Mercurial > repos > bgruening > repeat_masker

comparison repeatmasker.xml @ 7:d7540a923c7b draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 133126ca40437cebd8ead4ec14400dcc22b5ce21"
author iuc
date Sun, 01 Dec 2019 09:31:09 -0500
parents 65ab76d58c41
children ade773848c3d
comparison
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6:65ab76d58c41 7:d7540a923c7b
1 <tool id="repeatmasker_wrapper" name="RepeatMasker" version="4.0.7+galaxy2" profile="17.01"> 1 <tool id="repeatmasker_wrapper" name="RepeatMasker" version="4.0.7+galaxy2" profile="17.01">
2 <description>RepeatMasker</description> 2 <description>screen DNA sequences for interspersed repeats and low complexity regions</description>
3 3
4 <requirements> 4 <requirements>
5 <requirement type="package" version="4.0.7">repeatmasker</requirement> 5 <requirement type="package" version="4.0.7">repeatmasker</requirement>
6 </requirements> 6 </requirements>
7 7
54 ${advanced.xsmall} 54 ${advanced.xsmall}
55 ${advanced.poly} 55 ${advanced.poly}
56 rm_input.fasta && 56 rm_input.fasta &&
57 #if $advanced.is_only != '-is_only': 57 #if $advanced.is_only != '-is_only':
58 mv rm_input.fasta.masked '${output_masked_genome}' && 58 mv rm_input.fasta.masked '${output_masked_genome}' &&
59 sed -r 's/^ *// ; s/ *$//; s/\+ //; s/ +/\t/g ; 1,2c SW score\t% div.\t% del.\t% ins.\tquery sequence\tpos in query: begin\tend\t(left)\trepeat\tclass/family\tpos in repeat: begin\tend\t(left)\tID' rm_input.fasta.out >'${output_log}' && 59 sed -E 's/^ *// ; s/ *$//; s/\+ //; s/ +/\t/g ; 1,2c SW score\t% div.\t% del.\t% ins.\tquery sequence\tpos in query: begin\tend\t(left)\trepeat\tclass/family\tpos in repeat: begin\tend\t(left)\tID' rm_input.fasta.out >'${output_log}' &&
60 mv rm_input.fasta.tbl '${output_table}' && 60 mv rm_input.fasta.tbl '${output_table}' &&
61 #if $gff == '-gff': 61 #if $gff == '-gff':
62 mv rm_input.fasta.out.gff '${output_gff}' && 62 mv rm_input.fasta.out.gff '${output_gff}' &&
63 #end if 63 #end if
64 #if $advanced.keep_alignments == '-ali': 64 #if $advanced.keep_alignments == '-ali':
65 mv rm_input.fasta.align '${output_alignment}' && 65 mv rm_input.fasta.align '${output_alignment}' &&
66 #end if 66 #end if
67 #if $advanced.poly == '-poly': 67 #if $advanced.poly == '-poly':
68 sed -r 's/^ *// ; s/ *$//; s/\+ //; s/ +/\t/g' rm_input.fasta.polyout >'${output_polymorphic}' && 68 sed -E 's/^ *// ; s/ *$//; s/\+ //; s/ +/\t/g' rm_input.fasta.polyout >'${output_polymorphic}' &&
69 #end if 69 #end if
70 #end if 70 #end if
71 if [ -f 'rm_input.fasta.cat.gz' ]; then 71 if [ -f 'rm_input.fasta.cat.gz' ]; then
72 zcat 'rm_input.fasta.cat.gz' > '${output_repeat_catalog}'; 72 zcat 'rm_input.fasta.cat.gz' > '${output_repeat_catalog}';
73 else 73 else
189 <test expect_num_outputs="4"> 189 <test expect_num_outputs="4">
190 <param name="input_fasta" value="small.fasta" ftype="fasta" /> 190 <param name="input_fasta" value="small.fasta" ftype="fasta" />
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="4" /> 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" />
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" />