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changeset 3:13bcc2f459b0 draft

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planemo upload commit 801bf168032a13f6405518bddb35a24c9e9a8cd4-dirty
author nick
date Mon, 23 Nov 2015 18:07:11 -0500
parents 71ace43428ca
children af383638de66
files align_families.xml duplex.xml make_families.xml
diffstat 3 files changed, 11 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/align_families.xml	Mon Nov 23 17:57:34 2015 -0500
+++ b/align_families.xml	Mon Nov 23 18:07:11 2015 -0500
@@ -1,6 +1,10 @@
 <?xml version="1.0"?>
 <tool id="align_families" name="Align families" version="0.1">
   <description>from duplex sequencing data</description>
+  <requirements>
+    <requirement type="package" version="7.221">mafft</requirement>
+    <requirement type="package" version="0.1">duplex</requirement>
+  </requirements>
   <command interpreter="python" detect_errors="exit_code">align_families.py $input &gt; $output
   </command>
   <inputs>
@@ -9,10 +13,6 @@
   <outputs>
     <data name="output" format="tabular"/>
   </outputs>
-  <requirements>
-    <requirement type="package" version="7.221">mafft</requirement>
-    <requirement type="package" version="0.1">duplex</requirement>
-  </requirements>
   <tests>
     <test>
       <param name="input" value="smoke.families.tsv"/>
--- a/duplex.xml	Mon Nov 23 17:57:34 2015 -0500
+++ b/duplex.xml	Mon Nov 23 18:07:11 2015 -0500
@@ -1,6 +1,9 @@
 <?xml version="1.0"?>
 <tool id="duplex" name="Make consensus reads" version="0.1">
   <description>from duplex sequencing data</description>
+  <requirements>
+    <requirement type="package" version="0.1">duplex</requirement>
+  </requirements>
   <command interpreter="python" detect_errors="exit_code"><![CDATA[
     duplex.py -r $min_reads -q $qual_thres -F $qual_format $input
     #if $keep_sscs:
--- a/make_families.xml	Mon Nov 23 17:57:34 2015 -0500
+++ b/make_families.xml	Mon Nov 23 18:07:11 2015 -0500
@@ -1,6 +1,10 @@
 <?xml version="1.0"?>
 <tool id="make_families" name="Make families" version="0.1">
   <description>from duplex sequencing data</description>
+  <requirements>
+    <requirement type="package" version="0.1">duplex</requirement>
+    <!-- <requirement type="set_environment">DUPLEX_DIR</requirement> -->
+  </requirements>
   <command>paste $fastq1 $fastq2
     | paste - - - -
     | awk -f \$DUPLEX_DIR/make-barcodes.awk -v TAG_LEN=$taglen -v INVARIANT=$invariant