openms: FeatureFinderMultiplex.xml comparison

comparison FeatureFinderMultiplex.xml @ 4:6ead64a594bd draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty

author	bgruening
date	Wed, 27 Jan 2016 10:06:49 -0500
parents	3d84209d3178
children

comparison

equal deleted inserted replaced

-:ec62782f6c68
+:6ead64a594bd
-<?xml version='1.0' encoding='UTF-8'?>
+<?xml version="1.0" encoding="UTF-8"?>
-<tool id="FeatureFinderMultiplex" name="FeatureFinderMultiplex" version="1.12.0">
+<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
-<description>Determination of peak ratios in LC-MS data</description>
+<!--Proposed Tool Section: [Quantitation]-->
-<macros>
+<tool id="FeatureFinderMultiplex" name="FeatureFinderMultiplex" version="2.0.0">
-<token name="@EXECUTABLE@">FeatureFinderMultiplex</token>
+<description>Determination of peak ratios in LC-MS data</description>
-<import>macros.xml</import>
+<macros>
-</macros>
+<token name="@EXECUTABLE@">FeatureFinderMultiplex</token>
-<expand macro="stdio"/>
+<import>macros.xml</import>
-<expand macro="requirements"/>
+</macros>
-<command>FeatureFinderMultiplex
+<expand macro="references"/>
+<expand macro="stdio"/>
+<expand macro="requirements"/>
+<command>FeatureFinderMultiplex
--in ${param_in}
+#if $param_in:
--out ${param_out}
+-in $param_in
--threads \${GALAXY_SLOTS:-24}
+#end if
--algorithm:labels ${param_labels}
+#if $param_out:
--algorithm:charge ${param_charge}
+-out $param_out
--algorithm:rt_typical ${param_rt_typical}
+#end if
--algorithm:rt_min ${param_rt_min}
+#if $param_out_features:
--algorithm:mz_tolerance ${param_mz_tolerance}
+-out_features $param_out_features
--algorithm:mz_unit ${param_mz_unit}
+#end if
--algorithm:intensity_cutoff ${param_intensity_cutoff}
+#if $param_out_mzq:
--algorithm:peptide_similarity ${param_peptide_similarity}
+-out_mzq $param_out_mzq
--algorithm:averagine_similarity ${param_averagine_similarity}
+#end if
--algorithm:missed_cleavages ${param_missed_cleavages}
+-threads \${GALAXY_SLOTS:-24}
+#if $param_algorithm_labels:
+-algorithm:labels     &quot;$param_algorithm_labels&quot;
+#end if
+#if $param_algorithm_charge:
+-algorithm:charge     &quot;$param_algorithm_charge&quot;
+#end if
+#if $param_algorithm_rt_typical:
+-algorithm:rt_typical $param_algorithm_rt_typical
+#end if
+#if $param_algorithm_rt_min:
+-algorithm:rt_min $param_algorithm_rt_min
+#end if
+#if $param_algorithm_mz_tolerance:
+-algorithm:mz_tolerance $param_algorithm_mz_tolerance
+#end if
+#if $param_algorithm_mz_unit:
+-algorithm:mz_unit
+#if &quot; &quot; in str($param_algorithm_mz_unit):
+&quot;$param_algorithm_mz_unit&quot;
+#else
+$param_algorithm_mz_unit
+#end if
+#end if
+#if $param_algorithm_intensity_cutoff:
+-algorithm:intensity_cutoff $param_algorithm_intensity_cutoff
+#end if
+#if $param_algorithm_peptide_similarity:
+-algorithm:peptide_similarity $param_algorithm_peptide_similarity
+#end if
+#if $param_algorithm_averagine_similarity:
+-algorithm:averagine_similarity $param_algorithm_averagine_similarity
+#end if
+#if $param_algorithm_missed_cleavages:
+-algorithm:missed_cleavages $param_algorithm_missed_cleavages
+#end if
 #if $adv_opts.adv_opts_selector=='advanced':
--out_features ${adv_opts.param_out_features}
+#if $adv_opts.param_force:
--out_mzq ${adv_opts.param_out_mzq}
+-force
--out_debug ${adv_opts.param_out_debug}
+#end if
--algorithm:isotopes_per_peptide ${adv_opts.param_isotopes_per_peptide}
+#if $adv_opts.param_algorithm_isotopes_per_peptide:
-${adv_opts.param_knock_out}
+-algorithm:isotopes_per_peptide     &quot;$adv_opts.param_algorithm_isotopes_per_peptide&quot;
--labels:Arg6 ${adv_opts.param_Arg6}
+#end if
--labels:Arg10 ${adv_opts.param_Arg10}
+#if $adv_opts.param_algorithm_averagine_similarity_scaling:
--labels:Lys4 ${adv_opts.param_Lys4}
+-algorithm:averagine_similarity_scaling $adv_opts.param_algorithm_averagine_similarity_scaling
--labels:Lys6 ${adv_opts.param_Lys6}
+#end if
--labels:Lys8 ${adv_opts.param_Lys8}
+#if $adv_opts.param_algorithm_knock_out:
--labels:Dimethyl0 ${adv_opts.param_Dimethyl0}
+-algorithm:knock_out
--labels:Dimethyl4 ${adv_opts.param_Dimethyl4}
+#end if
--labels:Dimethyl6 ${adv_opts.param_Dimethyl6}
+#if $adv_opts.param_labels_Arg6:
--labels:Dimethyl8 ${adv_opts.param_Dimethyl8}
+-labels:Arg6 $adv_opts.param_labels_Arg6
--labels:ICPL0 ${adv_opts.param_ICPL0}
+#end if
--labels:ICPL4 ${adv_opts.param_ICPL4}
+#if $adv_opts.param_labels_Arg10:
--labels:ICPL6 ${adv_opts.param_ICPL6}
+-labels:Arg10 $adv_opts.param_labels_Arg10
--labels:ICPL10 ${adv_opts.param_ICPL10}
+#end if
+#if $adv_opts.param_labels_Lys4:
+-labels:Lys4 $adv_opts.param_labels_Lys4
+#end if
+#if $adv_opts.param_labels_Lys6:
+-labels:Lys6 $adv_opts.param_labels_Lys6
+#end if
+#if $adv_opts.param_labels_Lys8:
+-labels:Lys8 $adv_opts.param_labels_Lys8
+#end if
+#if $adv_opts.param_labels_Dimethyl0:
+-labels:Dimethyl0 $adv_opts.param_labels_Dimethyl0
+#end if
+#if $adv_opts.param_labels_Dimethyl4:
+-labels:Dimethyl4 $adv_opts.param_labels_Dimethyl4
+#end if
+#if $adv_opts.param_labels_Dimethyl6:
+-labels:Dimethyl6 $adv_opts.param_labels_Dimethyl6
+#end if
+#if $adv_opts.param_labels_Dimethyl8:
+-labels:Dimethyl8 $adv_opts.param_labels_Dimethyl8
+#end if
+#if $adv_opts.param_labels_ICPL0:
+-labels:ICPL0 $adv_opts.param_labels_ICPL0
+#end if
+#if $adv_opts.param_labels_ICPL4:
+-labels:ICPL4 $adv_opts.param_labels_ICPL4
+#end if
+#if $adv_opts.param_labels_ICPL6:
+-labels:ICPL6 $adv_opts.param_labels_ICPL6
+#end if
+#if $adv_opts.param_labels_ICPL10:
+-labels:ICPL10 $adv_opts.param_labels_ICPL10
+#end if
 #end if
 </command>
 <inputs>
-<param name="param_in" type="data" format="mzML" optional="False" label="Raw LC-MS data to be analyzed. (Profile data required. Will not work with centroided data!)" help="(-in)"/>
+<param format="mzml" help="(-in) " label="LC-MS dataset in centroid or profile mode" name="param_in" optional="False" type="data"/>
-<param name="param_labels" type="text" size="20" value="[][Lys8,Arg10]" label="Labels used for labelling the samples. [...] specifies the labels for a single sample. For example#br##br#[][Lys8,Arg10]        ... SILAC#br#[][Lys4,Arg6][Lys8,Arg10]        ... triple-SILAC#br#[Dimethyl0][Dimethyl6]        ... Dimethyl#br#[Dimethyl0][Dimethyl4][Dimethyl8]        ... triple Dimethyl#br#[ICPL0][ICPL4][ICPL6][ICPL10]        ... ICPL" help="(-labels)"/>
+<param help="(-labels) [...] specifies the labels for a single sample. For example &lt;br&gt; &lt;br&gt;[][Lys8,Arg10]        ... SILAC &lt;br&gt;[][Lys4,Arg6][Lys8,Arg10]        ... triple-SILAC &lt;br&gt;[Dimethyl0][Dimethyl6]        ... Dimethyl &lt;br&gt;[Dimethyl0][Dimethyl4][Dimethyl8]        ... triple Dimethyl &lt;br&gt;[ICPL0][ICPL4][ICPL6][ICPL10]        ... ICPL" label="Labels used for labelling the samples" name="param_algorithm_labels" size="30" type="text" value="[][Lys8,Arg10]">
-<param name="param_charge" type="text" size="20" value="1:4" label="Range of charge states in the sample, i.e. min charge : max charge." help="(-charge)"/>
+<sanitizer>
-<param name="param_rt_typical" type="float" min="0.0" optional="True" value="40.0" label="Typical retention time [s] over which a characteristic peptide elutes. (This is not an upper bound. Peptides that elute for longer will be reported.)" help="(-rt_typical)"/>
+<valid initial="string.printable">
-<param name="param_rt_min" type="float" min="0.0" optional="True" value="2.0" label="Lower bound for the retention time [s]. (Any peptides seen for a shorter time period are not reported.)" help="(-rt_min)"/>
+<remove value="'"/>
-<param name="param_mz_tolerance" type="float" min="0.0" optional="True" value="6.0" label="m/z tolerance for search of peak patterns." help="(-mz_tolerance)"/>
+<remove value="&quot;"/>
-<param name="param_mz_unit" type="select" optional="True" value="ppm" label="Unit of the 'mz_tolerance' parameter." help="(-mz_unit)">
+</valid>
-<option value="Da">Da</option>
+</sanitizer>
-<option value="ppm">ppm</option>
+</param>
-</param>
+<param help="(-charge) min charge : max charge" label="Range of charge states in the sample, i.e" name="param_algorithm_charge" size="30" type="text" value="1:4">
-<param name="param_intensity_cutoff" type="float" min="0.0" optional="True" value="1000.0" label="Lower bound for the intensity of isotopic peaks." help="(-intensity_cutoff)"/>
+<sanitizer>
-<param name="param_peptide_similarity" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Two peptides in a multiplet are expected to have the same isotopic pattern. This parameter is a lower bound on their similarity." help="(-peptide_similarity)"/>
+<valid initial="string.printable">
-<param name="param_averagine_similarity" type="float" min="0.0" max="1.0" optional="True" value="0.4" label="The isotopic pattern of a peptide should resemble the averagine model at this m/z position. This parameter is a lower bound on similarity between measured isotopic pattern and the averagine model." help="(-averagine_similarity)"/>
+<remove value="'"/>
-<param name="param_missed_cleavages" type="integer" min="0" optional="True" value="0" label="Maximum number of missed cleavages due to incomplete digestion." help="(-missed_cleavages)"/>
+<remove value="&quot;"/>
-<expand macro="advanced_options">
+</valid>
-<param name="param_out_debug" type="text" size="20" label="Directory for debug output." help="(-out_debug)"/>
+</sanitizer>
-<param name="param_isotopes_per_peptide" type="text" size="20" value="3:6" label="Range of isotopes per peptide in the sample. For example 3:6, if isotopic peptide patterns in the sample consist of either three, four, five or six isotopic peaks. " help="(-isotopes_per_peptide)"/>
+</param>
-<param name="param_knock_out" type="boolean" truevalue="-algorithm:knock_out true" falsevalue="-algorithm:knock_out false" checked="true" optional="True" label="Is it likely that knock-outs are present? (Supported for doublex, triplex and quadruplex experiments only.)" help="(-knock_out)"/>
+<param help="(-rt_typical) (This is not an upper bound. Peptides that elute for longer will be reported.)" label="Typical retention time [s] over which a characteristic peptide elutes" min="0.0" name="param_algorithm_rt_typical" optional="True" type="float" value="40.0"/>
-<param name="param_Arg6" type="float" min="0.0" optional="True" value="6.0201290268" label="Label:13C(6)  |  C(-6) 13C(6)  |  unimod #188" help="(-Arg6)"/>
+<param help="(-rt_min) (Any peptides seen for a shorter time period are not reported.)" label="Lower bound for the retention time [s]" min="0.0" name="param_algorithm_rt_min" optional="True" type="float" value="2.0"/>
-<param name="param_Arg10" type="float" min="0.0" optional="True" value="10.0082686" label="Label:13C(6)15N(4)  |  C(-6) 13C(6) N(-4) 15N(4)  |  unimod #267" help="(-Arg10)"/>
+<param help="(-mz_tolerance) " label="m/z tolerance for search of peak patterns" min="0.0" name="param_algorithm_mz_tolerance" optional="True" type="float" value="6.0"/>
-<param name="param_Lys4" type="float" min="0.0" optional="True" value="4.0251069836" label="Label:2H(4)  |  H(-4) 2H(4)  |  unimod #481" help="(-Lys4)"/>
+<param help="(-mz_unit) " label="Unit of the 'mz_tolerance' paramete" name="param_algorithm_mz_unit" optional="True" type="select" value="ppm">
-<param name="param_Lys6" type="float" min="0.0" optional="True" value="6.0201290268" label="Label:13C(6)  |  C(-6) 13C(6)  |  unimod #188" help="(-Lys6)"/>
+<option value="Da">Da</option>
-<param name="param_Lys8" type="float" min="0.0" optional="True" value="8.0141988132" label="Label:13C(6)15N(2)  |  C(-6) 13C(6) N(-2) 15N(2)  |  unimod #259" help="(-Lys8)"/>
+<option value="ppm">ppm</option>
-<param name="param_Dimethyl0" type="float" min="0.0" optional="True" value="28.0313" label="Dimethyl  |  H(4) C(2)  |  unimod #36" help="(-Dimethyl0)"/>
+</param>
-<param name="param_Dimethyl4" type="float" min="0.0" optional="True" value="32.056407" label="Dimethyl:2H(4)  |  2H(4) C(2)  |  unimod #199" help="(-Dimethyl4)"/>
+<param help="(-intensity_cutoff) " label="Lower bound for the intensity of isotopic peaks" min="0.0" name="param_algorithm_intensity_cutoff" optional="True" type="float" value="1000.0"/>
-<param name="param_Dimethyl6" type="float" min="0.0" optional="True" value="34.063117" label="Dimethyl:2H(4)13C(2)  |  2H(4) 13C(2)  |  unimod #510" help="(-Dimethyl6)"/>
+<param help="(-peptide_similarity) This parameter is a lower bound on their similarity" label="Two peptides in a multiplet are expected to have the same isotopic pattern" max="1.0" min="-1.0" name="param_algorithm_peptide_similarity" optional="True" type="float" value="0.5"/>
-<param name="param_Dimethyl8" type="float" min="0.0" optional="True" value="36.07567" label="Dimethyl:2H(6)13C(2)  |  H(-2) 2H(6) 13C(2)  |  unimod #330" help="(-Dimethyl8)"/>
+<param help="(-averagine_similarity) This parameter is a lower bound on similarity between measured isotopic pattern and the averagine model" label="The isotopic pattern of a peptide should resemble the averagine model at this m/z position" max="1.0" min="-1.0" name="param_algorithm_averagine_similarity" optional="True" type="float" value="0.4"/>
-<param name="param_ICPL0" type="float" min="0.0" optional="True" value="105.021464" label="ICPL  |  H(3) C(6) N O  |  unimod #365" help="(-ICPL0)"/>
+<param help="(-missed_cleavages) " label="Maximum number of missed cleavages due to incomplete digestion" min="0" name="param_algorithm_missed_cleavages" optional="True" type="integer" value="0"/>
-<param name="param_ICPL4" type="float" min="0.0" optional="True" value="109.046571" label="ICPL:2H(4)  |  H(-1) 2H(4) C(6) N O  |  unimod #687" help="(-ICPL4)"/>
+<expand macro="advanced_options">
-<param name="param_ICPL6" type="float" min="0.0" optional="True" value="111.041593" label="ICPL:13C(6)  |  H(3) 13C(6) N O  |  unimod #364" help="(-ICPL6)"/>
+<param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
-<param name="param_ICPL10" type="float" min="0.0" optional="True" value="115.0667" label="ICPL:13C(6)2H(4)  |  H(-1) 2H(4) 13C(6) N O  |  unimod #866" help="(-ICPL10)"/>
+<param help="(-isotopes_per_peptide) For example 3:6, if isotopic peptide patterns in the sample consist of either three, four, five or six isotopic peaks. " label="Range of isotopes per peptide in the sample" name="param_algorithm_isotopes_per_peptide" size="30" type="text" value="3:6">
-</expand>
+<sanitizer>
-</inputs>
+<valid initial="string.printable">
-<outputs>
+<remove value="'"/>
-<data name="param_out" label="Set of all identified peptide groups (i.e. peptide pairs or triplets or singlets or ..). The m/z-RT positions correspond to the lightest peptide in each group." format="consensusXML"/>
+<remove value="&quot;"/>
-<data name="param_out_features" label="Optional output file containing the individual peptide features in 'out'." format="featureXML"/>
+</valid>
-<data name="param_out_mzq" label="Optional output file of MzQuantML." format="data"/>
+</sanitizer>
-</outputs>
+</param>
-<help>**What it does**
+<param help="(-averagine_similarity_scaling) 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.)" label="Let x denote this scaling factor, and p the averagine similarity paramete" max="1.0" min="0.0" name="param_algorithm_averagine_similarity_scaling" optional="True" type="float" value="0.75"/>
+<param checked="false" falsevalue="" help="(-knock_out) (Supported for doublex, triplex and quadruplex experiments only.)" label="Is it likely that knock-outs are present?" name="param_algorithm_knock_out" optional="True" truevalue="-algorithm:knock_out" type="boolean"/>
-Determination of peak ratios in LC-MS data
+<param help="(-Arg6) " label="Label:13C(6)  |  C(-6) 13C(6)  |  unimod #188" min="0.0" name="param_labels_Arg6" optional="True" type="float" value="6.0201290268"/>
+<param help="(-Arg10) " label="Label:13C(6)15N(4)  |  C(-6) 13C(6) N(-4) 15N(4)  |  unimod #267" min="0.0" name="param_labels_Arg10" optional="True" type="float" value="10.0082686"/>
+<param help="(-Lys4) " label="Label:2H(4)  |  H(-4) 2H(4)  |  unimod #481" min="0.0" name="param_labels_Lys4" optional="True" type="float" value="4.0251069836"/>
+<param help="(-Lys6) " label="Label:13C(6)  |  C(-6) 13C(6)  |  unimod #188" min="0.0" name="param_labels_Lys6" optional="True" type="float" value="6.0201290268"/>
+<param help="(-Lys8) " label="Label:13C(6)15N(2)  |  C(-6) 13C(6) N(-2) 15N(2)  |  unimod #259" min="0.0" name="param_labels_Lys8" optional="True" type="float" value="8.0141988132"/>
+<param help="(-Dimethyl0) " label="Dimethyl  |  H(4) C(2)  |  unimod #36" min="0.0" name="param_labels_Dimethyl0" optional="True" type="float" value="28.0313"/>
+<param help="(-Dimethyl4) " label="Dimethyl:2H(4)  |  2H(4) C(2)  |  unimod #199" min="0.0" name="param_labels_Dimethyl4" optional="True" type="float" value="32.056407"/>
+<param help="(-Dimethyl6) " label="Dimethyl:2H(4)13C(2)  |  2H(4) 13C(2)  |  unimod #510" min="0.0" name="param_labels_Dimethyl6" optional="True" type="float" value="34.063117"/>
+<param help="(-Dimethyl8) " label="Dimethyl:2H(6)13C(2)  |  H(-2) 2H(6) 13C(2)  |  unimod #330" min="0.0" name="param_labels_Dimethyl8" optional="True" type="float" value="36.07567"/>
+<param help="(-ICPL0) " label="ICPL  |  H(3) C(6) N O  |  unimod #365" min="0.0" name="param_labels_ICPL0" optional="True" type="float" value="105.021464"/>
+<param help="(-ICPL4) " label="ICPL:2H(4)  |  H(-1) 2H(4) C(6) N O  |  unimod #687" min="0.0" name="param_labels_ICPL4" optional="True" type="float" value="109.046571"/>
+<param help="(-ICPL6) " label="ICPL:13C(6)  |  H(3) 13C(6) N O  |  unimod #364" min="0.0" name="param_labels_ICPL6" optional="True" type="float" value="111.041593"/>
+<param help="(-ICPL10) " label="ICPL:13C(6)2H(4)  |  H(-1) 2H(4) 13C(6) N O  |  unimod #866" min="0.0" name="param_labels_ICPL10" optional="True" type="float" value="115.0667"/>
+</expand>
+</inputs>
+<outputs>
+<data format="consensusxml" name="param_out"/>
+<data format="xml" name="param_out_features"/>
+<data format="mzq" name="param_out_mzq"/>
+</outputs>
+<help>Determination of peak ratios in LC-MS data
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderMultiplex.html
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderMultiplex.html</help>
+</tool>
-@REFERENCES@
-</help>
-</tool>

Mercurial > repos > bgruening > openms

comparison FeatureFinderMultiplex.xml @ 4:6ead64a594bd draft default tip