Mercurial > repos > galaxyp > openms_tmtanalyzer
diff TMTAnalyzer.xml @ 0:d05c7c810dd8 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
| author | galaxyp |
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| date | Wed, 01 Mar 2017 12:32:02 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/TMTAnalyzer.xml Wed Mar 01 12:32:02 2017 -0500 @@ -0,0 +1,142 @@ +<?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="2.1.0"> + <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 + +#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 +#if $param_id_pool: + -id_pool "$param_id_pool" +#end if +#if $param_algorithm_Extraction_select_activation: + -algorithm:Extraction:select_activation $param_algorithm_Extraction_select_activation +#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': + #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="30" label="ID pool file to DocumentID's for all generated output files" help="(-id_pool) Disabled by default. (Set to 'main' to use /home/ubuntu/miniconda3/envs/py2test/share/OpenMS/IDPool/IDPool.txt)"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_algorithm_Extraction_select_activation" type="select" optional="False" 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)" help="(-select_activation) Set to empty string if you want to disable filtering"> + <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" selected="true">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_algorithm_Extraction_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) "/> + <repeat name="rep_param_algorithm_Extraction_channel_active" min="0" max="1" title="param_algorithm_Extraction_channel_active"> + <param name="param_algorithm_Extraction_channel_active" type="text" size="30" 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>," help="(-channel_active) e.g. "114:myref","115:liver""> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + </repeat> + <param name="param_algorithm_Quantification_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_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> + <repeat name="rep_param_algorithm_Quantification_isotope_correction_tmt_6plex" min="0" max="1" title="param_algorithm_Quantification_isotope_correction_tmt_6plex"> + <param name="param_algorithm_Quantification_isotope_correction_tmt_6plex" type="text" size="30" 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> ;" help="(-tmt-6plex) e.g. '126:0/0.3/4/0' , '128:0.1/0.3/3/0.2'"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + </repeat> + <param name="param_algorithm_Quantification_do_normalization" display="radio" type="boolean" truevalue="-algorithm:Quantification:do_normalization" falsevalue="" checked="false" optional="True" label="Normalize channels?" 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!"/> + <param name="param_algorithm_MetaInformation_Program" type="text" size="30" value="OpenMS::TMTAnalyzer" label="" help="(-Program) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + </expand> + </inputs> + <outputs> + <data name="param_out" format="consensusxml"/> + <data name="param_out_mzq" format="mzq"/> + <data name="param_out_stats" format="tabular"/> + </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</help> +</tool>