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comparison FeatureFinderMultiplex.xml @ 12:9e6747a47a04 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
author galaxyp
date Wed, 15 May 2019 05:30:01 -0400
parents 10cf202b7035
children 7397f644139b
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11:10cf202b7035 12:9e6747a47a04
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
3 <!--Proposed Tool Section: [Quantitation]--> 3 <!--Proposed Tool Section: [Quantitation]-->
4 <tool id="FeatureFinderMultiplex" name="FeatureFinderMultiplex" version="2.2.0.1"> 4 <tool id="FeatureFinderMultiplex" name="FeatureFinderMultiplex" version="2.3.0">
5 <description>Determination of peak ratios in LC-MS data</description> 5 <description>Determination of peak ratios in LC-MS data</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">FeatureFinderMultiplex</token> 7 <token name="@EXECUTABLE@">FeatureFinderMultiplex</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
10 <expand macro="references"/> 10 <expand macro="references"/>
11 <expand macro="stdio"/> 11 <expand macro="stdio"/>
12 <expand macro="requirements"/> 12 <expand macro="requirements"/>
13 <command>FeatureFinderMultiplex 13 <command detect_errors="aggressive"><![CDATA[FeatureFinderMultiplex
14 14
15 #if $param_in: 15 #if $param_in:
16 -in $param_in 16 -in $param_in
17 #end if 17 #end if
18 #if $param_out: 18 #if $param_out:
129 #end if 129 #end if
130 #if $adv_opts.param_labels_ICPL10: 130 #if $adv_opts.param_labels_ICPL10:
131 -labels:ICPL10 $adv_opts.param_labels_ICPL10 131 -labels:ICPL10 $adv_opts.param_labels_ICPL10
132 #end if 132 #end if
133 #end if 133 #end if
134 </command> 134 -threads "\${GALAXY_SLOTS:-1}"
135 ]]></command>
135 <inputs> 136 <inputs>
136 <param name="param_in" type="data" format="mzml" optional="False" label="LC-MS dataset in centroid or profile mode" help="(-in) "/> 137 <param name="param_in" type="data" format="mzml" optional="False" label="LC-MS dataset in centroid or profile mode" help="(-in) "/>
137 <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 &lt;br&gt; &lt;br&gt;[][Lys8,Arg10] ... SILAC &lt;br&gt;[][Lys4,Arg6][Lys8,Arg10] ... triple-SILAC &lt;br&gt;[Dimethyl0][Dimethyl6] ... Dimethyl &lt;br&gt;[Dimethyl0][Dimethyl4][Dimethyl8] ... triple Dimethyl &lt;br&gt;[ICPL0][ICPL4][ICPL6][ICPL10] ... ICPL"> 138 <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 &lt;br&gt; &lt;br&gt;[][Lys8,Arg10] ... SILAC &lt;br&gt;[][Lys4,Arg6][Lys8,Arg10] ... triple-SILAC &lt;br&gt;[Dimethyl0][Dimethyl6] ... Dimethyl &lt;br&gt;[Dimethyl0][Dimethyl4][Dimethyl8] ... triple Dimethyl &lt;br&gt;[ICPL0][ICPL4][ICPL6][ICPL10] ... ICPL">
138 <sanitizer> 139 <sanitizer>
139 <valid initial="string.printable"> 140 <valid initial="string.printable">
198 <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) "/> 199 <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) "/>
199 <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) "/> 200 <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) "/>
200 </expand> 201 </expand>
201 </inputs> 202 </inputs>
202 <outputs> 203 <outputs>
203 <data name="param_out" format="consensusxml"/> 204 <data name="param_out" format="consensusxml" label="${tool.name} on ${on_string}: consensusxml"/>
204 <data name="param_out_features" format="featurexml"/> 205 <data name="param_out_features" format="featurexml" label="${tool.name} on ${on_string}: featurexml"/>
205 <data name="param_out_mzq" format="mzq"/> 206 <data name="param_out_mzq" format="mzq" label="${tool.name} on ${on_string}: mzq"/>
206 </outputs> 207 </outputs>
207 <help>Determination of peak ratios in LC-MS data 208 <help>Determination of peak ratios in LC-MS data
208 209
209 210
210 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderMultiplex.html</help> 211 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_FeatureFinderMultiplex.html</help>
211 </tool> 212 </tool>