Mercurial > repos > jpetteng > ectyper

changeset 4:e07f3859a242 draft

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Updated xml file to require ectyper itself as it should be available via conda.
author jpetteng
date Fri, 05 Jan 2018 10:59:51 -0500
parents 19b25805275f
children a202cc394af8
files ecoli_serotyping/ectyper.xml
diffstat 1 files changed, 2 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/ecoli_serotyping/ectyper.xml	Fri Jan 05 10:58:47 2018 -0500
+++ b/ecoli_serotyping/ectyper.xml	Fri Jan 05 10:59:51 2018 -0500
@@ -1,6 +1,7 @@
 <tool id="ectyper" name="ectyper" version="2.0">
     <requirements>
       <requirement type="package" version="3.6.3">python</requirement>
+      <requirement type="package">ectyper</requirement>
       <requirement type="package">biopython</requirement>
       <requirement type="package">blast</requirement>
       <requirement type="package">samtools</requirement>
@@ -32,7 +33,7 @@
         -i sample_1.fastq sample_2.fastq
       #end if
       -b $maptype.select;
-      cat  SeqSero_result*/Seqsero_result.txt > results.txt; 
+      cat  ectyper_result*/ectyper_result.txt > results.txt; 
 
     ]]></command>
     <inputs>