Mercurial > repos > yhoogstrate > edger_with_design_matrix

comparison edgeR_Design_from_Expression_Matrix.xml @ 8:31a23ae7c61e draft default tip

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/edger_with_design_matrix commit eb5cd7834861d8ddbffce974ed0ca6f1c0ecccf2
author erasmus-medical-center
date Tue, 14 Feb 2017 10:01:51 -0500
parents 55f4e42f91ba
children
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7:55f4e42f91ba 8:31a23ae7c61e
5 <macros> 5 <macros>
6 <import>edgeR_macros.xml</import> 6 <import>edgeR_macros.xml</import>
7 </macros> 7 </macros>
8 8
9 <requirements> 9 <requirements>
10 <requirement type="package" version="1.0.0">design_matrix_creator</requirement> 10 <requirement type="package" version="2.7">python</requirement>
11 </requirements> 11 </requirements>
12 12
13 <command> 13 <command>
14 design_matrix_creator 14 python '${__tool_directory__}/bin/design_matrix_creator'
15 -c $expression_matrix 15 -c $expression_matrix
16 16
17 #set $unique_columns = [] 17 #set $unique_columns = []
18 #for $factor in $treatments: 18 #for $factor in $treatments:
19 #for $level in $factor.rep_factorLevel: 19 #for $level in $factor.rep_factorLevel:
55 55
56 -o $design_matrix 56 -o $design_matrix
57 </command> 57 </command>
58 58
59 <inputs> 59 <inputs>
60 <param format="tabular" name="expression_matrix" type="data" label="Expression matrix (read counts)" help="You can create a count matrix with the tool" /> 60 <param name="expression_matrix" format="tabular" type="data" label="Expression matrix (read counts)" help="You can create a count matrix with the tool" />
61 61
62 <repeat name="treatments" title="Factor/Condition" min="1"> 62 <repeat name="treatments" title="Factor/Condition" min="1">
63 <param name="name" type="text" value="FactorName" label="Specify a name for the factor / condition" help="e.g. 'Tumor vs. Normal', 'Timepoint' or 'DiseaseState'. Field must be non-numerical, preferably only letters!!" /> 63 <param name="name" type="text" value="FactorName" label="Specify a name for the factor / condition" help="e.g. 'Tumor vs. Normal', 'Timepoint' or 'DiseaseState'. Field must be non-numerical, preferably only letters!!" />
64 <repeat name="rep_factorLevel" title="Factor level" min="1"> 64 <repeat name="rep_factorLevel" title="Factor level" min="1">
65 <param name="factorLevel" type="text" value="FactorLevel" label="Specify a condition" help="e.g. Tumor or Normal; Treated, untreaded or placebo. Field must be non-numerical, preferably only letters!!" /> 65 <param name="factorLevel" type="text" value="FactorLevel" label="Specify a condition" help="e.g. Tumor or Normal; Treated, untreaded or placebo. Field must be non-numerical, preferably only letters!!" />
94 94
95 <tests> 95 <tests>
96 <test> 96 <test>
97 <param name="expression_matrix" value="GSE51403/GSE51403_expression_matrix_full.txt" /> 97 <param name="expression_matrix" value="GSE51403/GSE51403_expression_matrix_full.txt" />
98 98
99 <!-- <repeat name="treatments"> --> 99 <repeat name="treatments">
100 <param name="treatments_0|name" value="Treatment" /> 100 <repeat name="rep_factorLevel">
101 <!-- <repeat name="rep_factorLevel"> --> 101 <param name="factorLevel" value="Control" />
102 <param name="treatments_0|rep_factorLevel_0|factorLevel" value="Control" /> 102 <param name="factorIndex" value="2,3,4,5,6,7,8" />
103 <param name="treatments_0|rep_factorLevel_0|factorIndex" value="2,3,4,5,6,7,8" /> 103 </repeat>
104 <!-- </repeat> --> 104 <repeat name="rep_factorLevel">
105 <!-- <repeat name="rep_factorLevel"> --> 105 <param name="factorLevel" value="E2" />
106 <param name="treatments_0|rep_factorLevel_1|factorLevel" value="E2" /> 106 <param name="factorIndex" value="9,10,11,12,13,14,15" />
107 <param name="treatments_0|rep_factorLevel_1|factorIndex" value="9,10,11,12,13,14,15" /> 107 </repeat>
108 <!-- </repeat> --> 108 </repeat>
109 <!-- </repeat> -->
110 109
111 <conditional name="choose_blocking"> 110 <conditional name="choose_blocking">
112 <param value="false" /> 111 <param name="choice" value="false" />
113 </conditional> 112 </conditional>
114 113
115 <output name="design_matrix" file="GSE51403/GSE51403_design_matrix_full_depth.txt" /> 114 <output name="design_matrix" file="GSE51403/GSE51403_design_matrix_full_depth.txt" />
116 </test> 115 </test>
117 </tests> 116 </tests>