Mercurial > repos > bgruening > openms
diff TMTAnalyzer.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/TMTAnalyzer.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/TMTAnalyzer.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,69 +1,137 @@ -<?xml version='1.0' encoding='UTF-8'?> -<tool id="TMTAnalyzer" name="TMTAnalyzer" version="1.12.0"> - <description>Calculates TMT quantitative values for peptides</description> - <macros> - <token name="@EXECUTABLE@">TMTAnalyzer</token> - <import>macros.xml</import> - </macros> - <expand macro="stdio"/> - <expand macro="requirements"/> - <command>TMTAnalyzer +<?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="TMTAnalyzer" name="TMTAnalyzer" version="2.0.0"> + <description>Calculates TMT quantitative values for peptides</description> + <macros> + <token name="@EXECUTABLE@">TMTAnalyzer</token> + <import>macros.xml</import> + </macros> + <expand macro="references"/> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>TMTAnalyzer --in ${param_in} --out ${param_out} --out_stats ${param_out_stats} --threads \${GALAXY_SLOTS:-24} --id_pool ${param_id_pool} --algorithm:Extraction:select_activation ${param_select_activation} --algorithm:Extraction:reporter_mass_shift ${param_reporter_mass_shift} --algorithm:Extraction:channel_active ${param_channel_active} --algorithm:Quantification:channel_reference ${param_channel_reference} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_out_mzq: + -out_mzq $param_out_mzq +#end if +#if $param_out_stats: + -out_stats $param_out_stats +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_algorithm_Extraction_select_activation: + -algorithm:Extraction:select_activation + #if " " in str($param_algorithm_Extraction_select_activation): + "$param_algorithm_Extraction_select_activation" + #else + $param_algorithm_Extraction_select_activation + #end if +#end if +#if $param_algorithm_Extraction_reporter_mass_shift: + -algorithm:Extraction:reporter_mass_shift $param_algorithm_Extraction_reporter_mass_shift +#end if + +#if $rep_param_algorithm_Extraction_channel_active: +-algorithm:Extraction:channel_active + #for token in $rep_param_algorithm_Extraction_channel_active: + #if " " in str(token): + "$token.param_algorithm_Extraction_channel_active" + #else + $token.param_algorithm_Extraction_channel_active + #end if + #end for +#end if +#if $param_algorithm_Quantification_channel_reference: + -algorithm:Quantification:channel_reference $param_algorithm_Quantification_channel_reference +#end if #if $adv_opts.adv_opts_selector=='advanced': - -out_mzq ${adv_opts.param_out_mzq} - -algorithm:Quantification:isotope_correction:tmt-6plex ${adv_opts.param_tmt-6plex} - ${adv_opts.param_do_normalization} - -algorithm:MetaInformation:Program ${adv_opts.param_Program} + #if $adv_opts.param_force: + -force +#end if + +#if $rep_param_algorithm_Quantification_isotope_correction_tmt_6plex: +-algorithm:Quantification:isotope_correction:tmt-6plex + #for token in $rep_param_algorithm_Quantification_isotope_correction_tmt_6plex: + #if " " in str(token): + "$token.param_algorithm_Quantification_isotope_correction_tmt_6plex" + #else + $token.param_algorithm_Quantification_isotope_correction_tmt_6plex + #end if + #end for +#end if + #if $adv_opts.param_algorithm_Quantification_do_normalization: + -algorithm:Quantification:do_normalization +#end if + #if $adv_opts.param_algorithm_MetaInformation_Program: + -algorithm:MetaInformation:Program "$adv_opts.param_algorithm_MetaInformation_Program" +#end if #end if </command> - <inputs> - <param name="param_in" type="data" format="mzML" optional="False" label="input raw/picked data file " help="(-in)"/> - <param name="param_id_pool" type="text" size="20" label="ID pool file to DocumentID's for all generated output files. Disabled by default. (Set to 'main' to use /home/thouwaar/Projects/OpenMS/share/OpenMS/IDPool/IDPool.txt)" help="(-id_pool)"/> - <param name="param_select_activation" type="select" optional="True" value="High-energy collision-induced dissociation" label="Operate only on MSn scans where any of its precursors features a certain activation method (usually HCD for iTRAQ). Set to empty string if you want to disable filtering." help="(-select_activation)"> - <option value="Collision-induced dissociation">Collision-induced dissociation</option> - <option value="Post-source decay">Post-source decay</option> - <option value="Plasma desorption">Plasma desorption</option> - <option value="Surface-induced dissociation">Surface-induced dissociation</option> - <option value="Blackbody infrared radiative dissociation">Blackbody infrared radiative dissociation</option> - <option value="Electron capture dissociation">Electron capture dissociation</option> - <option value="Infrared multiphoton dissociation">Infrared multiphoton dissociation</option> - <option value="Sustained off-resonance irradiation">Sustained off-resonance irradiation</option> - <option value="High-energy collision-induced dissociation">High-energy collision-induced dissociation</option> - <option value="Low-energy collision-induced dissociation">Low-energy collision-induced dissociation</option> - <option value="Photodissociation">Photodissociation</option> - <option value="Electron transfer dissociation">Electron transfer dissociation</option> - <option value=""></option> - </param> - <param name="param_reporter_mass_shift" type="float" min="1e-08" max="0.5" optional="True" value="0.1" label="Allowed shift (left to right) in Da from the expected position." help="(-reporter_mass_shift)"/> - <param name="param_channel_active" type="text" size="20" value="126:liver 131:lung" label="Each channel that was used in the experiment and its description (126-131 for TMT-6-plex) in format <channel>:<name>, e.g. "114:myref","115:liver"." help="(-channel_active)"/> - <param name="param_channel_reference" type="integer" min="126" max="131" optional="True" value="126" label="Number of the reference channel (126-131)." help="(-channel_reference)"/> - <expand macro="advanced_options"> - <param name="param_tmt-6plex" type="text" size="20" value="126:0/0/0/0 127:0/0/0/0 128:0/0/0/0 129:0/0/0/0 130:0/0/0/0 131:0/0/0/0" label="Override default values (see Documentation); use the following format: <channel>:<-2Da>/<-1Da>/<+1Da>/<+2Da> ; e.g. '126:0/0.3/4/0' , '128:0.1/0.3/3/0.2'." help="(-tmt-6plex)"/> - <param name="param_do_normalization" type="boolean" truevalue="-algorithm:Quantification:do_normalization true" falsevalue="-algorithm:Quantification:do_normalization false" checked="false" optional="True" label="Normalize channels? Done by using the Median of Ratios (every channel / Reference). Also the ratio of medians (from any channel and reference) is provided as control measure!" help="(-do_normalization)"/> - <param name="param_Program" type="text" size="20" value="OpenMS::TMTAnalyzer" label="" help="(-Program)"/> - </expand> - </inputs> - <outputs> - <data name="param_out" label="output consensusXML file with quantitative information" format="consensusXML"/> - <data name="param_out_mzq" label="Optional output file of MzQuantML." format="data"/> - <data name="param_out_stats" label="output statistics as tab-separated file (readable by R or Excel or ...)" format="data"/> - </outputs> - <help>**What it does** - -Calculates TMT quantitative values for peptides + <inputs> + <param format="mzml" help="(-in) " label="input raw/picked data file" name="param_in" optional="False" type="data"/> + <param help="(-select_activation) Set to empty string if you want to disable filtering" label="Operate only on MSn scans where any of its precursors features a certain activation method (usually HCD for iTRAQ)" name="param_algorithm_Extraction_select_activation" optional="True" type="select" value="High-energy collision-induced dissociation"> + <option value="Collision-induced dissociation">Collision-induced dissociation</option> + <option value="Post-source decay">Post-source decay</option> + <option value="Plasma desorption">Plasma desorption</option> + <option value="Surface-induced dissociation">Surface-induced dissociation</option> + <option value="Blackbody infrared radiative dissociation">Blackbody infrared radiative dissociation</option> + <option value="Electron capture dissociation">Electron capture dissociation</option> + <option value="Infrared multiphoton dissociation">Infrared multiphoton dissociation</option> + <option value="Sustained off-resonance irradiation">Sustained off-resonance irradiation</option> + <option value="High-energy collision-induced dissociation">High-energy collision-induced dissociation</option> + <option value="Low-energy collision-induced dissociation">Low-energy collision-induced dissociation</option> + <option value="Photodissociation">Photodissociation</option> + <option value="Electron transfer dissociation">Electron transfer dissociation</option> + <option value=""></option> + </param> + <param help="(-reporter_mass_shift) " label="Allowed shift (left to right) in Da from the expected position" max="0.5" min="1e-08" name="param_algorithm_Extraction_reporter_mass_shift" optional="True" type="float" value="0.1"/> + <repeat max="1" min="0" name="rep_param_algorithm_Extraction_channel_active" title="param_algorithm_Extraction_channel_active"> + <param help="(-channel_active) e.g. "114:myref","115:liver"" label="Each channel that was used in the experiment and its description (126-131 for TMT-6-plex) in format <channel>:<name>," name="param_algorithm_Extraction_channel_active" size="30" type="text" value="126:liver 131:lung"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + </repeat> + <param help="(-channel_reference) " label="Number of the reference channel (126-131)" max="131" min="126" name="param_algorithm_Quantification_channel_reference" optional="True" type="integer" value="126"/> + <expand macro="advanced_options"> + <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/> + <repeat max="1" min="0" name="rep_param_algorithm_Quantification_isotope_correction_tmt_6plex" title="param_algorithm_Quantification_isotope_correction_tmt_6plex"> + <param help="(-tmt-6plex) e.g. '126:0/0.3/4/0' , '128:0.1/0.3/3/0.2'" label="Override default values (see Documentation); use the following format: <channel>:<-2Da>/<-1Da>/<+1Da>/<+2Da> ;" name="param_algorithm_Quantification_isotope_correction_tmt_6plex" size="30" type="text" value="126:0/0/0/0 127:0/0/0/0 128:0/0/0/0 129:0/0/0/0 130:0/0/0/0 131:0/0/0/0"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + </repeat> + <param checked="false" falsevalue="" help="(-do_normalization) Done by using the Median of Ratios (every channel / Reference). Also the ratio of medians (from any channel and reference) is provided as control measure!" label="Normalize channels?" name="param_algorithm_Quantification_do_normalization" optional="True" truevalue="-algorithm:Quantification:do_normalization" type="boolean"/> + <param help="(-Program) " label="" name="param_algorithm_MetaInformation_Program" size="30" type="text" value="OpenMS::TMTAnalyzer"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + </expand> + </inputs> + <outputs> + <data format="consensusxml" name="param_out"/> + <data format="mzq" name="param_out_mzq"/> + <data format="tabular" name="param_out_stats"/> + </outputs> + <help>Calculates TMT quantitative values for peptides -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_TMTAnalyzer.html - -@REFERENCES@ -</help> -</tool> +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_TMTAnalyzer.html</help> + </tool>