Mercurial > repos > bgruening > repeat_masker

comparison repeatmasker.xml @ 8:ade773848c3d draft

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"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
comparison
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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