annotate FeatureFinderMultiplex.xml @ 13:18f63fd679e3 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"

<?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: [Quantitation]-->
<tool id="FeatureFinderMultiplex" name="FeatureFinderMultiplex" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
  <description>Determination of peak ratios in LC-MS data</description>
  <macros>
    <token name="@EXECUTABLE@">FeatureFinderMultiplex</token>
    <import>macros.xml</import>
    <import>macros_autotest.xml</import>
    <import>macros_test.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
@EXT_FOO@
#import re

## Preprocessing
mkdir in &&
ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  mkdir out &&
#end if
#if "out_multiplets_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  mkdir out_multiplets &&
#end if
#if "out_blacklist_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  mkdir out_blacklist &&
#end if

## Main program call

set -o pipefail &&
@EXECUTABLE@ -write_ctd ./ &&
python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
@EXECUTABLE@ -ini @EXECUTABLE@.ctd
-in
'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  -out
  'out/output.${gxy2omsext("featurexml")}'
#end if
#if "out_multiplets_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  -out_multiplets
  'out_multiplets/output.${gxy2omsext("consensusxml")}'
#end if
#if "out_blacklist_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  -out_blacklist
  'out_blacklist/output.${gxy2omsext("mzml")}'
#end if
#if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
  | tee '$stdout'
#end if

## Postprocessing
#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  && mv 'out/output.${gxy2omsext("featurexml")}' '$out'
#end if
#if "out_multiplets_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  && mv 'out_multiplets/output.${gxy2omsext("consensusxml")}' '$out_multiplets'
#end if
#if "out_blacklist_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  && mv 'out_blacklist/output.${gxy2omsext("mzml")}' '$out_blacklist'
#end if
#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
  && mv '@EXECUTABLE@.ctd' '$ctd_out'
#end if]]></command>
  <configfiles>
    <inputs name="args_json" data_style="paths"/>
    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
  </configfiles>
  <inputs>
    <param name="in" argument="-in" type="data" format="mzml" optional="false" label="LC-MS dataset in either centroid or profile mode" help=" select mzml data sets(s)"/>
    <section name="algorithm" title="algorithmic parameters" help="" expanded="false">
      <param name="labels" argument="-algorithm:labels" type="text" optional="true" value="[][Lys8,Arg10]" label="Labels used for labelling the samples" help="If the sample is unlabelled (i.e. you want to detect only single peptide features) please leave this parameter empty. [...] specifies the labels for a single sample. For example. . [][Lys8,Arg10]        ... SILAC. [][Lys4,Arg6][Lys8,Arg10]        ... triple-SILAC. [Dimethyl0][Dimethyl6]        ... Dimethyl. [Dimethyl0][Dimethyl4][Dimethyl8]        ... triple Dimethyl. [ICPL0][ICPL4][ICPL6][ICPL10]        ... ICPL">
        <expand macro="list_string_san"/>
      </param>
      <param name="charge" argument="-algorithm:charge" type="text" optional="true" value="1:4" label="Range of charge states in the sample" help="i.e. min charge : max charge">
        <expand macro="list_string_san"/>
      </param>
      <param name="isotopes_per_peptide" argument="-algorithm:isotopes_per_peptide" type="text" optional="true" value="3:6" label="Range of isotopes per peptide in the sample" help="For example 3:6, if isotopic peptide patterns in the sample consist of either three, four, five or six isotopic peaks. ">
        <expand macro="list_string_san"/>
      </param>
      <param name="rt_typical" argument="-algorithm:rt_typical" type="float" optional="true" min="0.0" value="40.0" label="Typical retention time [s] over which a characteristic peptide elutes" help="(This is not an upper bound. Peptides that elute for longer will be reported.)"/>
      <param name="rt_band" argument="-algorithm:rt_band" type="float" optional="true" min="0.0" value="0.0" label="The algorithm searches for characteristic isotopic peak patterns, spectrum by spectrum" help="For some low-intensity peptides, an important peak might be missing in one spectrum but be present in one of the neighbouring ones. The algorithm takes a bundle of neighbouring spectra with width rt_band into account. For example with rt_band = 0, all characteristic isotopic peaks have to be present in one and the same spectrum. As rt_band increases, the sensitivity of the algorithm but also the likelihood of false detections increases"/>
      <param name="rt_min" argument="-algorithm:rt_min" type="float" optional="true" min="0.0" value="2.0" label="Lower bound for the retention time [s]" help="(Any peptides seen for a shorter time period are not reported.)"/>
      <param name="mz_tolerance" argument="-algorithm:mz_tolerance" type="float" optional="true" min="0.0" value="6.0" label="m/z tolerance for search of peak patterns" help=""/>
      <param name="mz_unit" argument="-algorithm:mz_unit" display="radio" type="select" optional="false" label="Unit of the 'mz_tolerance' paramete" help="">
        <option value="Da">Da</option>
        <option value="ppm" selected="true">ppm</option>
        <expand macro="list_string_san"/>
      </param>
      <param name="intensity_cutoff" argument="-algorithm:intensity_cutoff" type="float" optional="true" min="0.0" value="1000.0" label="Lower bound for the intensity of isotopic peaks" help=""/>
      <param name="peptide_similarity" argument="-algorithm:peptide_similarity" type="float" optional="true" min="-1.0" max="1.0" value="0.5" label="Two peptides in a multiplet are expected to have the same isotopic pattern" help="This parameter is a lower bound on their similarity"/>
      <param name="averagine_similarity" argument="-algorithm:averagine_similarity" type="float" optional="true" min="-1.0" max="1.0" value="0.4" label="The isotopic pattern of a peptide should resemble the averagine model at this m/z position" help="This parameter is a lower bound on similarity between measured isotopic pattern and the averagine model"/>
      <param name="averagine_similarity_scaling" argument="-algorithm:averagine_similarity_scaling" type="float" optional="true" min="0.0" max="1.0" value="0.95" label="Let x denote this scaling factor, and p the averagine similarity paramete" help="For the detection of single peptides, the averagine parameter p is replaced by p' = p + x(1-p), i.e. x = 0 -&gt; p' = p and x = 1 -&gt; p' = 1. (For knock_out = true, peptide doublets and singlets are detected simulataneously. For singlets, the peptide similarity filter is irreleavant. In order to compensate for this 'missing filter', the averagine parameter p is replaced by the more restrictive p' when searching for singlets.)"/>
      <param name="missed_cleavages" argument="-algorithm:missed_cleavages" type="integer" optional="true" min="0" value="0" label="Maximum number of missed cleavages due to incomplete digestion" help="(Only relevant if enzymatic cutting site coincides with labelling site. For example, Arg/Lys in the case of trypsin digestion and SILAC labelling.)"/>
      <param name="spectrum_type" argument="-algorithm:spectrum_type" display="radio" type="select" optional="false" label="Type of MS1 spectra in input mzML file" help="'automatic' determines the spectrum type directly from the input mzML file">
        <option value="profile">profile</option>
        <option value="centroid">centroid</option>
        <option value="automatic" selected="true">automatic</option>
        <expand macro="list_string_san"/>
      </param>
      <param name="averagine_type" argument="-algorithm:averagine_type" display="radio" type="select" optional="false" label="The type of averagine to use, currently RNA, DNA or peptide" help="">
        <option value="peptide" selected="true">peptide</option>
        <option value="RNA">RNA</option>
        <option value="DNA">DNA</option>
        <expand macro="list_string_san"/>
      </param>
      <param name="knock_out" argument="-algorithm:knock_out" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Is it likely that knock-outs are present" help="(Supported for doublex, triplex and quadruplex experiments only.)"/>
    </section>
    <section name="labels" title="mass shifts for all possible labels" help="" expanded="false">
      <param name="Arg6" argument="-labels:Arg6" type="float" optional="true" min="0.0" value="6.0201290268" label="Label:13C(6)  |  C(-6) 13C(6)  |  unimod #188" help=""/>
      <param name="Arg10" argument="-labels:Arg10" type="float" optional="true" min="0.0" value="10.0082686" label="Label:13C(6)15N(4)  |  C(-6) 13C(6) N(-4) 15N(4)  |  unimod #267" help=""/>
      <param name="Lys4" argument="-labels:Lys4" type="float" optional="true" min="0.0" value="4.0251069836" label="Label:2H(4)  |  H(-4) 2H(4)  |  unimod #481" help=""/>
      <param name="Lys6" argument="-labels:Lys6" type="float" optional="true" min="0.0" value="6.0201290268" label="Label:13C(6)  |  C(-6) 13C(6)  |  unimod #188" help=""/>
      <param name="Lys8" argument="-labels:Lys8" type="float" optional="true" min="0.0" value="8.0141988132" label="Label:13C(6)15N(2)  |  C(-6) 13C(6) N(-2) 15N(2)  |  unimod #259" help=""/>
      <param name="Leu3" argument="-labels:Leu3" type="float" optional="true" min="0.0" value="3.01883" label="Label:2H(3)  |  H(-3) 2H(3)  |  unimod #262" help=""/>
      <param name="Dimethyl0" argument="-labels:Dimethyl0" type="float" optional="true" min="0.0" value="28.0313" label="Dimethyl  |  H(4) C(2)  |  unimod #36" help=""/>
      <param name="Dimethyl4" argument="-labels:Dimethyl4" type="float" optional="true" min="0.0" value="32.056407" label="Dimethyl:2H(4)  |  2H(4) C(2)  |  unimod #199" help=""/>
      <param name="Dimethyl6" argument="-labels:Dimethyl6" type="float" optional="true" min="0.0" value="34.063117" label="Dimethyl:2H(4)13C(2)  |  2H(4) 13C(2)  |  unimod #510" help=""/>
      <param name="Dimethyl8" argument="-labels:Dimethyl8" type="float" optional="true" min="0.0" value="36.07567" label="Dimethyl:2H(6)13C(2)  |  H(-2) 2H(6) 13C(2)  |  unimod #330" help=""/>
      <param name="ICPL0" argument="-labels:ICPL0" type="float" optional="true" min="0.0" value="105.021464" label="ICPL  |  H(3) C(6) N O  |  unimod #365" help=""/>
      <param name="ICPL4" argument="-labels:ICPL4" type="float" optional="true" min="0.0" value="109.046571" label="ICPL:2H(4)  |  H(-1) 2H(4) C(6) N O  |  unimod #687" help=""/>
      <param name="ICPL6" argument="-labels:ICPL6" type="float" optional="true" min="0.0" value="111.041593" label="ICPL:13C(6)  |  H(3) 13C(6) N O  |  unimod #364" help=""/>
      <param name="ICPL10" argument="-labels:ICPL10" type="float" optional="true" min="0.0" value="115.0667" label="ICPL:13C(6)2H(4)  |  H(-1) 2H(4) 13C(6) N O  |  unimod #866" help=""/>
    </section>
    <expand macro="adv_opts_macro">
      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
      <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
        <expand macro="list_string_san"/>
      </param>
    </expand>
    <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="false">
      <option value="out_FLAG">out (ICPL:13C(6)2H(4)  |  H(-1) 2H(4) 13C(6) N O  |  unimod #866)</option>
      <option value="out_multiplets_FLAG">out_multiplets (ICPL:13C(6)2H(4)  |  H(-1) 2H(4) 13C(6) N O  |  unimod #866)</option>
      <option value="out_blacklist_FLAG">out_blacklist (ICPL:13C(6)2H(4)  |  H(-1) 2H(4) 13C(6) N O  |  unimod #866)</option>
      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
    </param>
  </inputs>
  <outputs>
    <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml">
      <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
    <data name="out_multiplets" label="${tool.name} on ${on_string}: out_multiplets" format="consensusxml">
      <filter>OPTIONAL_OUTPUTS is not None and "out_multiplets_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
    <data name="out_blacklist" label="${tool.name} on ${on_string}: out_blacklist" format="mzml">
      <filter>OPTIONAL_OUTPUTS is not None and "out_blacklist_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
    <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
      <filter>OPTIONAL_OUTPUTS is None</filter>
    </data>
    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
  </outputs>
  <tests>
    <expand macro="autotest_FeatureFinderMultiplex"/>
    <expand macro="manutest_FeatureFinderMultiplex"/>
  </tests>
  <help><![CDATA[Determination of peak ratios in LC-MS data


For more information, visit http://www.openms.de/documentation/TOPP_FeatureFinderMultiplex.html]]></help>
  <expand macro="references"/>
</tool>