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comparison fuma.xml @ 3:4966079d474b draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2-dirty
author yhoogstrate
date Tue, 20 Oct 2015 10:12:08 -0400
parents 86526900cb8f
children cb0543909e83
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2:86526900cb8f 3:4966079d474b
111 </outputs> 111 </outputs>
112 112
113 <tests> 113 <tests>
114 <test> 114 <test>
115 <!-- <repeat name="datasets"> --> 115 <!-- <repeat name="datasets"> -->
116 <param name="datasets_0|sample" value="chimerascan.txt" ftype="tabular" /> 116 <param name="datasets_0|sample" value="edgren_chimerascan.txt" ftype="tabular" />
117 <param name="datasets_0|format" value="chimerascan" /> 117 <param name="datasets_0|format" value="chimerascan" />
118 <param name="datasets_0|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" /> 118 <param name="datasets_0|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
119 <!-- </repeat> --> 119 <!-- </repeat> -->
120 <!-- <repeat name="datasets"> --> 120 <!-- <repeat name="datasets"> -->
121 <param name="datasets_1|sample" value="defuse.txt" ftype="tabular" /> 121 <param name="datasets_1|sample" value="edgren_defuse.txt" ftype="tabular" />
122 <param name="datasets_1|format" value="defuse" /> 122 <param name="datasets_1|format" value="defuse" />
123 <param name="datasets_1|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" /> 123 <param name="datasets_1|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
124 <!-- </repeat> --> 124 <!-- </repeat> -->
125 <!-- <repeat name="datasets"> --> 125 <!-- <repeat name="datasets"> -->
126 <param name="datasets_2|sample" value="fusion-map.txt" ftype="tabular" /> 126 <param name="datasets_2|sample" value="edgren_fusion-map.txt" ftype="tabular" />
127 <param name="datasets_2|format" value="fusionmap" /> 127 <param name="datasets_2|format" value="fusionmap" />
128 <param name="datasets_2|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" /> 128 <param name="datasets_2|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
129 <!-- </repeat> --> 129 <!-- </repeat> -->
130 <!-- <repeat name="datasets"> --> 130 <!-- <repeat name="datasets"> -->
131 <param name="datasets_3|sample" value="edgren_tp.txt" ftype="tabular" /> 131 <param name="datasets_3|sample" value="edgren_true_positives.txt" ftype="tabular" />
132 <param name="datasets_3|format" value="fusionmap" /> 132 <param name="datasets_3|format" value="fusionmap" />
133 <param name="datasets_3|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" /> 133 <param name="datasets_3|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
134 <!-- </repeat> --> 134 <!-- </repeat> -->
135 135
136 <param name="settingsType" value="full" /> 136 <param name="settingsType" value="full" />
138 <param name="matching_method" value="subset" /> 138 <param name="matching_method" value="subset" />
139 <param name="strand_specific_matching" value="--strand-specific-matching" /> 139 <param name="strand_specific_matching" value="--strand-specific-matching" />
140 <param name="acceptor_donor_order_specific_matchig" value="--acceptor-donor-order-specific-matching" /> 140 <param name="acceptor_donor_order_specific_matchig" value="--acceptor-donor-order-specific-matching" />
141 <param name="output_format" value="list_boolean" /> 141 <param name="output_format" value="list_boolean" />
142 142
143 <output name="fuma_overview" file="output_test_1.txt" /> 143 <output name="fuma_overview" file="edgren_test_01_specifc_matching_output.txt" />
144 </test> 144 </test>
145 <test> 145 <test>
146 <!-- <repeat name="datasets"> --> 146 <!-- <repeat name="datasets"> -->
147 <param name="datasets_0|sample" value="chimerascan.txt" ftype="tabular" /> 147 <param name="datasets_0|sample" value="edgren_chimerascan.txt" ftype="tabular" />
148 <param name="datasets_0|format" value="chimerascan" /> 148 <param name="datasets_0|format" value="chimerascan" />
149 <param name="datasets_0|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" /> 149 <param name="datasets_0|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
150 <!-- </repeat> --> 150 <!-- </repeat> -->
151 <!-- <repeat name="datasets"> --> 151 <!-- <repeat name="datasets"> -->
152 <param name="datasets_1|sample" value="defuse.txt" ftype="tabular" /> 152 <param name="datasets_1|sample" value="edgren_defuse.txt" ftype="tabular" />
153 <param name="datasets_1|format" value="defuse" /> 153 <param name="datasets_1|format" value="defuse" />
154 <param name="datasets_1|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" /> 154 <param name="datasets_1|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
155 <!-- </repeat> --> 155 <!-- </repeat> -->
156 <!-- <repeat name="datasets"> --> 156 <!-- <repeat name="datasets"> -->
157 <param name="datasets_2|sample" value="fusion-map.txt" ftype="tabular" /> 157 <param name="datasets_2|sample" value="edgren_fusion-map.txt" ftype="tabular" />
158 <param name="datasets_2|format" value="fusionmap" /> 158 <param name="datasets_2|format" value="fusionmap" />
159 <param name="datasets_2|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" /> 159 <param name="datasets_2|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
160 <!-- </repeat> --> 160 <!-- </repeat> -->
161 <!-- <repeat name="datasets"> --> 161 <!-- <repeat name="datasets"> -->
162 <param name="datasets_3|sample" value="edgren_tp.txt" ftype="tabular" /> 162 <param name="datasets_3|sample" value="edgren_true_positives.txt" ftype="tabular" />
163 <param name="datasets_3|format" value="fusionmap" /> 163 <param name="datasets_3|format" value="fusionmap" />
164 <param name="datasets_3|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" /> 164 <param name="datasets_3|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />
165 <!-- </repeat> --> 165 <!-- </repeat> -->
166 166
167 <param name="settingsType" value="full" /> 167 <param name="settingsType" value="full" />
169 <param name="matching_method" value="subset" /> 169 <param name="matching_method" value="subset" />
170 <param name="strand_specific_matching" value="" /> 170 <param name="strand_specific_matching" value="" />
171 <param name="acceptor_donor_order_specific_matchig" value="" /> 171 <param name="acceptor_donor_order_specific_matchig" value="" />
172 <param name="output_format" value="list_boolean" /> 172 <param name="output_format" value="list_boolean" />
173 173
174 <output name="fuma_overview" file="output_test_2.txt" /> 174 <output name="fuma_overview" file="edgren_test_02_unspecifc_matching_output.txt" />
175 </test> 175 </test>
176 </tests> 176 </tests>
177 177
178 <help><![CDATA[ 178 <help><![CDATA[
179 ============ 179 ============