Mercurial > repos > bgruening > repeat_masker

comparison repeatmasker.xml @ 13:3f987772e283 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker commit 66afa14fe355603b05936eb4575d4b65a9861838"
author iuc
date Thu, 21 Oct 2021 15:49:31 +0000
parents 39b40a9a6296
children
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12:39b40a9a6296 13:3f987772e283
1 <tool id="repeatmasker_wrapper" name="RepeatMasker" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@" profile="20.01"> 1 <tool id="repeatmasker_wrapper" name="RepeatMasker" version="@TOOL_VERSION@+@VERSION_SUFFIX@" profile="20.01">
2 <description>screen DNA sequences for interspersed repeats and low complexity regions</description> 2 <description>screen DNA sequences for interspersed repeats and low complexity regions</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro='xrefs'/> 6 <expand macro='xrefs'/>
56 ${advanced.gccalc} 56 ${advanced.gccalc}
57 ${advanced.nocut} 57 ${advanced.nocut}
58 ${advanced.keep_alignments} 58 ${advanced.keep_alignments}
59 ${advanced.invert_alignments} 59 ${advanced.invert_alignments}
60 ${advanced.xout} 60 ${advanced.xout}
61 ${advanced.xsmall} 61 ${xsmall}
62 ${advanced.poly} 62 ${advanced.poly}
63 rm_input.fasta && 63 rm_input.fasta &&
64 #if $advanced.is_only != '-is_only': 64 #if $advanced.is_only != '-is_only':
65 mv rm_input.fasta.masked '${output_masked_genome}' && 65 mv rm_input.fasta.masked '${output_masked_genome}' &&
66 sed -E 's/^ *// ; s/ *$//; 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 >'${output_log}' && 66 sed -E 's/^ *// ; s/ *$//; 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}' &&
122 <param name="cutoff" type="integer" argument="-cutoff" value="225" label="Cutoff score for masking repeats" /> 122 <param name="cutoff" type="integer" argument="-cutoff" value="225" label="Cutoff score for masking repeats" />
123 </when> 123 </when>
124 </conditional> 124 </conditional>
125 <param type="boolean" argument="-gff" truevalue="-gff" falsevalue="" label="Output annotation of repeats in GFF format" checked="false" /> 125 <param type="boolean" argument="-gff" truevalue="-gff" falsevalue="" label="Output annotation of repeats in GFF format" checked="false" />
126 <param argument="-excln" type="boolean" truevalue="-excln" falsevalue="" label="Ignore stretches of Ns when computing statistics" checked="true" help="Scaffolds are sometimes joined with stretches of 25 or more Ns. This option ignores them when calculating repeat statistics" /> 126 <param argument="-excln" type="boolean" truevalue="-excln" falsevalue="" label="Ignore stretches of Ns when computing statistics" checked="true" help="Scaffolds are sometimes joined with stretches of 25 or more Ns. This option ignores them when calculating repeat statistics" />
127 <param type="boolean" argument="-xsmall" truevalue="-xsmall" falsevalue="" checked="false" label="Perform softmasking instead of hardmasking" help="Output repetitive regions as lowercase, non-repetitive regions as uppercase (instead of replacing repetitive regions with 'N's)" />
127 <section name="advanced" title="Advanced options" expanded="false"> 128 <section name="advanced" title="Advanced options" expanded="false">
128 <param argument="-is_only" type="boolean" truevalue="-is_only" falsevalue="" checked="false" label="Only clip E coli insertion elements" /> 129 <param argument="-is_only" type="boolean" truevalue="-is_only" falsevalue="" checked="false" label="Only clip E coli insertion elements" />
129 <param argument="-is_clip" type="boolean" truevalue="-is_clip" falsevalue="" checked="false" label="Clip IS elements before analysis" help="Normally RepeatMasker will report on IS element, with this option selected it will clip them before analysis" /> 130 <param argument="-is_clip" type="boolean" truevalue="-is_clip" falsevalue="" checked="false" label="Clip IS elements before analysis" help="Normally RepeatMasker will report on IS element, with this option selected it will clip them before analysis" />
130 <param argument="-no_is" type="boolean" truevalue="-no_is" falsevalue="" checked="false" label="Skip bacterial insertion element check" /> 131 <param argument="-no_is" type="boolean" truevalue="-no_is" falsevalue="" checked="false" label="Skip bacterial insertion element check" />
131 <param argument="-rodspec" type="boolean" truevalue="-rodspec" falsevalue="" checked="false" label="Only check for rodent specific repeats" help="If this option is select a check for rodent specific repeats is done instead of a full RepeatMasker run" /> 132 <param argument="-rodspec" type="boolean" truevalue="-rodspec" falsevalue="" checked="false" label="Only check for rodent specific repeats" help="If this option is select a check for rodent specific repeats is done instead of a full RepeatMasker run" />
148 <param type="boolean" argument="-gccalc" truevalue="-gcccalc" falsevalue="" checked="false" label="Calculate GC % for all sequences" help="By default RepeatMasker skips calculating GC % for small sequences" /> 149 <param type="boolean" argument="-gccalc" truevalue="-gcccalc" falsevalue="" checked="false" label="Calculate GC % for all sequences" help="By default RepeatMasker skips calculating GC % for small sequences" />
149 <param type="boolean" argument="-nocut" truevalue="-nocut" falsevalue="" checked="false" label="Skips cutting of repeats" /> 150 <param type="boolean" argument="-nocut" truevalue="-nocut" falsevalue="" checked="false" label="Skips cutting of repeats" />
150 <param name="xout" type="boolean" argument="-x" truevalue="-x" falsevalue="" checked="false" label="Mask with X instead of N characters" /> 151 <param name="xout" type="boolean" argument="-x" truevalue="-x" falsevalue="" checked="false" label="Mask with X instead of N characters" />
151 <param name="keep_alignments" type="boolean" argument="-ali" truevalue="-ali" falsevalue="" checked="false" label="Output alignments file" /> 152 <param name="keep_alignments" type="boolean" argument="-ali" truevalue="-ali" falsevalue="" checked="false" label="Output alignments file" />
152 <param name="invert_alignments" type="boolean" argument="-inv" truevalue="-inv" falsevalue="" checked="false" label="Invert alignments in alignment file" help="Show alignments in the orientation of the repeat sequence, not the query sequence" /> 153 <param name="invert_alignments" type="boolean" argument="-inv" truevalue="-inv" falsevalue="" checked="false" label="Invert alignments in alignment file" help="Show alignments in the orientation of the repeat sequence, not the query sequence" />
153 <param type="boolean" argument="-xsmall" truevalue="-xsmall" falsevalue="" checked="false" label="Output repetitive regions as lowercase, non-repetitive regions as uppercase" />
154 <param type="boolean" argument="-poly" truevalue="-poly" falsevalue="" checked="false" label="Output list of potentially polymorphic microsatellites" /> 154 <param type="boolean" argument="-poly" truevalue="-poly" falsevalue="" checked="false" label="Output list of potentially polymorphic microsatellites" />
155 </section> 155 </section>
156 </inputs> 156 </inputs>
157 <outputs> 157 <outputs>
158 <data name="output_masked_genome" format="fasta" label="RepeatMasker masked sequence on ${on_string}"> 158 <data name="output_masked_genome" format="fasta" label="RepeatMasker masked sequence on ${on_string}">