Mercurial > repos > lparsons > htseq_count

comparison htseq-count.xml @ 26:7f5a8d427b39 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 3e7db651397e9a42de15c5d6f60cec780f4b32df
author iuc
date Sun, 29 Apr 2018 09:53:13 -0400
parents f1368427a79c
children 67b0b160903a
comparison
equal deleted inserted replaced
25:f1368427a79c 26:7f5a8d427b39
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" />