# HG changeset patch
# User pjbriggs
# Date 1535554671 14400
# Node ID 545f2377695398784c82beecdef88923ceaad9de
# Parent  eb7d118dd3228aecc550706fbebef6fc3eeaa3ad
planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 993dae6791b28d776b116153e834192435084ef5

diff -r eb7d118dd322 -r 545f23776953 amplicon_analysis_pipeline.xml
--- 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:" />
diff -r eb7d118dd322 -r 545f23776953 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Jul 04 06:56:48 2018 -0400
+++ b/tool_dependencies.xml	Wed Aug 29 10:57:51 2018 -0400
@@ -35,6 +35,23 @@
       </install>
   </package>
   <!--
+      microbiomeutil provides ChimeraSlayer
+  -->
+  <package name="microbiomeutil-chimeraslayer" version="2010-04-29">
+    <install version="1.0">
+      <actions>
+	<action type="download_by_url">https://sourceforge.net/projects/microbiomeutil/files/__OLD_VERSIONS/microbiomeutil_2010-04-29.tar.gz</action>
+	<action type="move_directory_files">
+	  <source_directory>ChimeraSlayer</source_directory>
+	  <destination_directory>$INSTALL_DIR/ChimeraSlayer</destination_directory>
+	</action>
+	<action type="set_environment">
+	    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/ChimeraSlayer</environment_variable>
+	</action>
+      </actions>
+    </install>
+  </package>
+  <!--
       uclust required for QIIME/pyNAST
       License only allows this version to be used with those two packages
       See: