Mercurial > repos > bgruening > openms
diff 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 |
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--- a/FeatureFinderMultiplex.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/FeatureFinderMultiplex.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,94 +1,182 @@ -<?xml version='1.0' encoding='UTF-8'?> -<tool id="FeatureFinderMultiplex" name="FeatureFinderMultiplex" version="1.12.0"> - <description>Determination of peak ratios in LC-MS data</description> - <macros> - <token name="@EXECUTABLE@">FeatureFinderMultiplex</token> - <import>macros.xml</import> - </macros> - <expand macro="stdio"/> - <expand macro="requirements"/> - <command>FeatureFinderMultiplex +<?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="FeatureFinderMultiplex" name="FeatureFinderMultiplex" version="2.0.0"> + <description>Determination of peak ratios in LC-MS data</description> + <macros> + <token name="@EXECUTABLE@">FeatureFinderMultiplex</token> + <import>macros.xml</import> + </macros> + <expand macro="references"/> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>FeatureFinderMultiplex --in ${param_in} --out ${param_out} --threads \${GALAXY_SLOTS:-24} --algorithm:labels ${param_labels} --algorithm:charge ${param_charge} --algorithm:rt_typical ${param_rt_typical} --algorithm:rt_min ${param_rt_min} --algorithm:mz_tolerance ${param_mz_tolerance} --algorithm:mz_unit ${param_mz_unit} --algorithm:intensity_cutoff ${param_intensity_cutoff} --algorithm:peptide_similarity ${param_peptide_similarity} --algorithm:averagine_similarity ${param_averagine_similarity} --algorithm:missed_cleavages ${param_missed_cleavages} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_out_features: + -out_features $param_out_features +#end if +#if $param_out_mzq: + -out_mzq $param_out_mzq +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_algorithm_labels: + -algorithm:labels "$param_algorithm_labels" +#end if +#if $param_algorithm_charge: + -algorithm:charge "$param_algorithm_charge" +#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 $param_algorithm_mz_unit: + -algorithm:mz_unit + #if " " in str($param_algorithm_mz_unit): + "$param_algorithm_mz_unit" + #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} - -out_mzq ${adv_opts.param_out_mzq} - -out_debug ${adv_opts.param_out_debug} - -algorithm:isotopes_per_peptide ${adv_opts.param_isotopes_per_peptide} - ${adv_opts.param_knock_out} - -labels:Arg6 ${adv_opts.param_Arg6} - -labels:Arg10 ${adv_opts.param_Arg10} - -labels:Lys4 ${adv_opts.param_Lys4} - -labels:Lys6 ${adv_opts.param_Lys6} - -labels:Lys8 ${adv_opts.param_Lys8} - -labels:Dimethyl0 ${adv_opts.param_Dimethyl0} - -labels:Dimethyl4 ${adv_opts.param_Dimethyl4} - -labels:Dimethyl6 ${adv_opts.param_Dimethyl6} - -labels:Dimethyl8 ${adv_opts.param_Dimethyl8} - -labels:ICPL0 ${adv_opts.param_ICPL0} - -labels:ICPL4 ${adv_opts.param_ICPL4} - -labels:ICPL6 ${adv_opts.param_ICPL6} - -labels:ICPL10 ${adv_opts.param_ICPL10} + #if $adv_opts.param_force: + -force +#end if + #if $adv_opts.param_algorithm_isotopes_per_peptide: + -algorithm:isotopes_per_peptide "$adv_opts.param_algorithm_isotopes_per_peptide" +#end if + #if $adv_opts.param_algorithm_averagine_similarity_scaling: + -algorithm:averagine_similarity_scaling $adv_opts.param_algorithm_averagine_similarity_scaling +#end if + #if $adv_opts.param_algorithm_knock_out: + -algorithm:knock_out +#end if + #if $adv_opts.param_labels_Arg6: + -labels:Arg6 $adv_opts.param_labels_Arg6 +#end if + #if $adv_opts.param_labels_Arg10: + -labels:Arg10 $adv_opts.param_labels_Arg10 +#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 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 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)"/> - <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)"/> - <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)"/> - <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)"/> - <param name="param_mz_unit" type="select" optional="True" value="ppm" label="Unit of the 'mz_tolerance' parameter." help="(-mz_unit)"> - <option value="Da">Da</option> - <option value="ppm">ppm</option> - </param> - <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)"/> - <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)"/> - <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)"/> - <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)"/> - <expand macro="advanced_options"> - <param name="param_out_debug" type="text" size="20" label="Directory for debug output." help="(-out_debug)"/> - <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 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 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 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 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 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)"/> - <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)"/> - <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 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 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 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 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 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)"/> - <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 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)"/> - </expand> - </inputs> - <outputs> - <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"/> - <data name="param_out_features" label="Optional output file containing the individual peptide features in 'out'." format="featureXML"/> - <data name="param_out_mzq" label="Optional output file of MzQuantML." format="data"/> - </outputs> - <help>**What it does** - -Determination of peak ratios in LC-MS data + <inputs> + <param format="mzml" help="(-in) " label="LC-MS dataset in centroid or profile mode" name="param_in" optional="False" type="data"/> + <param help="(-labels) [...] 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" label="Labels used for labelling the samples" name="param_algorithm_labels" size="30" type="text" value="[][Lys8,Arg10]"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </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"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <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 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 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 help="(-mz_unit) " label="Unit of the 'mz_tolerance' paramete" name="param_algorithm_mz_unit" optional="True" type="select" value="ppm"> + <option value="Da">Da</option> + <option value="ppm">ppm</option> + </param> + <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 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 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 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"/> + <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="(-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"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <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 -> p' = p and x = 1 -> 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"/> + <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 - -@REFERENCES@ -</help> -</tool> +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderMultiplex.html</help> + </tool>