comparison Decharger.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="Decharger" name="Decharger" version="1.12.0">
  <description>Decharges and merges different feature charge variants of the same peptide.</description>
  <macros>
    <token name="@EXECUTABLE@">Decharger</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>Decharger

-in ${param_in}
-out_cm ${param_out_cm}
-out_fm ${param_out_fm}
-outpairs ${param_outpairs}
-threads \${GALAXY_SLOTS:-24} 
-algorithm:FeatureDeconvolution:charge_min ${param_charge_min}
-algorithm:FeatureDeconvolution:charge_max ${param_charge_max}
-algorithm:FeatureDeconvolution:charge_span_max ${param_charge_span_max}
-algorithm:FeatureDeconvolution:q_try ${param_q_try}
-algorithm:FeatureDeconvolution:retention_max_diff ${param_retention_max_diff}
-algorithm:FeatureDeconvolution:retention_max_diff_local ${param_retention_max_diff_local}
-algorithm:FeatureDeconvolution:mass_max_diff ${param_mass_max_diff}
-algorithm:FeatureDeconvolution:potential_adducts ${param_potential_adducts}
-algorithm:FeatureDeconvolution:max_neutrals ${param_max_neutrals}
-algorithm:FeatureDeconvolution:max_minority_bound ${param_max_minority_bound}
-algorithm:FeatureDeconvolution:min_rt_overlap ${param_min_rt_overlap}
${param_intensity_filter}
#if $adv_opts.adv_opts_selector=='advanced':
    -algorithm:FeatureDeconvolution:default_map_label ${adv_opts.param_default_map_label}
    -algorithm:FeatureDeconvolution:verbose_level ${adv_opts.param_verbose_level}
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="featureXML" optional="False" label="input file " help="(-in)"/>
    <param name="param_charge_min" type="integer" value="1" label="Minimal possible charge" help="(-charge_min)"/>
    <param name="param_charge_max" type="integer" value="10" label="Maximal possible charge" help="(-charge_max)"/>
    <param name="param_charge_span_max" type="integer" min="1" optional="True" value="4" label="Maximal range of charges for a single analyte, i.e. observing q1=[5,6,7] implies span=3. Setting this to 1 will only find adduct variants of the same charge" help="(-charge_span_max)"/>
    <param name="param_q_try" type="select" optional="True" value="feature" label="Try different values of charge for each feature according to the above settings ('heuristic' [does not test all charges, just the likely ones] or 'all' ), or leave feature charge untouched ('feature')." help="(-q_try)">
      <option value="feature">feature</option>
      <option value="heuristic">heuristic</option>
      <option value="all">all</option>
    </param>
    <param name="param_retention_max_diff" type="float" value="1.0" label="Maximum allowed RT difference between any two features if their relation shall be determined" help="(-retention_max_diff)"/>
    <param name="param_retention_max_diff_local" type="float" value="1.0" label="Maximum allowed RT difference between between two co-features, after adduct shifts have been accounted for (if you do not have any adduct shifts, this value should be equal to 'retention_max_diff', otherwise it should be smaller!)" help="(-retention_max_diff_local)"/>
    <param name="param_mass_max_diff" type="float" value="0.5" label="Maximum allowed mass difference [in Th] for a single feature." help="(-mass_max_diff)"/>
    <param name="param_potential_adducts" type="text" size="20" value="H+:0.9" label="Adducts used to explain mass differences in format: 'Element(+)*:Probability[:RTShift[:Label]]', i.e. the number of '+' indicate the charge, e.g. 'Ca++:0.5' indicates +2. Probabilites have to be in (0,1]. RTShift param is optional and indicates the expected RT shift caused by this adduct, e.g. '(2)H4H-4:1:-3' indicates a 4 deuterium label, which causes early elution by 3 seconds. As a fourth parameter you can add a label which is tagged on every feature which has this adduct. This also determines the map number in the consensus file." help="(-potential_adducts)"/>
    <param name="param_max_neutrals" type="integer" value="0" label="Maximal number of neutral adducts(q=0) allowed. Add them in the 'potential_adducts' section!" help="(-max_neutrals)"/>
    <param name="param_max_minority_bound" type="integer" min="0" optional="True" value="2" label="Maximum count of the least probable adduct (according to 'potential_adducts' param) within a charge variant. E.g. setting this to 2 will not allow an adduct composition of '1(H+),3(Na+)' if Na+ is the least probable adduct" help="(-max_minority_bound)"/>
    <param name="param_min_rt_overlap" type="float" min="0.0" max="1.0" optional="True" value="0.66" label="Minimum overlap of the convex hull' RT intersection measured against the union from two features (if CHs are given)" help="(-min_rt_overlap)"/>
    <param name="param_intensity_filter" type="boolean" truevalue="-algorithm:FeatureDeconvolution:intensity_filter true" falsevalue="-algorithm:FeatureDeconvolution:intensity_filter false" checked="false" optional="True" label="Enable the intensity filter, which will only allow edges between two equally charged features if the intensity of the feature with less likely adducts is smaller than that of the other feature. It is not used for features of different charge." help="(-intensity_filter)"/>
    <expand macro="advanced_options">
      <param name="param_default_map_label" type="text" size="20" value="decharged features" label="Label of map in output consensus file where all features are put by default" help="(-default_map_label)"/>
      <param name="param_verbose_level" type="integer" min="0" max="3" optional="True" value="0" label="Amount of debug information given during processing." help="(-verbose_level)"/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out_cm" label="output consensus map" format="consensusXML"/>
    <data name="param_out_fm" label="output feature map" format="featureXML"/>
    <data name="param_outpairs" label="output file" format="consensusXML"/>
  </outputs>
  <help>**What it does**

Decharges and merges different feature charge variants of the same peptide.


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_Decharger.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: [Quantitation]-->
  <tool id="Decharger" name="Decharger" version="2.0.0">
    <description>Decharges and merges different feature charge variants of the same peptide.</description>
    <macros>
      <token name="@EXECUTABLE@">Decharger</token>
      <import>macros.xml</import>
    </macros>
    <expand macro="references"/>
    <expand macro="stdio"/>
    <expand macro="requirements"/>
    <command>Decharger

#if $param_in:
  -in $param_in
#end if
#if $param_out_cm:
  -out_cm $param_out_cm
#end if
#if $param_out_fm:
  -out_fm $param_out_fm
#end if
#if $param_outpairs:
  -outpairs $param_outpairs
#end if
-threads \${GALAXY_SLOTS:-24}
#if $param_algorithm_FeatureDeconvolution_charge_min:
  -algorithm:FeatureDeconvolution:charge_min $param_algorithm_FeatureDeconvolution_charge_min
#end if
#if $param_algorithm_FeatureDeconvolution_charge_max:
  -algorithm:FeatureDeconvolution:charge_max $param_algorithm_FeatureDeconvolution_charge_max
#end if
#if $param_algorithm_FeatureDeconvolution_charge_span_max:
  -algorithm:FeatureDeconvolution:charge_span_max $param_algorithm_FeatureDeconvolution_charge_span_max
#end if
#if $param_algorithm_FeatureDeconvolution_q_try:
  -algorithm:FeatureDeconvolution:q_try
  #if &quot; &quot; in str($param_algorithm_FeatureDeconvolution_q_try):
    &quot;$param_algorithm_FeatureDeconvolution_q_try&quot;
  #else
    $param_algorithm_FeatureDeconvolution_q_try
  #end if
#end if
#if $param_algorithm_FeatureDeconvolution_retention_max_diff:
  -algorithm:FeatureDeconvolution:retention_max_diff $param_algorithm_FeatureDeconvolution_retention_max_diff
#end if
#if $param_algorithm_FeatureDeconvolution_retention_max_diff_local:
  -algorithm:FeatureDeconvolution:retention_max_diff_local $param_algorithm_FeatureDeconvolution_retention_max_diff_local
#end if
#if $param_algorithm_FeatureDeconvolution_mass_max_diff:
  -algorithm:FeatureDeconvolution:mass_max_diff $param_algorithm_FeatureDeconvolution_mass_max_diff
#end if

#if $rep_param_algorithm_FeatureDeconvolution_potential_adducts:
-algorithm:FeatureDeconvolution:potential_adducts
  #for token in $rep_param_algorithm_FeatureDeconvolution_potential_adducts:
    #if &quot; &quot; in str(token):
      &quot;$token.param_algorithm_FeatureDeconvolution_potential_adducts&quot;
    #else
      $token.param_algorithm_FeatureDeconvolution_potential_adducts
    #end if
  #end for
#end if
#if $param_algorithm_FeatureDeconvolution_max_neutrals:
  -algorithm:FeatureDeconvolution:max_neutrals $param_algorithm_FeatureDeconvolution_max_neutrals
#end if
#if $param_algorithm_FeatureDeconvolution_max_minority_bound:
  -algorithm:FeatureDeconvolution:max_minority_bound $param_algorithm_FeatureDeconvolution_max_minority_bound
#end if
#if $param_algorithm_FeatureDeconvolution_min_rt_overlap:
  -algorithm:FeatureDeconvolution:min_rt_overlap $param_algorithm_FeatureDeconvolution_min_rt_overlap
#end if
#if $param_algorithm_FeatureDeconvolution_intensity_filter:
  -algorithm:FeatureDeconvolution:intensity_filter
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
    #if $adv_opts.param_algorithm_FeatureDeconvolution_default_map_label:
  -algorithm:FeatureDeconvolution:default_map_label     &quot;$adv_opts.param_algorithm_FeatureDeconvolution_default_map_label&quot;
#end if
    #if $adv_opts.param_algorithm_FeatureDeconvolution_verbose_level:
  -algorithm:FeatureDeconvolution:verbose_level $adv_opts.param_algorithm_FeatureDeconvolution_verbose_level
#end if
#end if
</command>
    <inputs>
      <param format="xml" help="(-in) " label="input file" name="param_in" optional="False" type="data"/>
      <param help="(-charge_min) " label="Minimal possible charge" name="param_algorithm_FeatureDeconvolution_charge_min" type="integer" value="1"/>
      <param help="(-charge_max) " label="Maximal possible charge" name="param_algorithm_FeatureDeconvolution_charge_max" type="integer" value="10"/>
      <param help="(-charge_span_max) observing q1=[5,6,7] implies span=3. Setting this to 1 will only find adduct variants of the same charge" label="Maximal range of charges for a single analyte, i.e" min="1" name="param_algorithm_FeatureDeconvolution_charge_span_max" optional="True" type="integer" value="4"/>
      <param help="(-q_try) " label="Try different values of charge for each feature according to the above settings ('heuristic' [does not test all charges, just the likely ones] or 'all' ), or leave feature charge untouched ('feature')" name="param_algorithm_FeatureDeconvolution_q_try" optional="True" type="select" value="feature">
        <option value="feature">feature</option>
        <option value="heuristic">heuristic</option>
        <option value="all">all</option>
      </param>
      <param help="(-retention_max_diff) " label="Maximum allowed RT difference between any two features if their relation shall be determined" name="param_algorithm_FeatureDeconvolution_retention_max_diff" type="float" value="1.0"/>
      <param help="(-retention_max_diff_local) " label="Maximum allowed RT difference between between two co-features, after adduct shifts have been accounted for (if you do not have any adduct shifts, this value should be equal to 'retention_max_diff', otherwise it should be smaller!)" name="param_algorithm_FeatureDeconvolution_retention_max_diff_local" type="float" value="1.0"/>
      <param help="(-mass_max_diff) " label="Maximum allowed mass difference [in Th] for a single feature" name="param_algorithm_FeatureDeconvolution_mass_max_diff" type="float" value="0.5"/>
      <repeat max="1" min="0" name="rep_param_algorithm_FeatureDeconvolution_potential_adducts" title="param_algorithm_FeatureDeconvolution_potential_adducts">
        <param help="(-potential_adducts) e.g. 'Ca++:0.5' indicates +2. Probabilites have to be in (0,1]. RTShift param is optional and indicates the expected RT shift caused by this adduct, e.g. '(2)H4H-4:1:-3' indicates a 4 deuterium label, which causes early elution by 3 seconds. As a fourth parameter you can add a label which is tagged on every feature which has this adduct. This also determines the map number in the consensus file" label="Adducts used to explain mass differences in format: 'Element(+)*:Probability[:RTShift[:Label]]', i.e. the number of '+' indicate the charge," name="param_algorithm_FeatureDeconvolution_potential_adducts" size="30" type="text" value="H+:0.9">
          <sanitizer>
            <valid initial="string.printable">
              <remove value="'"/>
              <remove value="&quot;"/>
            </valid>
          </sanitizer>
        </param>
      </repeat>
      <param help="(-max_neutrals) Add them in the 'potential_adducts' section!" label="Maximal number of neutral adducts(q=0) allowed" name="param_algorithm_FeatureDeconvolution_max_neutrals" type="integer" value="0"/>
      <param help="(-max_minority_bound) E.g. setting this to 2 will not allow an adduct composition of '1(H+),3(Na+)' if Na+ is the least probable adduct" label="Maximum count of the least probable adduct (according to 'potential_adducts' param) within a charge variant" min="0" name="param_algorithm_FeatureDeconvolution_max_minority_bound" optional="True" type="integer" value="2"/>
      <param help="(-min_rt_overlap) " label="Minimum overlap of the convex hull' RT intersection measured against the union from two features (if CHs are given)" max="1.0" min="0.0" name="param_algorithm_FeatureDeconvolution_min_rt_overlap" optional="True" type="float" value="0.66"/>
      <param checked="false" falsevalue="" help="(-intensity_filter) It is not used for features of different charge" label="Enable the intensity filter, which will only allow edges between two equally charged features if the intensity of the feature with less likely adducts is smaller than that of the other feature" name="param_algorithm_FeatureDeconvolution_intensity_filter" optional="True" truevalue="-algorithm:FeatureDeconvolution:intensity_filter" 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"/>
        <param help="(-default_map_label) " label="Label of map in output consensus file where all features are put by default" name="param_algorithm_FeatureDeconvolution_default_map_label" size="30" type="text" value="decharged features">
          <sanitizer>
            <valid initial="string.printable">
              <remove value="'"/>
              <remove value="&quot;"/>
            </valid>
          </sanitizer>
        </param>
        <param help="(-verbose_level) " label="Amount of debug information given during processing" max="3" min="0" name="param_algorithm_FeatureDeconvolution_verbose_level" optional="True" type="integer" value="0"/>
      </expand>
    </inputs>
    <outputs>
      <data format="consensusxml" name="param_out_cm"/>
      <data format="xml" name="param_out_fm"/>
      <data format="consensusxml" name="param_outpairs"/>
    </outputs>
    <help>Decharges and merges different feature charge variants of the same peptide.


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