comparison MapAlignerPoseClustering.xml @ 1:40ca4302e603 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 42171f39c42277bcfb50271180dcc9c82d3e8e74

0:70f729e59244

    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command><![CDATA[
  MapAlignerPoseClustering
-in $param_in
-out $out
-trafo_out $trafo_out

-threads "\${GALAXY_SLOTS:-1}"

#if $param_reference_file:
  -reference:file $param_reference_file

  #else
    $adv_opts.param_algorithm_pairfinder_distance_intensity_log_transform
  #end if
#end if
#end if
 ]]>
</command>
  <inputs>
    <param name="param_in" type="data" format="mzML,featureXML" label="Input files to align (all must have the same file type)" help="(-in) "/>
    <param name="param_reference_file" type="data" format="mzML,featureXML" optional="True" label="File to use as reference (same file format as input files required)" help="(-file) "/>
    <param name="param_reference_index" type="integer" min="0" optional="True" value="0" label="Use one of the input files as reference ('1' for the first file, etc.)" help="(-index) &lt;br&gt;If '0', no explicit reference is set - the algorithm will select a reference"/>
    <param name="param_algorithm_max_num_peaks_considered" type="integer" min="-1" optional="True" value="1000" label="The maximal number of peaks/features to be considered per map" help="(-max_num_peaks_considered) To use all, set to '-1'"/>
    <param name="param_algorithm_superimposer_mz_pair_max_distance" type="float" min="0.0" optional="True" value="0.5" label="Maximum of m/z deviation of corresponding elements in different maps" help="(-mz_pair_max_distance)  This condition applies to the pairs considered in hashing"/>
    <param name="param_algorithm_superimposer_num_used_points" type="integer" min="-1" optional="True" value="2000" label="Maximum number of elements considered in each map (selected by intensity)" help="(-num_used_points)  Use this to reduce the running time and to disregard weak signals during alignment.  For using all points, set this to -1"/>

        <option value="disabled" selected="true">disabled</option>
      </param>
    </expand>
    </inputs>
    <outputs>
        <data name="out" format_source="param_in" metadata_source="param_in" />
        <data name="trafo_out" format_source="param_in" metadata_source="param_in" />
    </outputs>
    <help>Corrects retention time distortions between maps using a pose clustering approach.


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

1:40ca4302e603

    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command><![CDATA[

  mkdir -p ./results_trafoxml ./results_out &&
  MapAlignerPoseClustering

-in
#for $infile in $param_in:
    '$infile'
#end for

-out
#for $counter,$infile in enumerate($param_in):
    ./results_out/${infile.element_identifier}.${infile.extension}
#end for

-trafo_out
#for $counter,$infile in enumerate($param_in):
    ./results_trafoxml/${infile.element_identifier}.trafoxml
#end for

-threads "\${GALAXY_SLOTS:-1}"

#if $param_reference_file:
  -reference:file $param_reference_file

  #else
    $adv_opts.param_algorithm_pairfinder_distance_intensity_log_transform
  #end if
#end if
#end if

 ]]>
</command>
  <inputs>
    <param name="param_in" type="data" format="mzML,featureXML" multiple="true" label="Input files to align (all must have the same file type)" help="(-in) "/>
    <param name="param_reference_file" type="data" format="mzML,featureXML" optional="True" label="File to use as reference (same file format as input files required)" help="(-file) "/>
    <param name="param_reference_index" type="integer" min="0" optional="True" value="0" label="Use one of the input files as reference ('1' for the first file, etc.)" help="(-index) &lt;br&gt;If '0', no explicit reference is set - the algorithm will select a reference"/>
    <param name="param_algorithm_max_num_peaks_considered" type="integer" min="-1" optional="True" value="1000" label="The maximal number of peaks/features to be considered per map" help="(-max_num_peaks_considered) To use all, set to '-1'"/>
    <param name="param_algorithm_superimposer_mz_pair_max_distance" type="float" min="0.0" optional="True" value="0.5" label="Maximum of m/z deviation of corresponding elements in different maps" help="(-mz_pair_max_distance)  This condition applies to the pairs considered in hashing"/>
    <param name="param_algorithm_superimposer_num_used_points" type="integer" min="-1" optional="True" value="2000" label="Maximum number of elements considered in each map (selected by intensity)" help="(-num_used_points)  Use this to reduce the running time and to disregard weak signals during alignment.  For using all points, set this to -1"/>

        <option value="disabled" selected="true">disabled</option>
      </param>
    </expand>
    </inputs>
    <outputs>
        <collection name="out" type="list">
            <discover_datasets pattern="__designation_and_ext__" directory="results_out"/>
        </collection>

        <collection name="trafo_out" type="list">
            <discover_datasets pattern="__designation_and_ext__" directory="results_trafoxml"/>
        </collection>
    </outputs>
    <help>Corrects retention time distortions between maps using a pose clustering approach.


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