Mercurial > repos > galaxyp > openms_featurefindermultiplex
diff FeatureFinderMultiplex.xml @ 12:3098bea02bd8 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
| author | galaxyp |
|---|---|
| date | Wed, 09 Sep 2020 12:50:38 +0000 |
| parents | e8651e585689 |
| children | 5e5771b511a3 |
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--- a/FeatureFinderMultiplex.xml Fri May 17 09:48:25 2019 -0400 +++ b/FeatureFinderMultiplex.xml Wed Sep 09 12:50:38 2020 +0000 @@ -1,212 +1,167 @@ <?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="2.3.0"> +<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="references"/> - <expand macro="stdio"/> <expand macro="requirements"/> - <command detect_errors="aggressive"><![CDATA[FeatureFinderMultiplex + <expand macro="stdio"/> + <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ +@EXT_FOO@ +#import re -#if $param_in: - -in $param_in +## Preprocessing +mkdir in && +ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + mkdir out && #end if -#if $param_out: - -out $param_out +#if "out_multiplets_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + mkdir out_multiplets && #end if -#if $param_out_features: - -out_features $param_out_features -#end if -#if $param_out_mzq: - -out_mzq $param_out_mzq +#if "out_blacklist_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + mkdir out_blacklist && #end if --algorithm:labels '$param_algorithm_labels' +## Main program call -#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 $param_algorithm_mz_tolerance +set -o pipefail && +@EXECUTABLE@ -write_ctd ./ && +python3 '$__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 $param_algorithm_mz_unit: - -algorithm:mz_unit - #if " " in str($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 $param_algorithm_missed_cleavages +#if "out_multiplets_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + -out_multiplets + 'out_multiplets/output.${gxy2omsext("consensusxml")}' #end if -#if $adv_opts.adv_opts_selector=='advanced': - #if $adv_opts.param_force: - -force +#if "out_blacklist_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + -out_blacklist + 'out_blacklist/output.${gxy2omsext("mzml")}' #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 $adv_opts.param_algorithm_knock_out: - -algorithm:knock_out +#if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 + | tee '$stdout' #end if - #if $adv_opts.param_algorithm_spectrum_type: - -algorithm:spectrum_type - #if " " in str($adv_opts.param_algorithm_spectrum_type): - "$adv_opts.param_algorithm_spectrum_type" - #else - $adv_opts.param_algorithm_spectrum_type - #end if + +## Postprocessing +#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + && mv 'out/output.${gxy2omsext("featurexml")}' '$out' #end if - #if $adv_opts.param_algorithm_averagine_type: - -algorithm:averagine_type - #if " " in str($adv_opts.param_algorithm_averagine_type): - "$adv_opts.param_algorithm_averagine_type" - #else - $adv_opts.param_algorithm_averagine_type - #end if +#if "out_multiplets_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + && mv 'out_multiplets/output.${gxy2omsext("consensusxml")}' '$out_multiplets' #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 $adv_opts.param_labels_Lys6 +#if "out_blacklist_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + && mv 'out_blacklist/output.${gxy2omsext("mzml")}' '$out_blacklist' #end if - #if $adv_opts.param_labels_Lys8: - -labels:Lys8 $adv_opts.param_labels_Lys8 -#end if - #if $adv_opts.param_labels_Leu3: - -labels:Leu3 $adv_opts.param_labels_Leu3 -#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 --threads "\${GALAXY_SLOTS:-1}" -]]></command> +#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="param_in" type="data" format="mzml" optional="False" label="LC-MS dataset in centroid or profile mode" help="(-in) "/> - <param name="param_algorithm_labels" type="text" size="30" value="[][Lys8,Arg10]" label="Labels used for labelling the samples" 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"> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <param name="param_algorithm_charge" type="text" size="30" value="1:4" label="Range of charge states in the sample, i.e" help="(-charge) min charge : max charge"> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - <param name="param_algorithm_rt_typical" type="float" min="0.0" optional="True" value="40.0" label="Typical retention time [s] over which a characteristic peptide elutes" help="(-rt_typical) (This is not an upper bound. Peptides that elute for longer will be reported.)"/> - <param name="param_algorithm_rt_min" type="float" min="0.0" optional="True" value="2.0" label="Lower bound for the retention time [s]" help="(-rt_min) (Any peptides seen for a shorter time period are not reported.)"/> - <param name="param_algorithm_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_algorithm_mz_unit" display="radio" type="select" optional="False" value="ppm" label="Unit of the 'mz_tolerance' paramete" help="(-mz_unit) "> - <option value="Da">Da</option> - <option value="ppm" selected="true">ppm</option> - </param> - <param name="param_algorithm_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_algorithm_peptide_similarity" type="float" min="-1.0" max="1.0" optional="True" value="0.5" label="Two peptides in a multiplet are expected to have the same isotopic pattern" help="(-peptide_similarity) This parameter is a lower bound on their similarity"/> - <param name="param_algorithm_averagine_similarity" type="float" min="-1.0" 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" help="(-averagine_similarity) This parameter is a lower bound on similarity between measured isotopic pattern and the averagine model"/> - <param name="param_algorithm_missed_cleavages" type="integer" min="0" optional="True" value="0" label="Maximum number of missed cleavages due to incomplete digestion" help="(-missed_cleavages) (Only relevant if enzymatic cutting site coincides with labelling site. For example, Arg/Lys in the case of trypsin digestion and SILAC labelling.)"/> - <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_isotopes_per_peptide" type="text" size="30" value="3:6" label="Range of isotopes per peptide in the sample" 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. "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> + <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="param_algorithm_averagine_similarity_scaling" type="float" min="0.0" max="1.0" optional="True" value="0.75" label="Let x denote this scaling factor, and p the averagine similarity paramete" 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.)"/> - <param name="param_algorithm_knock_out" display="radio" type="boolean" truevalue="-algorithm:knock_out" falsevalue="" checked="false" optional="True" label="Is it likely that knock-outs are present?" help="(-knock_out) (Supported for doublex, triplex and quadruplex experiments only.)"/> - <param name="param_algorithm_spectrum_type" display="radio" type="select" optional="False" value="automatic" label="Type of MS1 spectra in input mzML file" help="(-spectrum_type) 'automatic' determines the spectrum type directly from the input mzML file"> + <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 -> 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.)"/> + <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="param_algorithm_averagine_type" display="radio" type="select" optional="False" value="peptide" label="The type of averagine to use, currently RNA, DNA or peptide" help="(-averagine_type) "> + <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="param_labels_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_labels_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_labels_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_labels_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_labels_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_labels_Leu3" type="float" min="0.0" optional="True" value="3.01883" label="Label:2H(3) | H(-3) 2H(3) | unimod #262" help="(-Leu3) "/> - <param name="param_labels_Dimethyl0" type="float" min="0.0" optional="True" value="28.0313" label="Dimethyl | H(4) C(2) | unimod #36" help="(-Dimethyl0) "/> - <param name="param_labels_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_labels_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_labels_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_labels_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_labels_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_labels_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_labels_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 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="param_out" format="consensusxml" label="${tool.name} on ${on_string}: consensusxml"/> - <data name="param_out_features" format="featurexml" label="${tool.name} on ${on_string}: featurexml"/> - <data name="param_out_mzq" format="mzq" label="${tool.name} on ${on_string}: mzq"/> + <data name="out" label="${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> - <help>Determination of peak ratios in LC-MS data + <tests> + <expand macro="autotest_FeatureFinderMultiplex"/> + <expand macro="manutest_FeatureFinderMultiplex"/> + </tests> + <help><![CDATA[Determination of peak ratios in LC-MS data -For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_FeatureFinderMultiplex.html</help> +For more information, visit http://www.openms.de/documentation/TOPP_FeatureFinderMultiplex.html]]></help> + <expand macro="references"/> </tool>