Mercurial > repos > bgruening > repeat_masker
comparison repeatmasker.xml @ 8:ade773848c3d draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit b0aaae4488b95b54eaf85010f999b2638dfadd3e"
| author | iuc |
|---|---|
| date | Thu, 23 Jan 2020 04:40:29 -0500 |
| parents | d7540a923c7b |
| children | 438f65cb1d14 |
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| 7:d7540a923c7b | 8:ade773848c3d |
|---|---|
| 191 <param name="source_type" value="library" /> | 191 <param name="source_type" value="library" /> |
| 192 <param name="repeat_lib" value="repeats.fasta" ftype="fasta" /> | 192 <param name="repeat_lib" value="repeats.fasta" ftype="fasta" /> |
| 193 <output name="output_masked_genome" file="small.fasta.masked" /> | 193 <output name="output_masked_genome" file="small.fasta.masked" /> |
| 194 <output name="output_table" file="small.fasta.stats" lines_diff="6" /> | 194 <output name="output_table" file="small.fasta.stats" lines_diff="6" /> |
| 195 <output name="output_repeat_catalog" file="small.fasta.cat" lines_diff="2" /> | 195 <output name="output_repeat_catalog" file="small.fasta.cat" lines_diff="2" /> |
| 196 <output name="output_log" file="small.fasta.log" /> | 196 <output name="output_log" file="small.fasta.log" lines_diff="2"/> |
| 197 </test> | 197 </test> |
| 198 <test expect_num_outputs="7"> | 198 <test expect_num_outputs="7"> |
| 199 <param name="input_fasta" value="small.fasta" ftype="fasta" /> | 199 <param name="input_fasta" value="small.fasta" ftype="fasta" /> |
| 200 <param name="source_type" value="library" /> | 200 <param name="source_type" value="library" /> |
| 201 <param name="gff" value="-gff" /> | 201 <param name="gff" value="-gff" /> |
| 204 <param name="poly" value="-poly" /> | 204 <param name="poly" value="-poly" /> |
| 205 <param name="repeat_lib" value="repeats.fasta" ftype="fasta" /> | 205 <param name="repeat_lib" value="repeats.fasta" ftype="fasta" /> |
| 206 <output name="output_masked_genome" file="small.fasta.masked" /> | 206 <output name="output_masked_genome" file="small.fasta.masked" /> |
| 207 <output name="output_table" file="small.fasta.stats" lines_diff="6" /> | 207 <output name="output_table" file="small.fasta.stats" lines_diff="6" /> |
| 208 <output name="output_repeat_catalog" file="small.fasta.cat" lines_diff="2" /> | 208 <output name="output_repeat_catalog" file="small.fasta.cat" lines_diff="2" /> |
| 209 <output name="output_log" file="small.fasta.log" /> | 209 <output name="output_log" file="small.fasta.log" lines_diff="2"/> |
| 210 <output name="output_alignment" file="small.fasta.align" /> | 210 <output name="output_alignment" file="small.fasta.align" /> |
| 211 <output name="output_polymorphic" file="small.fasta.poly" /> | 211 <output name="output_polymorphic" file="small.fasta.poly" /> |
| 212 <output name="output_gff" file="small.fasta.gff" lines_diff="4" /> | 212 <output name="output_gff" file="small.fasta.gff" lines_diff="4" /> |
| 213 </test> | 213 </test> |
| 214 <test expect_num_outputs="4"> | 214 <test expect_num_outputs="4"> |
| 218 <param name="repbase_file_name" value="fake.embl" /> | 218 <param name="repbase_file_name" value="fake.embl" /> |
| 219 <param name="species_list" value="anopheles" /> | 219 <param name="species_list" value="anopheles" /> |
| 220 <output name="output_masked_genome" file="small.fasta.masked" /> | 220 <output name="output_masked_genome" file="small.fasta.masked" /> |
| 221 <output name="output_table" file="small_repbase.fasta.stats" lines_diff="2" /> | 221 <output name="output_table" file="small_repbase.fasta.stats" lines_diff="2" /> |
| 222 <output name="output_repeat_catalog" file="small.fasta.cat" lines_diff="2" /> | 222 <output name="output_repeat_catalog" file="small.fasta.cat" lines_diff="2" /> |
| 223 <output name="output_log" file="small_repbase.fasta.log" /> | 223 <output name="output_log" file="small_repbase.fasta.log" lines_diff="2"/> |
| 224 </test> | 224 </test> |
| 225 </tests> | 225 </tests> |
| 226 <help><![CDATA[ | 226 <help><![CDATA[ |
| 227 RepeatMasker is a program that screens DNA for interspersed repeats and low | 227 RepeatMasker is a program that screens DNA for interspersed repeats and low |
| 228 complexity DNA sequences. The database of repeats to screen for can be | 228 complexity DNA sequences. The database of repeats to screen for can be |