Mercurial > repos > yhoogstrate > fuma
comparison fuma.xml @ 3:4966079d474b draft
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 ============ |