Mercurial > repos > lparsons > htseq_count

diff htseq-count.xml @ 28:916cb26bd9d3 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 9b894593cf3c0156faf679300ded731e0796f792"
author iuc
date Sun, 26 Jan 2020 23:43:52 -0500
parents 67b0b160903a
children 4418229c501e
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line diff
--- a/htseq-count.xml	Thu Oct 17 03:01:55 2019 -0400
+++ b/htseq-count.xml	Sun Jan 26 23:43:52 2020 -0500
@@ -1,4 +1,4 @@
-<tool id="htseq_count" name="htseq-count" version="0.9.1" profile="16.04">
+<tool id="htseq_count" name="htseq-count" version="0.9.1+galaxy1" profile="16.04">
     <description> - Count aligned reads in a BAM file that overlap features in a GFF file</description>
     <requirements>
         <requirement type="package" version="0.9.1">htseq</requirement>
@@ -49,7 +49,7 @@
         --secondary-alignments=${advanced_options.secondary_alignments}
         --supplementary-alignments=${advanced_options.supplementary_alignments}
         #if $advanced_options.samout_conditional.samout == "Yes":
-            --samout='$__new_file_path__/${samoutfile.id}_tmp.sam'
+            --samout=samout.sam
         #end if
     #end if
 
@@ -65,7 +65,7 @@
         #if $advanced_options.samout_conditional.samout == "Yes":
             && samtools view -Su
                 -t '${reference_fasta_filename}.fai'
-                '$__new_file_path__/${samoutfile.id}_tmp.sam'
+                samout.sam
             | samtools sort -T "\${TMPDIR:-.}" -o '$samoutfile' -
         #end if
     #end if