comparison TextExporter.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="TextExporter" name="TextExporter" version="1.12.0">
  <description>Exports various XML formats to a text file.</description>
  <macros>
    <token name="@EXECUTABLE@">TextExporter</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>TextExporter

-in ${param_in}
-out ${param_out}
-separator ${param_separator}
-replacement ${param_replacement}
-quoting ${param_quoting}
${param_no_ids}
-threads \${GALAXY_SLOTS:-24} 
${param_minimal}
${param_proteins_only}
${param_peptides_only}
${param_first_dim_rt}
-consensus:centroids ${param_centroids}
-consensus:elements ${param_elements}
-consensus:features ${param_features}
-consensus:sorting_method ${param_sorting_method}
${param_sort_by_maps}
${param_sort_by_size}
</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="20" label="The used separator character(s); if not set the 'tab' character is used" help="(-separator)"/>
    <param name="param_replacement" type="text" size="20" value="_" label="Used to replace occurrences of the separator in strings before writing, if 'quoting' is 'none'" help="(-replacement)"/>
    <param name="param_quoting" type="select" optional="True" value="none" label="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes,#br#'escape' for quoting with backslash-escaping of embedded quotes" help="(-quoting)">
      <option value="none">none</option>
      <option value="double">double</option>
      <option value="escape">escape</option>
    </param>
    <param name="param_no_ids" type="boolean" truevalue="-no_ids true" falsevalue="-no_ids false" checked="false" optional="True" label="Supresses output of identification data." help="(-no_ids)"/>
    <param name="param_minimal" type="boolean" truevalue="-feature:minimal true" falsevalue="-feature:minimal false" checked="false" optional="True" label="Set this flag to write only three attributes: RT, m/z, and intensity." help="(-minimal)"/>
    <param name="param_proteins_only" type="boolean" truevalue="-id:proteins_only true" falsevalue="-id:proteins_only false" checked="false" optional="True" label="Set this flag if you want only protein information from an idXML file" help="(-proteins_only)"/>
    <param name="param_peptides_only" type="boolean" truevalue="-id:peptides_only true" falsevalue="-id:peptides_only false" checked="false" optional="True" label="Set this flag if you want only peptide information from an idXML file" help="(-peptides_only)"/>
    <param name="param_first_dim_rt" type="boolean" truevalue="-id:first_dim_rt true" falsevalue="-id:first_dim_rt false" 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_sorting_method" type="select" optional="True" value="none" label="Sorting options can be combined. The precedence is: sort_by_size, sort_by_maps, sorting_method" help="(-sorting_method)">
      <option value="none">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_sort_by_maps" type="boolean" truevalue="-consensus:sort_by_maps true" falsevalue="-consensus:sort_by_maps false" checked="false" optional="True" label="Apply a stable sort by the covered maps, lexicographically" help="(-sort_by_maps)"/>
    <param name="param_sort_by_size" type="boolean" truevalue="-consensus:sort_by_size true" falsevalue="-consensus:sort_by_size false" checked="false" optional="True" label="Apply a stable sort by decreasing size (i.e., the number of elements)" help="(-sort_by_size)"/>
  </inputs>
  <outputs>
    <data name="param_out" label="Output file (mandatory for featureXML and idXML)" format="tabular"/>
    <data name="param_centroids" label="Output file for centroids of consensus features" format="tabular"/>
    <data name="param_elements" label="Output file for elements of consensus features" format="tabular"/>
    <data name="param_features" label="Output file for consensus features and contained elements from all maps (writes 'nan's if elements are missing)" format="tabular"/>
  </outputs>
  <help>**What it does**

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

@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: [File Handling]-->
  <tool id="TextExporter" name="TextExporter" version="2.0.0">
    <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 $param_separator:
  -separator     &quot;$param_separator&quot;
#end if
#if $param_replacement:
  -replacement     &quot;$param_replacement&quot;
#end if
#if $param_quoting:
  -quoting
  #if &quot; &quot; in str($param_quoting):
    &quot;$param_quoting&quot;
  #else
    $param_quoting
  #end if
#end if
#if $param_no_ids:
  -no_ids
#end if
-threads \${GALAXY_SLOTS:-24}
#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_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 $param_consensus_sorting_method:
  -consensus:sorting_method
  #if &quot; &quot; in str($param_consensus_sorting_method):
    &quot;$param_consensus_sorting_method&quot;
  #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 format="xml,consensusxml,mzml" help="(-in) " label="Input file" name="param_in" optional="False" type="data"/>
      <param help="(-separator) " label="The used separator character(s); if not set the 'tab' character is used" name="param_separator" size="30" type="text">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
      <param help="(-replacement) " label="Used to replace occurrences of the separator in strings before writing, if 'quoting' is 'none'" name="param_replacement" size="30" type="text" value="_">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
      <param help="(-quoting) " 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" name="param_quoting" optional="True" type="select" value="none">
        <option value="none">none</option>
        <option value="double">double</option>
        <option value="escape">escape</option>
      </param>
      <param checked="false" falsevalue="" help="(-no_ids) " label="Suppresses output of identification data" name="param_no_ids" optional="True" truevalue="-no_ids" type="boolean"/>
      <param checked="false" falsevalue="" help="(-minimal) " label="Set this flag to write only three attributes: RT, m/z, and intensity" name="param_feature_minimal" optional="True" truevalue="-feature:minimal" type="boolean"/>
      <param help="(-add_metavalues) Set to -1 to omit meta values (default)" label="Add columns for meta values which occur with a certain frequency (0-100%)" max="100" min="-1" name="param_feature_add_metavalues" optional="True" type="integer" value="-1"/>
      <param checked="false" falsevalue="" help="(-proteins_only) " label="Set this flag if you want only protein information from an idXML file" name="param_id_proteins_only" optional="True" truevalue="-id:proteins_only" type="boolean"/>
      <param checked="false" falsevalue="" help="(-peptides_only) " label="Set this flag if you want only peptide information from an idXML file" name="param_id_peptides_only" optional="True" truevalue="-id:peptides_only" type="boolean"/>
      <param checked="false" falsevalue="" help="(-first_dim_rt) " label="If this flag is set the first_dim RT of the peptide hits will also be printed (if present)" name="param_id_first_dim_rt" optional="True" truevalue="-id:first_dim_rt" type="boolean"/>
      <param help="(-sorting_method) The precedence is: sort_by_size, sort_by_maps, sorting_method" label="Sorting options can be combined" name="param_consensus_sorting_method" optional="True" type="select" value="none">
        <option value="none">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 checked="false" falsevalue="" help="(-sort_by_maps) " label="Apply a stable sort by the covered maps, lexicographically" name="param_consensus_sort_by_maps" optional="True" truevalue="-consensus:sort_by_maps" type="boolean"/>
      <param checked="false" falsevalue="" help="(-sort_by_size) " label="Apply a stable sort by decreasing size (i.e., the number of elements)" name="param_consensus_sort_by_size" optional="True" truevalue="-consensus:sort_by_size" type="boolean"/>
      <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="tabular" name="param_out"/>
      <data format="tabular" name="param_consensus_centroids"/>
      <data format="tabular" name="param_consensus_elements"/>
      <data format="tabular" name="param_consensus_features"/>
    </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>