Mercurial > repos > lparsons > htseq_count
comparison htseq-count.xml @ 27:4dd515072667 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 3e7db651397e9a42de15c5d6f60cec780f4b32df
| author | iuc |
|---|---|
| date | Sun, 29 Apr 2018 09:52:57 -0400 |
| parents | d8c5761a8ba7 |
| children | bc4ada69b61f |
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| 26:d8c5761a8ba7 | 27:4dd515072667 |
|---|---|
| 156 <actions> | 156 <actions> |
| 157 <action name="column_names" type="metadata" default="Category,${samfile.element_identifier}" /> | 157 <action name="column_names" type="metadata" default="Category,${samfile.element_identifier}" /> |
| 158 </actions> | 158 </actions> |
| 159 </data> | 159 </data> |
| 160 <data format="bam" name="samoutfile" metadata_source="samfile" label="${tool.name} on ${on_string} (BAM)"> | 160 <data format="bam" name="samoutfile" metadata_source="samfile" label="${tool.name} on ${on_string} (BAM)"> |
| 161 <filter>samout_conditional['samout'] == "Yes"</filter> | 161 <filter>advanced_options['advanced_options_selector'] == 'advanced' and advanced_options['samout_conditional']['samout'] == "Yes"</filter> |
| 162 </data> | 162 </data> |
| 163 </outputs> | 163 </outputs> |
| 164 | 164 |
| 165 <tests> | 165 <tests> |
| 166 <test> | 166 <test expect_num_outputs="2"> |
| 167 <param name="samfile" value="htseq-test.sam" /> | 167 <param name="samfile" value="htseq-test.sam" /> |
| 168 <param name="gfffile" value="htseq-test.gff" /> | 168 <param name="gfffile" value="htseq-test.gff" /> |
| 169 <output name="counts" file="htseq-test_counts.tsv" /> | 169 <output name="counts" file="htseq-test_counts.tsv" /> |
| 170 <output name="othercounts" file="htseq-test_othercounts.tsv" /> | 170 <output name="othercounts" file="htseq-test_othercounts.tsv" /> |
| 171 </test> | 171 </test> |
| 172 <test> | 172 <test expect_num_outputs="2"> |
| 173 <param name="samfile" value="htseq-test.sam" /> | 173 <param name="samfile" value="htseq-test.sam" /> |
| 174 <param name="gfffile" value="htseq-test.gff" /> | 174 <param name="gfffile" value="htseq-test.gff" /> |
| 175 <output name="counts" file="htseq-test_counts.tsv" /> | 175 <output name="counts" file="htseq-test_counts.tsv" /> |
| 176 <output name="othercounts" file="htseq-test_othercounts.tsv" /> | 176 <output name="othercounts" file="htseq-test_othercounts.tsv" /> |
| 177 </test> | 177 </test> |
| 178 <test> | 178 <test expect_num_outputs="2"> |
| 179 <param name="samfile" value="htseq-test.bam" /> | 179 <param name="samfile" value="htseq-test.bam" /> |
| 180 <param name="gfffile" value="htseq-test.gff" /> | 180 <param name="gfffile" value="htseq-test.gff" /> |
| 181 <output name="counts" file="htseq-test_counts.tsv" /> | 181 <output name="counts" file="htseq-test_counts.tsv" /> |
| 182 <output name="othercounts" file="htseq-test_othercounts.tsv" /> | 182 <output name="othercounts" file="htseq-test_othercounts.tsv" /> |
| 183 </test> | 183 </test> |
| 184 <test> | 184 <test expect_num_outputs="2"> |
| 185 <param name="samfile" value="htseq-test-paired.bam" /> | 185 <param name="samfile" value="htseq-test-paired.bam" /> |
| 186 <param name="gfffile" value="htseq-test.gff" /> | 186 <param name="gfffile" value="htseq-test.gff" /> |
| 187 <output name="counts" file="htseq-test-paired_counts.tsv" /> | 187 <output name="counts" file="htseq-test-paired_counts.tsv" /> |
| 188 <output name="othercounts" file="htseq-test-paired_othercounts.tsv" /> | 188 <output name="othercounts" file="htseq-test-paired_othercounts.tsv" /> |
| 189 </test> | 189 </test> |
| 190 <test> | 190 <test expect_num_outputs="2"> |
| 191 <param name="samfile" value="htseq-test-paired.bam" /> | 191 <param name="samfile" value="htseq-test-paired.bam" /> |
| 192 <param name="gfffile" value="htseq-test.gff" /> | 192 <param name="gfffile" value="htseq-test.gff" /> |
| 193 <param name="samout" value="No" /> | 193 <param name="samout" value="No" /> |
| 194 <output name="counts" file="htseq-test-paired_counts.tsv" /> | 194 <output name="counts" file="htseq-test-paired_counts.tsv" /> |
| 195 <output name="othercounts" file="htseq-test-paired_othercounts.tsv" /> | 195 <output name="othercounts" file="htseq-test-paired_othercounts.tsv" /> |
| 196 </test> | 196 </test> |
| 197 <test> | 197 <test expect_num_outputs="3"> |
| 198 <param name="samfile" value="htseq-test.sam" /> | 198 <param name="samfile" value="htseq-test.sam" /> |
| 199 <param name="gfffile" value="htseq-test.gff" /> | 199 <param name="gfffile" value="htseq-test.gff" /> |
| 200 <param name="advanced_options_selector" value="advanced" /> | 200 <param name="advanced_options_selector" value="advanced" /> |
| 201 <param name="samout" value="Yes" /> | 201 <param name="samout" value="Yes" /> |
| 202 <param name="reference_source_selector" value="history" /> | 202 <param name="reference_source_selector" value="history" /> |
| 203 <param name="ref_file" value="htseq-test_reference.fasta" /> | 203 <param name="ref_file" value="htseq-test_reference.fasta" /> |
| 204 <output name="counts" file="htseq-test_counts.tsv" /> | 204 <output name="counts" file="htseq-test_counts.tsv" /> |
| 205 <output name="othercounts" file="htseq-test_othercounts.tsv" /> | 205 <output name="othercounts" file="htseq-test_othercounts.tsv" /> |
| 206 <output name="samoutfile" file="htseq-test_samout.bam" /> | 206 <output name="samoutfile" file="htseq-test_samout.bam" /> |
| 207 </test> | 207 </test> |
| 208 <test> | 208 <test expect_num_outputs="2"> |
| 209 <param name="samfile" value="htseq-test.sam" /> | 209 <param name="samfile" value="htseq-test.sam" /> |
| 210 <param name="gfffile" value="htseq-test.gff" /> | 210 <param name="gfffile" value="htseq-test.gff" /> |
| 211 <param name="advanced_options_selector" value="advanced" /> | 211 <param name="advanced_options_selector" value="advanced" /> |
| 212 <param name="nonunique" value="all" /> | 212 <param name="nonunique" value="all" /> |
| 213 <param name="secondary_alignments" value="ignore" /> | 213 <param name="secondary_alignments" value="ignore" /> |