Mercurial > repos > bgruening > repeat_masker
changeset 5:19cc8c8f6f02 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 133126ca40437cebd8ead4ec14400dcc22b5ce21"
| author | iuc |
|---|---|
| date | Sun, 01 Dec 2019 14:30:49 +0000 |
| parents | 13b7842c72bc |
| children | d3c5701f265f |
| files | repeatmasker.xml |
| diffstat | 1 files changed, 4 insertions(+), 4 deletions(-) [+] |
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--- a/repeatmasker.xml Tue Dec 18 14:04:52 2018 -0500 +++ b/repeatmasker.xml Sun Dec 01 14:30:49 2019 +0000 @@ -1,5 +1,5 @@ <tool id="repeatmasker_wrapper" name="RepeatMasker" version="4.0.7+galaxy2" profile="17.01"> - <description>RepeatMasker</description> + <description>screen DNA sequences for interspersed repeats and low complexity regions</description> <requirements> <requirement type="package" version="4.0.7">repeatmasker</requirement> @@ -56,7 +56,7 @@ rm_input.fasta && #if $advanced.is_only != '-is_only': mv rm_input.fasta.masked '${output_masked_genome}' && - 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}' && + 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}' && mv rm_input.fasta.tbl '${output_table}' && #if $gff == '-gff': mv rm_input.fasta.out.gff '${output_gff}' && @@ -65,7 +65,7 @@ mv rm_input.fasta.align '${output_alignment}' && #end if #if $advanced.poly == '-poly': - sed -r 's/^ *// ; s/ *$//; s/\+ //; s/ +/\t/g' rm_input.fasta.polyout >'${output_polymorphic}' && + sed -E 's/^ *// ; s/ *$//; s/\+ //; s/ +/\t/g' rm_input.fasta.polyout >'${output_polymorphic}' && #end if #end if if [ -f 'rm_input.fasta.cat.gz' ]; then @@ -191,7 +191,7 @@ <param name="source_type" value="library" /> <param name="repeat_lib" value="repeats.fasta" ftype="fasta" /> <output name="output_masked_genome" file="small.fasta.masked" /> - <output name="output_table" file="small.fasta.stats" lines_diff="4" /> + <output name="output_table" file="small.fasta.stats" lines_diff="6" /> <output name="output_repeat_catalog" file="small.fasta.cat" lines_diff="2" /> <output name="output_log" file="small.fasta.log" /> </test>