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comparison proteomiqon_psmstatistics.xml @ 1:f831f7d721f8 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 28244fe226c9bd5326886bf21960cbb43a4be2ec"
author galaxyp
date Fri, 27 Aug 2021 07:28:43 +0000
parents b8590dea5e2d
children 9ac2e8232c5c
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0:b8590dea5e2d 1:f831f7d721f8
1 <tool id="proteomiqon_psmstatistics" name="ProteomIQon PSMStatistics" version="@VERSION@" profile="20.05"> 1 <tool id="proteomiqon_psmstatistics" name="ProteomIQon PSMStatistics" version="@VERSION@" profile="20.05">
2 <description> 2 <description>
3 utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score. 3 utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score.
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <token name="@VERSION@">0.0.6</token> 6 <token name="@VERSION@">0.0.7</token>
7 </macros> 7 </macros>
8 <requirements> 8 <requirements>
9 <requirement type="package" version="@VERSION@">proteomiqon-psmstatistics</requirement> 9 <requirement type="package" version="@VERSION@">proteomiqon-psmstatistics</requirement>
10 </requirements> 10 </requirements>
11 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
33 "QValueThreshold" : $ThresholdCond.QValueThreshold, 33 "QValueThreshold" : $ThresholdCond.QValueThreshold,
34 "PepValueThreshold" : $ThresholdCond.PepValueThreshold, 34 "PepValueThreshold" : $ThresholdCond.PepValueThreshold,
35 "MaxIterations" : $ThresholdCond.MaxIterations, 35 "MaxIterations" : $ThresholdCond.MaxIterations,
36 "MinimumIncreaseBetweenIterations" : $ThresholdCond.MinimumIncreaseBetweenIterations, 36 "MinimumIncreaseBetweenIterations" : $ThresholdCond.MinimumIncreaseBetweenIterations,
37 "PepValueFittingMethod" : { 37 "PepValueFittingMethod" : {
38 "Case":"$ThresholdCond.PepValueFittingMethod" 38 "Case":"LinearLogit"
39 } 39 }
40 } 40 }
41 ] 41 ]
42 #else if $ThresholdCond.ProcessingType == "Fixed" 42 #else if $ThresholdCond.ProcessingType == "Fixed"
43 "Case":"Fixed", 43 "Case":"Fixed",
67 <when value="Estimate"> 67 <when value="Estimate">
68 <param name="QValueThreshold" type="float" value="0.01" label="Q-Value threshold" /> 68 <param name="QValueThreshold" type="float" value="0.01" label="Q-Value threshold" />
69 <param name="PepValueThreshold" type="float" value="0.05" label="Pep-Value threshold" /> 69 <param name="PepValueThreshold" type="float" value="0.05" label="Pep-Value threshold" />
70 <param name="MaxIterations" type="integer" value="15" label="Max iterations" /> 70 <param name="MaxIterations" type="integer" value="15" label="Max iterations" />
71 <param name="MinimumIncreaseBetweenIterations" type="float" value="0.005" label="Minimum increase between iterations" /> 71 <param name="MinimumIncreaseBetweenIterations" type="float" value="0.005" label="Minimum increase between iterations" />
72 <param name="PepValueFittingMethod" type="select" label="Pep-Value fitting method">
73 <option value="LinearSpline">Linear Spline</option>
74 <option value="LogisticRegressionLogit" selected="true">Logistic Regression Logit</option>
75 </param>
76 </when> 72 </when>
77 <when value="Fixed"> 73 <when value="Fixed">
78 <param name="SequestLike" type="float" value="5.0" label="Sequest like" /> 74 <param name="SequestLike" type="float" value="5.0" label="Sequest like" />
79 <param name="Andromeda" type="float" value="40.0" label="Andromeda" /> 75 <param name="Andromeda" type="float" value="40.0" label="Andromeda" />
80 </when> 76 </when>
100 <param name="ProcessingType" value="Estimate"/> 96 <param name="ProcessingType" value="Estimate"/>
101 <param name="QValueThreshold" value="0.01"/> 97 <param name="QValueThreshold" value="0.01"/>
102 <param name="PepValueThreshold" value="0.05"/> 98 <param name="PepValueThreshold" value="0.05"/>
103 <param name="MaxIterations" value="15"/> 99 <param name="MaxIterations" value="15"/>
104 <param name="MinimumIncreaseBetweenIterations" value="0.005"/> 100 <param name="MinimumIncreaseBetweenIterations" value="0.005"/>
105 <param name="PepValueFittingMethod" value="LinearSpline"/>
106 </conditional> 101 </conditional>
107 </test> 102 </test>
108 <test expect_num_outputs="2"> 103 <test expect_num_outputs="2">
109 <param name="psm" value="sample.psm"/> 104 <param name="psm" value="sample.psm"/>
110 <param name="peptideDB" value="sample.db"/> 105 <param name="peptideDB" value="sample.db"/>
114 <param name="ProcessingType" value="Estimate"/> 109 <param name="ProcessingType" value="Estimate"/>
115 <param name="QValueThreshold" value="0.01"/> 110 <param name="QValueThreshold" value="0.01"/>
116 <param name="PepValueThreshold" value="0.05"/> 111 <param name="PepValueThreshold" value="0.05"/>
117 <param name="MaxIterations" value="15"/> 112 <param name="MaxIterations" value="15"/>
118 <param name="MinimumIncreaseBetweenIterations" value="0.005"/> 113 <param name="MinimumIncreaseBetweenIterations" value="0.005"/>
119 <param name="PepValueFittingMethod" value="LinearSpline"/>
120 </conditional> 114 </conditional>
121 <output name="out_paramfile" file="result_1.json"/> 115 <output name="out_paramfile" file="result_1.json"/>
122 </test> 116 </test>
123 <test expect_num_outputs="2"> 117 <test expect_num_outputs="2">
124 <param name="psm" value="sample.psm"/> 118 <param name="psm" value="sample.psm"/>
129 <param name="ProcessingType" value="Estimate"/> 123 <param name="ProcessingType" value="Estimate"/>
130 <param name="QValueThreshold" value="0.01"/> 124 <param name="QValueThreshold" value="0.01"/>
131 <param name="PepValueThreshold" value="0.05"/> 125 <param name="PepValueThreshold" value="0.05"/>
132 <param name="MaxIterations" value="15"/> 126 <param name="MaxIterations" value="15"/>
133 <param name="MinimumIncreaseBetweenIterations" value="0.005"/> 127 <param name="MinimumIncreaseBetweenIterations" value="0.005"/>
134 <param name="PepValueFittingMethod" value="LogisticRegressionLogit"/>
135 </conditional> 128 </conditional>
136 <output name="out_paramfile" file="result_2.json"/> 129 <output name="out_paramfile" file="result_2.json"/>
137 </test> 130 </test>
138 <test expect_num_outputs="2"> 131 <test expect_num_outputs="2">
139 <param name="psm" value="sample.psm"/> 132 <param name="psm" value="sample.psm"/>