annotate FeatureLinkerUnlabeled.xml @ 7:df7f4ac9a2c6 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: [Map Alignment]-->
<tool id="FeatureLinkerUnlabeled" name="FeatureLinkerUnlabeled" version="2.3.0">
  <description>Groups corresponding features from multiple maps.</description>
  <macros>
    <token name="@EXECUTABLE@">FeatureLinkerUnlabeled</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>FeatureLinkerUnlabeled

-in
  #for token in $param_in:
    $token
  #end for
#if $param_out:
  -out $param_out
#end if
#if $param_design:
  -design $param_design
#end if
#if $param_keep_subelements:
  -keep_subelements
#end if
#if $param_algorithm_second_nearest_gap:
  -algorithm:second_nearest_gap $param_algorithm_second_nearest_gap
#end if
#if $param_algorithm_use_identifications:
  -algorithm:use_identifications
#end if
#if $param_algorithm_ignore_charge:
  -algorithm:ignore_charge
#end if
#if $param_algorithm_distance_RT_max_difference:
  -algorithm:distance_RT:max_difference $param_algorithm_distance_RT_max_difference
#end if
#if $param_algorithm_distance_MZ_max_difference:
  -algorithm:distance_MZ:max_difference $param_algorithm_distance_MZ_max_difference
#end if
#if $param_algorithm_distance_MZ_unit:
  -algorithm:distance_MZ:unit
  #if " " in str($param_algorithm_distance_MZ_unit):
    "$param_algorithm_distance_MZ_unit"
  #else
    $param_algorithm_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_distance_RT_exponent:
  -algorithm:distance_RT:exponent $adv_opts.param_algorithm_distance_RT_exponent
#end if
    #if $adv_opts.param_algorithm_distance_RT_weight:
  -algorithm:distance_RT:weight $adv_opts.param_algorithm_distance_RT_weight
#end if
    #if $adv_opts.param_algorithm_distance_MZ_exponent:
  -algorithm:distance_MZ:exponent $adv_opts.param_algorithm_distance_MZ_exponent
#end if
    #if $adv_opts.param_algorithm_distance_MZ_weight:
  -algorithm:distance_MZ:weight $adv_opts.param_algorithm_distance_MZ_weight
#end if
    #if $adv_opts.param_algorithm_distance_intensity_exponent:
  -algorithm:distance_intensity:exponent $adv_opts.param_algorithm_distance_intensity_exponent
#end if
    #if $adv_opts.param_algorithm_distance_intensity_weight:
  -algorithm:distance_intensity:weight $adv_opts.param_algorithm_distance_intensity_weight
#end if
    #if $adv_opts.param_algorithm_distance_intensity_log_transform:
  -algorithm:distance_intensity:log_transform
  #if " " in str($adv_opts.param_algorithm_distance_intensity_log_transform):
    "$adv_opts.param_algorithm_distance_intensity_log_transform"
  #else
    $adv_opts.param_algorithm_distance_intensity_log_transform
  #end if
#end if
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="featurexml,consensusxml" multiple="true" optional="False" size="30" label="input files separated by blanks" help="(-in) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_design" type="data" format="tabular" optional="True" label="input file containing the experimental design" help="(-design) "/>
    <param name="param_keep_subelements" display="radio" type="boolean" truevalue="-keep_subelements" falsevalue="" checked="false" optional="True" label="For consensusXML input only: If set, the sub-features of the inputs are transferred to the output" help="(-keep_subelements) "/>
    <param name="param_algorithm_second_nearest_gap" type="float" min="1.0" optional="True" value="2.0" label="Only link features whose distance to the second nearest neighbors (for both sides) is larger by 'second_nearest_gap' than the distance between the matched pair itself" help="(-second_nearest_gap) "/>
    <param name="param_algorithm_use_identifications" display="radio" type="boolean" truevalue="-algorithm:use_identifications" falsevalue="" checked="false" optional="True" label="Never link features that are annotated with different peptides (features without ID's always match; only the best hit per peptide identification is considered)" help="(-use_identifications) "/>
    <param name="param_algorithm_ignore_charge" display="radio" type="boolean" truevalue="-algorithm:ignore_charge" falsevalue="" checked="false" optional="True" label="false [default]: pairing requires equal charge state (or at least one unknown charge '0'); true: Pairing irrespective of charge state" help="(-ignore_charge) "/>
    <param name="param_algorithm_distance_RT_max_difference" type="float" min="0.0" optional="True" value="100.0" label="Never pair features with a larger RT distance (in seconds)" help="(-max_difference) "/>
    <param name="param_algorithm_distance_MZ_max_difference" type="float" min="0.0" optional="True" value="0.3" label="Never pair features with larger m/z distance (unit defined by 'unit')" help="(-max_difference) "/>
    <param name="param_algorithm_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_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_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_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_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_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) "/>
      <param name="param_algorithm_distance_intensity_weight" type="float" min="0.0" optional="True" value="0.0" label="Final intensity distances are weighted by this facto" help="(-weight) "/>
      <param name="param_algorithm_distance_intensity_log_transform" display="radio" type="select" optional="False" value="disabled" label="Log-transform intensities?" help="(-log_transform) If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))">
        <option value="enabled">enabled</option>
        <option value="disabled" selected="true">disabled</option>
      </param>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" format="consensusxml"/>
  </outputs>
  <help>Groups corresponding features from multiple maps.


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