comparison MapAlignerPoseClustering.xml @ 2:304c13ce9577 draft

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

1:40ca4302e603

<tool id="MapAlignerPoseClustering" name="MapAlignerPoseClustering" version="2.2.0">
  <description>Corrects retention time distortions between maps using a pose clustering approach.</description>
  <macros>
    <token name="@EXECUTABLE@">MapAlignerPoseClustering</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command><![CDATA[

  mkdir -p ./results_trafoxml ./results_out &&

-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
#end if
#if $param_reference_index:

  #else
    $param_algorithm_pairfinder_distance_MZ_unit
  #end if
#end if
#if $adv_opts.adv_opts_selector=='advanced':

    #if $adv_opts.param_algorithm_superimposer_rt_pair_distance_fraction:
  -algorithm:superimposer:rt_pair_distance_fraction $adv_opts.param_algorithm_superimposer_rt_pair_distance_fraction
#end if
    #if $adv_opts.param_algorithm_superimposer_max_shift:
  -algorithm:superimposer:max_shift $adv_opts.param_algorithm_superimposer_max_shift
#end if
    #if $adv_opts.param_algorithm_superimposer_max_scaling:
  -algorithm:superimposer:max_scaling $adv_opts.param_algorithm_superimposer_max_scaling
#end if

#if $adv_opts.param_algorithm_pairfinder_distance_RT_exponent:
  -algorithm:pairfinder:distance_RT:exponent $adv_opts.param_algorithm_pairfinder_distance_RT_exponent
#end if
    #if $adv_opts.param_algorithm_pairfinder_distance_RT_weight:
  -algorithm:pairfinder:distance_RT:weight $adv_opts.param_algorithm_pairfinder_distance_RT_weight
#end if

  #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_algorithm_pairfinder_distance_MZ_unit" display="radio" type="select" optional="False" value="Da" label="Unit of the 'max_difference' paramete" help="(-unit) ">
      <option value="Da" selected="true">Da</option>
      <option value="ppm">ppm</option>
    </param>
    <expand macro="advanced_options">
      <param name="param_algorithm_superimposer_rt_pair_distance_fraction" type="float" min="0.0" max="1.0" optional="True" value="0.1" label="Within each of the two maps, the pairs considered for pose clustering must be separated by at least this fraction of the total elution time interval (i.e., max - min)" help="(-rt_pair_distance_fraction)  "/>
      <param name="param_algorithm_superimposer_max_shift" type="float" min="0.0" optional="True" value="1000.0" label="Maximal shift which is considered during histogramming (in seconds)" help="(-max_shift)  This applies for both directions"/>
      <param name="param_algorithm_superimposer_max_scaling" type="float" min="1.0" optional="True" value="2.0" label="Maximal scaling which is considered during histogramming" help="(-max_scaling)  The minimal scaling is the reciprocal of this"/>
      <param name="param_algorithm_pairfinder_distance_RT_exponent" type="float" min="0.0" optional="True" value="1.0" label="Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent) "/>
      <param name="param_algorithm_pairfinder_distance_RT_weight" type="float" min="0.0" optional="True" value="1.0" label="Final RT distances are weighted by this facto" help="(-weight) "/>
      <param name="param_algorithm_pairfinder_distance_MZ_exponent" type="float" min="0.0" optional="True" value="2.0" label="Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent) "/>
      <param name="param_algorithm_pairfinder_distance_MZ_weight" type="float" min="0.0" optional="True" value="1.0" label="Final m/z distances are weighted by this facto" help="(-weight) "/>
      <param name="param_algorithm_pairfinder_distance_intensity_exponent" type="float" min="0.0" optional="True" value="1.0" label="Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent) "/>

            <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>
</tool>

2:304c13ce9577

<?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: [Map Alignment]-->
<tool id="MapAlignerPoseClustering" name="MapAlignerPoseClustering" version="2.3.0">
  <description>Corrects retention time distortions between maps using a pose clustering approach.</description>
  <macros>
    <token name="@EXECUTABLE@">MapAlignerPoseClustering</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command><![CDATA[

  mkdir -p ./results_trafoxml ./results_out &&

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

#if $param_reference_file:
  -reference:file $param_reference_file
#end if
#if $param_reference_index:

  #else
    $param_algorithm_pairfinder_distance_MZ_unit
  #end if
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
    #if $adv_opts.param_algorithm_superimposer_rt_pair_distance_fraction:
  -algorithm:superimposer:rt_pair_distance_fraction $adv_opts.param_algorithm_superimposer_rt_pair_distance_fraction
#end if
    #if $adv_opts.param_algorithm_superimposer_max_shift:
  -algorithm:superimposer:max_shift $adv_opts.param_algorithm_superimposer_max_shift
#end if
    #if $adv_opts.param_algorithm_superimposer_max_scaling:
  -algorithm:superimposer:max_scaling $adv_opts.param_algorithm_superimposer_max_scaling
#end if
    #if $adv_opts.param_algorithm_superimposer_dump_buckets:
  -algorithm:superimposer:dump_buckets     "$adv_opts.param_algorithm_superimposer_dump_buckets"
#end if
    #if $adv_opts.param_algorithm_superimposer_dump_pairs:
  -algorithm:superimposer:dump_pairs     "$adv_opts.param_algorithm_superimposer_dump_pairs"
#end if
    #if $adv_opts.param_algorithm_pairfinder_distance_RT_exponent:
  -algorithm:pairfinder:distance_RT:exponent $adv_opts.param_algorithm_pairfinder_distance_RT_exponent
#end if
    #if $adv_opts.param_algorithm_pairfinder_distance_RT_weight:
  -algorithm:pairfinder:distance_RT:weight $adv_opts.param_algorithm_pairfinder_distance_RT_weight
#end if

  #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_algorithm_pairfinder_distance_MZ_unit" display="radio" type="select" optional="False" value="Da" label="Unit of the 'max_difference' paramete" help="(-unit) ">
      <option value="Da" selected="true">Da</option>
      <option value="ppm">ppm</option>
    </param>
    <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) "/>
      <param name="param_algorithm_superimposer_rt_pair_distance_fraction" type="float" min="0.0" max="1.0" optional="True" value="0.1" label="Within each of the two maps, the pairs considered for pose clustering must be separated by at least this fraction of the total elution time interval (i.e., max - min)" help="(-rt_pair_distance_fraction)  "/>
      <param name="param_algorithm_superimposer_max_shift" type="float" min="0.0" optional="True" value="1000.0" label="Maximal shift which is considered during histogramming (in seconds)" help="(-max_shift)  This applies for both directions"/>
      <param name="param_algorithm_superimposer_max_scaling" type="float" min="1.0" optional="True" value="2.0" label="Maximal scaling which is considered during histogramming" help="(-max_scaling)  The minimal scaling is the reciprocal of this"/>
      <param name="param_algorithm_superimposer_dump_buckets" type="text" size="30" label="[DEBUG] If non-empty, base filename where hash table buckets will be dumped to" help="(-dump_buckets)  A serial number for each invocation will be appended automatically">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
      <param name="param_algorithm_superimposer_dump_pairs" type="text" size="30" label="[DEBUG] If non-empty, base filename where the individual hashed pairs will be dumped to (large!)" help="(-dump_pairs)  A serial number for each invocation will be appended automatically">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
      <param name="param_algorithm_pairfinder_distance_RT_exponent" type="float" min="0.0" optional="True" value="1.0" label="Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent) "/>
      <param name="param_algorithm_pairfinder_distance_RT_weight" type="float" min="0.0" optional="True" value="1.0" label="Final RT distances are weighted by this facto" help="(-weight) "/>
      <param name="param_algorithm_pairfinder_distance_MZ_exponent" type="float" min="0.0" optional="True" value="2.0" label="Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent) "/>
      <param name="param_algorithm_pairfinder_distance_MZ_weight" type="float" min="0.0" optional="True" value="1.0" label="Final m/z distances are weighted by this facto" help="(-weight) "/>
      <param name="param_algorithm_pairfinder_distance_intensity_exponent" type="float" min="0.0" optional="True" value="1.0" label="Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent) "/>

            <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>
</tool>