# HG changeset patch
# User genouest
# Date 1639404763 0
# Node ID c57d7d83f3f8aeb604fddfa7eceba2092e78f8a2
# Parent  c42da0e5a671ebeebfaaa2e37c52f0f5b59e12c2
"planemo upload commit bbcbc29ef60120ea945879874ca92fb098dda8bf"

diff -r c42da0e5a671 -r c57d7d83f3f8 pep_match.xml
--- a/pep_match.xml	Fri Dec 10 10:35:58 2021 +0000
+++ b/pep_match.xml	Mon Dec 13 14:12:43 2021 +0000
@@ -4,9 +4,11 @@
         <container type="docker">dockerprotim/peptimapper</container>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-LXRunPepMatch -D $D -t $t -T $T -d $d '$fastafile' '$tagsfile' &&
-mv '${tagsfile}'.\$(basename '${fastafile}').trans.${D}.hit ${hitsfile} &&
-mv '${tagsfile}'.\$(basename '${fastafile}').trans.${D}.hit.${t}.${T}.${d}.clust '${clustersfile}'
+ln -s '$fastafile' 'in.fa' &&
+ln -s '$tagsfile' 'in.tags' &&
+LXRunPepMatch -D $D -t $t -T $T -d $d 'in.fa' 'in.tags' &&
+mv 'in.tags.in.fa.trans.${D}.hit' ${hitsfile} &&
+mv 'in.tags.in.fa.trans.${D}.hit.${t}.${T}.${d}.clust' '${clustersfile}'
     ]]></command>
     <inputs>
         <param name="tagsfile" type="data" format="txt" label="PSTs file (Text)" help="Peptide sequence tags file generated by PepnovoTag" />