Mercurial > repos > bgruening > repeat_masker
comparison repeatmasker.xml @ 13:3f987772e283 draft
"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 |
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| 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}"> |