Mercurial > repos > yhoogstrate > edger_with_design_matrix

comparison edgeR_Concatenate_Expression_Matrices.xml @ 94:46745f5666ac draft

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Added test
author yhoogstrate
date Sat, 28 Mar 2015 08:09:03 -0400
parents b2738b4d7c8c
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93:31335aa52b2e 94:46745f5666ac
84 <data format="tabular" name="expression_matrix" label="Expression matrix" /> 84 <data format="tabular" name="expression_matrix" label="Expression matrix" />
85 </outputs> 85 </outputs>
86 86
87 <tests> 87 <tests>
88 <test> 88 <test>
89 <param name="add_geneids.choice" value="true" /> 89 <conditional name="add_geneids">
90 <param name="choice" value="true" /> 90 <param name="choice" value="true" />
91 <param name="add_geneids" value="true" /> 91 <param name="sample_geneids" value="GSE51403/GSE51403_expression_matrix_GeneLengths.txt" />
92 92 <param name="column_geneids" value="1" />
93 93 </conditional>
94 <!-- 94
95 Add a gene-IDs column at the end of the file true 95 <param name="samples_0|sample" value="GSE51403/GSE51403_expression_matrix_Control_1.txt" />
96 Select Read-count dataset that contains a column for GeneIDs 21: MCF7_featureCounts_E2.txt 96 <param name="samples_0|column_index" value="2" />
97 Select GeneID column 1 97
98 Read-count dataset that belongs to a pair 14: MCF7_featureCounts_Control_1.txt 98 <conditional name="add_lengths">
99 Select columns that are associated with this factor level 2 99 <param name="choice" value="false" />
100 Read-count dataset that belongs to a pair 15: MCF7_featureCounts_Control_2.txt 100 </conditional>
101 Select columns that are associated with this factor level 2 101
102 Read-count dataset that belongs to a pair 16: MCF7_featureCounts_Control_3.txt 102 <param name="remove_comment_lines" value="false" />
103 Select columns that are associated with this factor level 2 103
104 Read-count dataset that belongs to a pair 17: MCF7_featureCounts_Control_4.txt 104 <output name="expression_matrix" file="GSE51403/GSE51403_expression_matrix_Control_1.txt" />
105 Select columns that are associated with this factor level 2 105 </test>
106 Read-count dataset that belongs to a pair 18: MCF7_featureCounts_Control_5.txt 106 <test>
107 Select columns that are associated with this factor level 2 107 <conditional name="add_geneids">
108 Read-count dataset that belongs to a pair 22: MCF7_featureCounts_Control_6.txt 108 <param name="choice" value="true" />
109 Select columns that are associated with this factor level 2 109 <param name="sample_geneids" value="GSE51403/GSE51403_expression_matrix_GeneLengths.txt" />
110 Read-count dataset that belongs to a pair 20: MCF7_featureCounts_Control_7.txt 110 <param name="column_geneids" value="1" />
111 Select columns that are associated with this factor level 2 111 </conditional>
112 Read-count dataset that belongs to a pair 21: MCF7_featureCounts_E2.txt 112
113 Select columns that are associated with this factor level 2 3 4 5 6 7 8 113 <!-- <repeat name="samples"> -->
114 Add a gene-lengths column at the end of the file true 114 <param name="samples_0|sample" value="GSE51403/GSE51403_expression_matrix_Control_1.txt" />
115 Read-count dataset that belongs to a pair 26: MCF7_featureCounts_GeneLengths.txt 115 <param name="samples_0|column_index" value="2" />
116 Select columns that are associated with this factor level 2 116 <!-- </repeat> -->
117 Automatically remove 'comment' lines starting with a '#' False 117
118 --> 118 <!-- <repeat name="samples"> -->
119 119 <param name="samples_1|sample" value="GSE51403/GSE51403_expression_matrix_Control_2.txt" />
120 <output name="expression_matrix" file="MCF7_featureCounts_concatenated.txt" /> 120 <param name="samples_1|column_index" value="2" />
121 <!-- </repeat> -->
122
123 <!-- <repeat name="samples"> -->
124 <param name="samples_2|sample" value="GSE51403/GSE51403_expression_matrix_Control_3.txt" />
125 <param name="samples_2|column_index" value="2" />
126 <!-- </repeat> -->
127
128 <!-- <repeat name="samples"> -->
129 <param name="samples_3|sample" value="GSE51403/GSE51403_expression_matrix_Control_4.txt" />
130 <param name="samples_3|column_index" value="2" />
131 <!-- </repeat> -->
132
133 <!-- <repeat name="samples"> -->
134 <param name="samples_4|sample" value="GSE51403/GSE51403_expression_matrix_Control_5.txt" />
135 <param name="samples_4|column_index" value="2" />
136 <!-- </repeat> -->
137
138 <!-- <repeat name="samples"> -->
139 <param name="samples_5|sample" value="GSE51403/GSE51403_expression_matrix_Control_6.txt" />
140 <param name="samples_5|column_index" value="2" />
141 <!-- </repeat> -->
142
143 <!-- <repeat name="samples"> -->
144 <param name="samples_6|sample" value="GSE51403/GSE51403_expression_matrix_Control_7.txt" />
145 <param name="samples_6|column_index" value="2" />
146 <!-- </repeat> -->
147
148 <!-- <repeat name="samples"> -->
149 <param name="samples_7|sample" value="GSE51403/GSE51403_expression_matrix_E2.txt" />
150 <param name="samples_7|column_index" value="2,3,4,5,6,7,8" />
151 <!-- </repeat> -->
152
153 <conditional name="add_lengths">
154 <param name="choice" value="true" />
155 <param name="sample_lengths" value="GSE51403/GSE51403_expression_matrix_GeneLengths.txt" />
156 <param name="column_lengths" value="2" />
157 </conditional>
158
159 <param name="remove_comment_lines" value="false" />
160
161 <output name="expression_matrix" file="GSE51403/GSE51403_expression_matrix_full.txt" />
121 </test> 162 </test>
122 </tests> 163 </tests>
123 164
124 <help> 165 <help>
125 edgeR: Concatenate Expression Matrices 166 edgeR: Concatenate Expression Matrices
155 196
156 http://toolshed.g2.bx.psu.edu 197 http://toolshed.g2.bx.psu.edu
157 198
158 http://testtoolshed.g2.bx.psu.edu/ 199 http://testtoolshed.g2.bx.psu.edu/
159 </help> 200 </help>
201
202 <citations>
203 <citation type="doi">10.1093/bioinformatics/btp616</citation>
204 <citation type="doi">10.1093/bioinformatics/btt688</citation>
205 </citations>
160 </tool> 206 </tool>