Mercurial > repos > estrain > seqsero2_v1_0_1

changeset 35:b99f3a65254d

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Uploaded
author estrain
date Sat, 07 Sep 2019 15:27:43 -0400
parents 4fcd9834e66b
children 2fb62709dc5e
files seqsero2.xml
diffstat 1 files changed, 8 insertions(+), 9 deletions(-) [+]
line wrap: on
line diff
--- a/seqsero2.xml	Sat Sep 07 14:52:22 2019 -0400
+++ b/seqsero2.xml	Sat Sep 07 15:27:43 2019 -0400
@@ -1,14 +1,13 @@
 <tool id="seqsero2_v1_0_1" name="SeqSero 2" version="1.0.1">
     <description>Salmonella serotype prediction</description>
     <requirements>
-      <requirement type="package" version="3.6">python</requirement>
-      <requirement type="package" version="1.74">biopython</requirement>
-      <requirement type="package" version="2.7.1">blast</requirement>
-      <requirement type="package" version="1.9">samtools</requirement>
-      <requirement type="package" version="2.9.1">sra-tools</requirement>
-      <requirement type="package" version="0.7.17">bwa</requirement>
-      <requirement type="package" version="3.13.1">spades</requirement>
-      <requirement type="package" version="2.27.1">bedtools</requirement>
+      <requirement type="package">biopython</requirement>
+      <requirement type="package">blast</requirement>
+      <requirement type="package">samtools</requirement>
+      <requirement type="package">sra-tools</requirement>
+      <requirement type="package">bwa</requirement>
+      <requirement type="package">spades</requirement>
+      <requirement type="package">bedtools</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
       echo "SeqSero 2 v. 1.0.1" ;
@@ -36,7 +35,7 @@
       ln -s $forward ${name}_1.fastq;
       ln -s $reverse ${name}_2.fastq;
       touch output/SeqSero_log.txt ;
-      python $__tool_directory__/SeqSero2_package.py
+      python3 $__tool_directory__/SeqSero2_package.py
         -p \${GALAXY_SLOTS:-4}
         -t 2
         -m $mode