Mercurial > repos > richard-burhans > segalign
comparison segalign.xml @ 6:6c95c380bfa7 draft
planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign commit a4be517dbe8277bed184b915721964820d7a3af0
| author | richard-burhans |
|---|---|
| date | Mon, 06 May 2024 17:44:50 +0000 |
| parents | 75e15ba3b4c1 |
| children | 150de8a3954a |
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| 5:75e15ba3b4c1 | 6:6c95c380bfa7 |
|---|---|
| 172 <param name="mode_selector" type="select" label="Choose the mode"> | 172 <param name="mode_selector" type="select" label="Choose the mode"> |
| 173 <option value="segalign" selected="true">SegAlign</option> | 173 <option value="segalign" selected="true">SegAlign</option> |
| 174 <option value="segalign_repeat_masker">SegAlign repeat masker</option> | 174 <option value="segalign_repeat_masker">SegAlign repeat masker</option> |
| 175 </param> | 175 </param> |
| 176 <when value="segalign"> | 176 <when value="segalign"> |
| 177 <param name="target" type="data" format="fasta" label="Target sequence file in FASTA format"/> | 177 <param name="target" type="data" format="fasta,fasta.gz" label="Target sequence file in FASTA format"/> |
| 178 <param name="query" type="data" format="fasta" label="Query sequence file in FASTA format"/> | 178 <param name="query" type="data" format="fasta,fasta.gz" label="Query sequence file in FASTA format"/> |
| 179 <expand macro="sequence_options"/> | 179 <expand macro="sequence_options"/> |
| 180 <expand macro="scoring_options"/> | 180 <expand macro="scoring_options"/> |
| 181 <expand macro="seeding_options"/> | 181 <expand macro="seeding_options"/> |
| 182 <expand macro="ungapped_extension_options"/> | 182 <expand macro="ungapped_extension_options"/> |
| 183 <expand macro="gapped_extension_options"/> | 183 <expand macro="gapped_extension_options"/> |
| 189 <param argument="--diagonal_partition" type="boolean" value="false" label="Enable diagonal partition optimization"/> | 189 <param argument="--diagonal_partition" type="boolean" value="false" label="Enable diagonal partition optimization"/> |
| 190 <param argument="--max_segments" type="integer" value="20000" label="Max segments"/> | 190 <param argument="--max_segments" type="integer" value="20000" label="Max segments"/> |
| 191 </section> | 191 </section> |
| 192 </when> | 192 </when> |
| 193 <when value="segalign_repeat_masker"> | 193 <when value="segalign_repeat_masker"> |
| 194 <param name="seq_file" type="data" format="fasta" label="Sequence file in FASTA format"/> | 194 <param name="seq_file" type="data" format="fasta,fasta.gz" label="Sequence file in FASTA format"/> |
| 195 <expand macro="sequence_options"> | 195 <expand macro="sequence_options"> |
| 196 <param argument="--neighbor_proportion" type="float" value="0.2" label="Proportion of neighbouring intervals to align the query interval to"/> | 196 <param argument="--neighbor_proportion" type="float" value="0.2" label="Proportion of neighbouring intervals to align the query interval to"/> |
| 197 </expand> | 197 </expand> |
| 198 <expand macro="scoring_options"/> | 198 <expand macro="scoring_options"/> |
| 199 <expand macro="seeding_options"/> | 199 <expand macro="seeding_options"/> |
| 222 </data> | 222 </data> |
| 223 </outputs> | 223 </outputs> |
| 224 <tests> | 224 <tests> |
| 225 <test expect_num_outputs="1" expect_test_failure="true"> | 225 <test expect_num_outputs="1" expect_test_failure="true"> |
| 226 <param name="mode_selector" value="segalign"/> | 226 <param name="mode_selector" value="segalign"/> |
| 227 <param name="target" value="hg38.chr20.chunk.fa.gz" ftype="fasta"/> | 227 <param name="target" value="hg38.chr20.chunk.fa.gz" ftype="fasta.gz"/> |
| 228 <param name="query" value="mm39.chr2.chunk.fa.gz" ftype="fasta"/> | 228 <param name="query" value="mm39.chr2.chunk.fa.gz" ftype="fasta.gz"/> |
| 229 <output name="segalign_output" decompress="true" file="segalign-output.maf.gz" ftype="maf"/> | 229 <output name="segalign_output" decompress="true" file="segalign-output.maf.gz" ftype="maf"/> |
| 230 </test> | 230 </test> |
| 231 <test expect_num_outputs="1" expect_test_failure="true"> | 231 <test expect_num_outputs="1" expect_test_failure="true"> |
| 232 <param name="mode_selector" value="segalign_repeat_masker"/> | 232 <param name="mode_selector" value="segalign_repeat_masker"/> |
| 233 <param name="seq_file" value="hg38.chr20.chunk.fa.gz" ftype="fasta"/> | 233 <param name="seq_file" value="hg38.chr20.chunk.fa.gz" ftype="fasta.gz"/> |
| 234 <output name="segalign_repeat_masker_output" decompress="true" file="segalign-repeat-masker-output.tab.gz" ftype="tabular"/> | 234 <output name="segalign_repeat_masker_output" decompress="true" file="segalign-repeat-masker-output.tab.gz" ftype="tabular"/> |
| 235 </test> | 235 </test> |
| 236 <test expect_num_outputs="1" expect_test_failure="true"> | 236 <test expect_num_outputs="1" expect_test_failure="true"> |
| 237 <param name="mode_selector" value="segalign"/> | 237 <param name="mode_selector" value="segalign"/> |
| 238 <param name="target" value="hg38.chr20.chunk.fa.gz" ftype="fasta"/> | 238 <param name="target" value="hg38.chr20.chunk.fa.gz" ftype="fasta.gz"/> |
| 239 <param name="query" value="mm39.chr2.chunk.fa.gz" ftype="fasta"/> | 239 <param name="query" value="mm39.chr2.chunk.fa.gz" ftype="fasta.gz"/> |
| 240 <param name="diagonal_partition" value="true"/> | 240 <param name="diagonal_partition" value="true"/> |
| 241 <output name="segalign_diagonal_partition_output" ftype="tgz"> | 241 <output name="segalign_diagonal_partition_output" ftype="tgz"> |
| 242 <assert_contents> | 242 <assert_contents> |
| 243 <has_archive_member path="galaxy/commands.json"/> | 243 <has_archive_member path="galaxy/commands.json"/> |
| 244 </assert_contents> | 244 </assert_contents> |