Mercurial > repos > jpetteng > ectyper0_1

changeset 17:80b1401a70ef draft

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Uploaded
author jpetteng
date Wed, 10 Jan 2018 13:22:00 -0500
parents a3b849d09c81
children b4fe4085b240
files ectyper.xml
diffstat 1 files changed, 4 insertions(+), 12 deletions(-) [+]
line wrap: on
line diff
--- a/ectyper.xml	Wed Jan 10 13:16:55 2018 -0500
+++ b/ectyper.xml	Wed Jan 10 13:22:00 2018 -0500
@@ -3,24 +3,16 @@
       <requirement type="package" version="0.1">ectyper</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-      #if $jobtype.select == "asm"
-        ln -s $jobtype.draft sample.fasta;  
-      #else if $jobtype.select == "se"
-        ln -s $jobtype.fastq1 sample_1.fastq;  
-      #else if $jobtype.select == "pe"
-        ln -s $jobtype.fastq1 sample_1.fastq;  
-        ln -s $jobtype.fastq2 sample_2.fastq;  
-      #end if
 
 	  $__tool_directory__/ectyper 
       #if $jobtype.select == "asm"
-        -i sample.fasta
+        -i $draft
       #else if $jobtype.select == "se"
-        -i sample_1.fastq
+        -i $fastq1
       #else if $jobtype.select == "pe"
-        -i sample_1.fastq sample_2.fastq
+        -i $fastq1 $fastq2
       #end if
-      -d  $percent_identity
+      -d $percent_identity
 	  -l $percent_length
   	  -o "./"; cat ./output/output.csv > results.csv;