diff repeatmasker.xml @ 7:d7540a923c7b draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 133126ca40437cebd8ead4ec14400dcc22b5ce21"

--- a/repeatmasker.xml	Tue Dec 18 14:05:17 2018 -0500
+++ b/repeatmasker.xml	Sun Dec 01 09:31:09 2019 -0500
@@ -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>