values which occur with a certain frequency (0-100%)" help="(-add_metavalues) Set to -1 to omit meta values (default)"/>
    <param name="param_id_add_hit_metavalues" type="integer" min="-1" max="100" optional="True" value="-1" label="Add columns for meta values which occur with a certain frequency (0-100%)" help="(-add_hit_metavalues) Set to -1 to omit meta values (default)"/>
    <param name="param_consensus_sorting_method" type="select" optional="False" value="none" label="Sorting options can be combined" help="(-sorting_method) The precedence is: sort_by_size, sort_by_maps, sorting_method">
      <option value="none" selected="true">none</option>
      <option value="RT">RT</option>
      <option value="MZ">MZ</option>
      <option value="RT_then_MZ">RT_then_MZ</option>
      <option value="intensity">intensity</option>
      <option value="quality_decreasing">quality_decreasing</option>
      <option value="quality_increasing">quality_increasing</option>
    </param>
    <param name="param_consensus_sort_by_maps" display="radio" type="boolean" truevalue="-consensus:sort_by_maps" falsevalue="" checked="false" optional="True" label="Apply a stable sort by the covered maps, lexicographically" help="(-sort_by_maps) "/>
    <param name="param_consensus_sort_by_size" display="radio" type="boolean" truevalue="-consensus:sort_by_size" falsevalue="" checked="false" optional="True" label="Apply a stable sort by decreasing size (i.e., the number of elements)" help="(-sort_by_size) "/>
    <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"/>
    <data name="param_consensus_centroids" format="tabular"/>
    <data name="param_consensus_elements" format="tabular"/>
    <data name="param_consensus_features" format="tabular"/>
  </outputs>
  <help>Exports various XML formats to a text file.


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