# HG changeset patch
# User pjbriggs
# Date 1539614441 14400
# Node ID 3512b135ecb04291063a8d7a3a92fa4061919804
# Parent  c4cde1f435f48b3668325d51ab52426ab16064a0
planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 601f7d1e21b25c583cc6e1a563029bab3f226921-dirty

diff -r c4cde1f435f4 -r 3512b135ecb0 amplicon_analysis_pipeline.xml
--- a/amplicon_analysis_pipeline.xml	Wed Oct 10 10:57:42 2018 -0400
+++ b/amplicon_analysis_pipeline.xml	Mon Oct 15 10:40:41 2018 -0400
@@ -2,25 +2,7 @@
   <description>analyse 16S rRNA data from Illumina Miseq paired-end reads</description>
   <requirements>
     <!-- non-bioconda dependencies -->
-    <requirement type="package" version="1.2.3">amplicon_analysis_pipeline</requirement>
-    <requirement type="package" version="2010-04-29">microbiomeutil-chimeraslayer</requirement>
-    <requirement type="package" version="1.2.22">uclust-qiime</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>
-    <requirement type="package" version="1.0">bioawk</requirement>
-    <requirement type="package" version="2.8.1">pandaseq</requirement>
-    <requirement type="package" version="3.5.0">spades</requirement>
-    <requirement type="package" version="0.11.3">fastqc</requirement>
-    <requirement type="package" version="1.8.0">qiime</requirement>
-    <requirement type="package" version="1.0">libgfortran</requirement>
-    <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>
-    <!-- toolshed dependencies -->
-    <requirement type="package" version="3.2.1">R</requirement>
+    <requirement type="package" version="1.2.3">amplicon_analysis_pipeline-all</requirement>
   </requirements>
   <stdio>
     <exit_code range="1:" />
diff -r c4cde1f435f4 -r 3512b135ecb0 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Oct 10 10:57:42 2018 -0400
+++ b/tool_dependencies.xml	Mon Oct 15 10:40:41 2018 -0400
@@ -1,80 +1,19 @@
 <?xml version="1.0"?>
 <tool_dependency>
-  <package name="amplicon_analysis_pipeline" version="1.2.3">
-      <install version="1.0">
-	<actions>
-	  <action type="download_by_url">https://github.com/MTutino/Amplicon_analysis/archive/v1.2.3.tar.gz</action>
-	  <action type="move_file">
-	    <source>Amplicon_analysis_pipeline.sh</source>
-	    <destination>$INSTALL_DIR/Amplicon_analysis_pipeline</destination>
-	  </action>
-	  <action type="move_file">
-	    <source>FIRST_STEP.sh</source>
-	    <destination>$INSTALL_DIR/Amplicon_analysis_pipeline</destination>
-	  </action>
-	  <action type="move_file">
-	    <source>VSEARCH.sh</source>
-	    <destination>$INSTALL_DIR/Amplicon_analysis_pipeline</destination>
-	  </action>
-	  <action type="move_file">
-	    <source>STAT_ANALYSIS.sh</source>
-	    <destination>$INSTALL_DIR/Amplicon_analysis_pipeline</destination>
-	  </action>
-	  <action type="move_file">
-	    <source>THIRD_STEP.sh</source>
-	    <destination>$INSTALL_DIR/Amplicon_analysis_pipeline</destination>
-	  </action>
-	  <action type="move_directory_files">
-	    <source_directory>uc2otutab</source_directory>
-	    <destination_directory>$INSTALL_DIR/Amplicon_analysis_pipeline/uc2otutab</destination_directory>
-	  </action>
-	  <action type="set_environment">
-	    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/Amplicon_analysis_pipeline</environment_variable>
-	  </action>
-	</actions>
-      </install>
-  </package>
-  <!--
-      microbiomeutil provides ChimeraSlayer
-  -->
-  <package name="microbiomeutil-chimeraslayer" version="2010-04-29">
+  <package name="amplicon_analysis_pipeline-all" version="1.2.3">
     <install version="1.0">
       <actions>
-	<action type="download_by_url">https://sourceforge.net/projects/microbiomeutil/files/__OLD_VERSIONS/microbiomeutil_2010-04-29.tar.gz</action>
-	<action type="move_directory_files">
-	  <source_directory>ChimeraSlayer</source_directory>
-	  <destination_directory>$INSTALL_DIR/ChimeraSlayer</destination_directory>
+	<action type="download_file">https://raw.githubusercontent.com/pjbriggs/Amplicon_analysis-galaxy/88289d6e8376bc94eb1a86391c3de9a81b1aa8a0/install_amplicon_analysis.sh</action>
+	<action type="chmod">
+	  <file mode="755">./install_amplicon_analysis.sh</file>
+	</action>
+	<action type="shell_command">
+	  ./install_amplicon_analysis.sh $INSTALL_DIR
 	</action>
 	<action type="set_environment">
-	    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/ChimeraSlayer</environment_variable>
+	    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/Amplicon_analysis-1.2.3/bin</environment_variable>
 	</action>
       </actions>
     </install>
   </package>
-  <!--
-      uclust required for QIIME/pyNAST
-      License only allows this version to be used with those two packages
-      See:
-      http://drive5.com/uclust/downloads1_2_22q.html
-  -->
-  <package name="uclust-qiime" version="1.2.22">
-    <install version="1.0">
-      <actions>
-	<action type="download_by_url">http://drive5.com/uclust/uclustq1.2.22_i86linux64</action>
-	<action rename_to="uclust" type="move_file">
-	  <source>uclustq1.2.22_i86linux64</source>
-	  <destination>$INSTALL_DIR/bin</destination>
-	</action>
-	<action type="chmod">
-	  <file mode="755">$INSTALL_DIR/bin/uclust</file>
-	</action>
-	<action type="set_environment">
-	    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-	</action>
-      </actions>
-    </install>
-  </package>
-  <package name="R" version="3.2.1">
-    <repository changeset_revision="77d439695328" name="package_r_3_2_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-  </package>
 </tool_dependency>