Mercurial > repos > nick > sequence_content_trimmer

changeset 3:d8b86dc67f84 draft default tip

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"planemo upload commit 8e52aac4afce4ab7c4d244e2b70f205f70c16749-dirty"
author nick
date Fri, 27 May 2022 23:27:43 +0000
parents a8fd651dcbd9
children
files trimmer.xml
diffstat 1 files changed, 7 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/trimmer.xml	Fri May 27 22:46:30 2022 +0000
+++ b/trimmer.xml	Fri May 27 23:27:43 2022 +0000
@@ -1,28 +1,28 @@
 <?xml version="1.0"?>
-<tool id="sequence_content_trimmer" version="0.2.2" name="Sequence Content Trimmer">
+<tool id="sequence_content_trimmer" version="0.2.3" name="Sequence Content Trimmer">
   <description>trim reads based on certain bases</description>
   <command detect_errors="exit_code"><![CDATA[
   #if $paired.is_paired and (('fasta' in $input1.extension and 'fastq' in $input2.extension) or \
       ('fastq' in $input1.extension and 'fasta' in $input2.extension))
     echo 'Both input files must be either fastq or fasta (no mixing the two).' >&2
   #else
-    trimmer.py $input1
+    python '$__tool_directory__/trimmer.py' '$input1'
     #if $paired.is_paired:
-      $input2 $output1 $output2
+      '$input2' '$output1' '$output2'
     #end if
     #if $input1.extension in ('fastq', 'fastqsanger', 'fastqillumina', 'fastqsolexa')
       -f fastq
     #elif $input1.extension == 'fasta'
       -f fasta
     #else
-      -f $input1.extension
+      -f '$input1.extension'
     #end if
-    -b '$bases' -t $thres -w $win_len $invert
+    -b '$bases' -t '$thres' -w '$win_len' $invert
     #if $min_len.has_min_len:
-      -m $min_len.value
+      -m '$min_len.value'
     #end if
     #if not $paired.is_paired:
-      > $output1
+      > '$output1'
     #end if
   #end if
   ]]>