Mercurial > repos > pjbriggs > amplicon_analysis_pipeline

diff amplicon_analysis_pipeline.xml @ 23:545f23776953 draft

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planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 993dae6791b28d776b116153e834192435084ef5
author pjbriggs
date Wed, 29 Aug 2018 10:57:51 -0400
parents 52052235644b
children fe354f5dd0ee
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--- a/amplicon_analysis_pipeline.xml	Wed Jul 04 06:56:48 2018 -0400
+++ b/amplicon_analysis_pipeline.xml	Wed Aug 29 10:57:51 2018 -0400
@@ -1,8 +1,12 @@
 <tool id="amplicon_analysis_pipeline" name="Amplicon Analysis Pipeline" version="1.2.2.1">
   <description>analyse 16S rRNA data from Illumina Miseq paired-end reads</description>
   <requirements>
-    <!-- amplicon_analysis_pipeline not available in bioconda -->
+    <!-- non-bioconda dependencies -->
     <requirement type="package" version="1.2.2">amplicon_analysis_pipeline</requirement>
+    <requirement type="package" version="2010-04-29">microbiomeutil-chimeraslayer</requirement>
+    <requirement type="package" version="1.2.22">uclust-qiime</requirement>
+    <requirement type="package">fasta_number</requirement>
+    <!-- bioconda dependencies -->
     <requirement type="package" version="2.7">python</requirement>
     <requirement type="package" version="1.11">cutadapt</requirement>
     <requirement type="package" version="1.33">sickle-trim</requirement>
@@ -14,13 +18,8 @@
     <requirement type="package" version="2.2.26">blast-legacy</requirement>
     <requirement type="package" version="0.2.4">fasta-splitter</requirement>
     <requirement type="package" version="2.2">rdp_classifier</requirement>
+    <requirement type="package" version="1.1.3">vsearch</requirement>
     <requirement type="package" version="3.2.1">R</requirement>
-    <requirement type="package" version="1.1.3">vsearch</requirement>
-    <requirement type="package" version="1.2.22">uclust-qiime</requirement>
-    <!-- microbiomeutil not available in bioconda -->
-    <requirement type="package" version="2010-04-29">microbiomeutil</requirement>
-    <!-- fastq_number not available in bioconda -->
-    <requirement type="package">fasta_number</requirement>
   </requirements>
   <stdio>
     <exit_code range="1:" />