Mercurial > repos > galaxyp > openms_featurefindermultiplex

comparison FeatureFinderMultiplex.xml @ 3:9ef0f56e82df draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
author galaxyp
date Wed, 09 Aug 2017 09:26:17 -0400
parents 23d1e0b5cf9f
children 3a462c96f2bd
comparison
equal deleted inserted replaced
2:ca88bd28f116 3:9ef0f56e82df
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 CTD2Galaxy.-->
3 <!--Proposed Tool Section: [Quantitation]--> 3 <!--Proposed Tool Section: [Quantitation]-->
4 <tool id="FeatureFinderMultiplex" name="FeatureFinderMultiplex" version="2.1.0"> 4 <tool id="FeatureFinderMultiplex" name="FeatureFinderMultiplex" version="2.2.0">
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>
69 #if $adv_opts.param_algorithm_averagine_similarity_scaling: 69 #if $adv_opts.param_algorithm_averagine_similarity_scaling:
70 -algorithm:averagine_similarity_scaling $adv_opts.param_algorithm_averagine_similarity_scaling 70 -algorithm:averagine_similarity_scaling $adv_opts.param_algorithm_averagine_similarity_scaling
71 #end if 71 #end if
72 #if $adv_opts.param_algorithm_knock_out: 72 #if $adv_opts.param_algorithm_knock_out:
73 -algorithm:knock_out 73 -algorithm:knock_out
74 #end if
75 #if $adv_opts.param_algorithm_spectrum_type:
76 -algorithm:spectrum_type
77 #if " " in str($adv_opts.param_algorithm_spectrum_type):
78 "$adv_opts.param_algorithm_spectrum_type"
79 #else
80 $adv_opts.param_algorithm_spectrum_type
81 #end if
74 #end if 82 #end if
75 #if $adv_opts.param_algorithm_averagine_type: 83 #if $adv_opts.param_algorithm_averagine_type:
76 -algorithm:averagine_type 84 -algorithm:averagine_type
77 #if " " in str($adv_opts.param_algorithm_averagine_type): 85 #if " " in str($adv_opts.param_algorithm_averagine_type):
78 "$adv_opts.param_algorithm_averagine_type" 86 "$adv_opts.param_algorithm_averagine_type"
163 </valid> 171 </valid>
164 </sanitizer> 172 </sanitizer>
165 </param> 173 </param>
166 <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 -&gt; p' = p and x = 1 -&gt; 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.)"/> 174 <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 -&gt; p' = p and x = 1 -&gt; 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.)"/>
167 <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.)"/> 175 <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.)"/>
176 <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">
177 <option value="profile">profile</option>
178 <option value="centroid">centroid</option>
179 <option value="automatic" selected="true">automatic</option>
180 </param>
168 <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) "> 181 <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) ">
169 <option value="peptide" selected="true">peptide</option> 182 <option value="peptide" selected="true">peptide</option>
170 <option value="RNA">RNA</option> 183 <option value="RNA">RNA</option>
171 <option value="DNA">DNA</option> 184 <option value="DNA">DNA</option>
172 </param> 185 </param>