Mercurial > repos > galaxyp > openms_multiplexresolver
diff MultiplexResolver.xml @ 0:c8871ea9a7b7 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
| author | galaxyp |
|---|---|
| date | Wed, 01 Mar 2017 10:14:59 -0500 |
| parents | |
| children | 2ba399876379 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/MultiplexResolver.xml Wed Mar 01 10:14:59 2017 -0500 @@ -0,0 +1,119 @@ +<?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: [Utilities]--> +<tool id="MultiplexResolver" name="MultiplexResolver" version="2.1.0"> + <description>Completes peptide multiplets and resolves conflicts within them.</description> + <macros> + <token name="@EXECUTABLE@">MultiplexResolver</token> + <import>macros.xml</import> + </macros> + <expand macro="references"/> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>MultiplexResolver + +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_out_conflicts: + -out_conflicts $param_out_conflicts +#end if +#if $param_algorithm_labels: + -algorithm:labels "$param_algorithm_labels" +#end if +#if $param_algorithm_missed_cleavages: + -algorithm:missed_cleavages $param_algorithm_missed_cleavages +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if + #if $adv_opts.param_algorithm_mass_tolerance: + -algorithm:mass_tolerance $adv_opts.param_algorithm_mass_tolerance +#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_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 +</command> + <inputs> + <param name="param_in" type="data" format="consensusxml" optional="False" label="Peptide multiplets with assigned sequence information" 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_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_mass_tolerance" type="float" value="0.1" label="Mass tolerance in Da for matching the detected to the theoretical mass shifts" help="(-mass_tolerance) "/> + <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) "/> + </expand> + </inputs> + <outputs> + <data name="param_out" format="consensusxml"/> + <data name="param_out_conflicts" format="consensusxml"/> + </outputs> + <help>Completes peptide multiplets and resolves conflicts within them. + + +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/doxygen/parameters/output/UTILS_MultiplexResolver.html</help> +</tool>