# HG changeset patch
# User pjbriggs
# Date 1538148497 14400
# Node ID b5e43dfe07ac7efc4a46ef85af469eba10567da3
# Parent  f0917c340f1329d9e2bdfee9b1f134beacd3e078
planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit e4cd2df591ac5b9da5a1731e81f921313ed9e979

diff -r f0917c340f13 -r b5e43dfe07ac README.rst
--- a/README.rst	Thu Aug 30 08:41:11 2018 -0400
+++ b/README.rst	Fri Sep 28 11:28:17 2018 -0400
@@ -29,8 +29,12 @@
 1. Install the dependencies
 ---------------------------
 
-The ``install_tool_deps.sh`` script can be used to fetch and install the
-dependencies locally, for example::
+If the tool is installed from the Galaxy toolshed (recommended) then
+the dependencies should be installed automatically and this step can
+be skipped.
+
+Otherwise the ``install_tool_deps.sh`` script can be used to fetch and
+install the dependencies locally, for example::
 
     install_tool_deps.sh /path/to/local_tool_dependencies
 
@@ -38,6 +42,8 @@
 created a set of directories containing the dependencies under the
 specified top level directory.
 
+*NB ``install_tool_deps.sh`` is no longer being maintained*
+
 2. Install the tool files
 -------------------------
 
@@ -203,9 +209,11 @@
 
 The following dependencies are currently unavailable:
 
- - fasta_number (need 02jun2015)
+ - R 3.2.1 (installed from the toolshed as the bioconda version
+   has conflicts )
  - microbiomeutil (need r20110519)
 
+
 (NB usearch 6.1.544 and 8.0.1623 are special cases which must be
 handled outside of Galaxy's dependency management systems.)
 
@@ -215,7 +223,8 @@
 ========== ======================================================================
 Version    Changes
 ---------- ----------------------------------------------------------------------
-1.2.2.1    Update to get dependencies from bioconda
+1.2.3.0    Updated to Amplicon_Analysis_Pipeline version 1.2.3; install
+           dependencies from bioconda and via tool_dependencies.xml
 1.2.2.0    Updated to Amplicon_Analysis_Pipeline version 1.2.2 (removes
            jackknifed analysis which is not captured by Galaxy tool)
 1.2.1.0    Updated to Amplicon_Analysis_Pipeline version 1.2.1 (adds
diff -r f0917c340f13 -r b5e43dfe07ac amplicon_analysis_pipeline.py
--- a/amplicon_analysis_pipeline.py	Thu Aug 30 08:41:11 2018 -0400
+++ b/amplicon_analysis_pipeline.py	Fri Sep 28 11:28:17 2018 -0400
@@ -190,7 +190,7 @@
         fasta_splitter = os.readlink(
             find_executable("fasta-splitter"))
     if fasta_splitter:
-        os.symlink(vsearch,os.path.join("bin","fasta-splitter.pl"))
+        os.symlink(fasta_splitter,os.path.join("bin","fasta-splitter.pl"))
         print "-- made symlink to %s" % fasta_splitter
     else:
         sys.stderr.write("Missing 'fasta-splitter[.pl]'\n")
@@ -234,17 +234,6 @@
                                find_executable("single_rarefaction.py")))
     os.environ["QIIME_CONFIG_FP"] = qiime_config_file
     print "-- set QIIME_CONFIG_FP: %s" % os.environ["QIIME_CONFIG_FP"]
-    # Check for fasta_number.py
-    fasta_number = find_executable("fasta_number.py")
-    if not fasta_number:
-        # Make a link to relabel_fasta.py
-        relabel_fasta_path = os.path.join(os.path.dirname(__file__),
-                                          "relabel_fasta.py")
-        fasta_number_path = os.path.join(os.path.abspath("bin"),
-                                         "fasta_number.py")
-        os.symlink(relabel_fasta_path,fasta_number_path)
-        print "-- linked %s to %s" % (relabel_fasta_path,
-                                      fasta_number_path)
 
     # Construct the pipeline command
     print "Amplicon analysis: constructing pipeline command"
diff -r f0917c340f13 -r b5e43dfe07ac amplicon_analysis_pipeline.xml
--- a/amplicon_analysis_pipeline.xml	Thu Aug 30 08:41:11 2018 -0400
+++ b/amplicon_analysis_pipeline.xml	Fri Sep 28 11:28:17 2018 -0400
@@ -1,8 +1,8 @@
-<tool id="amplicon_analysis_pipeline" name="Amplicon Analysis Pipeline" version="1.2.2.1">
+<tool id="amplicon_analysis_pipeline" name="Amplicon Analysis Pipeline" version="1.2.3.0">
   <description>analyse 16S rRNA data from Illumina Miseq paired-end reads</description>
   <requirements>
     <!-- non-bioconda dependencies -->
-    <requirement type="package" version="1.2.2">amplicon_analysis_pipeline</requirement>
+    <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 -->
@@ -18,6 +18,7 @@
     <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>
   </requirements>
   <stdio>
diff -r f0917c340f13 -r b5e43dfe07ac relabel_fasta.py
--- a/relabel_fasta.py	Thu Aug 30 08:41:11 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,88 +0,0 @@
-#!/usr/bin/env python
-
-DESCRIPTION = \
-"""Replace FASTA labels with new labels <PREFIX>1, <PREFIX>2,
-<PREFIX>3 ... (<PREFIX> is provided by the user via the command
-line).
-
-Can be used to label OTUs as OTU_1, OTU_2 etc.
-
-This reimplements the functionality of the fasta_number.py utility
-from https://drive5.com/python/fasta_number_py.html
-"""
-
-import argparse
-
-def relabel_fasta(fp,prefix,include_size=False):
-    """
-    Relabel sequence records in a FASTA file
-
-    Arguments:
-      fp (File): file-like object opened for reading
-        input FASTA data from
-      prefix (str): prefix to use in new labels
-      include_size (bool): if True then copy
-        'size=...' records into new labels (default
-        is not to copy the size)
-
-    Yields: updated lines from the input FASTA.
-    """
-    # Iterate over lines in file
-    nlabel = 0
-    for line in fp:
-        # Strip trailing newlines
-        line = line.rstrip('\n')
-        if not line:
-            # Skip blank lines
-            continue
-        elif line.startswith('>'):
-            # Deal with start of a sequence record
-            nlabel += 1
-            label = line[1:].strip()
-            if include_size:
-                # Extract size from the label
-                try:
-                    size = filter(
-                        lambda x: x.startswith("size="),
-                        label.split(';'))[0]
-                except Exception as ex:
-                    raise Exception("Couldn't locate 'size' in "
-                                    "label: %s" % label)
-                yield ">%s%d;%s" % (args.prefix,
-                                    nlabel,
-                                    size)
-            else:
-                yield ">%s%d" % (args.prefix,
-                                 nlabel)
-        else:
-            # Echo the line to output
-            yield line
-
-if __name__ == "__main__":
-    # Set up command line parser
-    p = argparse.ArgumentParser(description=DESCRIPTION)
-    p.add_argument("--needsize",
-                   action="store_true",
-                   help="include the size as part of the "
-                   "output label ('size=...' must be present "
-                   "in the input FASTA labels). Output labels "
-                   "will be '<PREFIX><NUMBER>;size=<SIZE>'")
-    p.add_argument("--nosize",
-                   action="store_true",
-                   help="don't include the size as part of "
-                   "the output label (this is the default)")
-    p.add_argument("fasta",
-                   metavar="FASTA",
-                   help="input FASTA file")
-    p.add_argument("prefix",
-                   metavar="PREFIX",
-                   help="prefix to use for labels in output")
-    # Process command line
-    args = p.parse_args()
-    # Relabel FASTA
-    with open(args.fasta,'rU') as fasta:
-        for line in relabel_fasta(fasta,
-                                  args.prefix,
-                                  include_size=args.needsize):
-            print line
-
diff -r f0917c340f13 -r b5e43dfe07ac tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Aug 30 08:41:11 2018 -0400
+++ b/tool_dependencies.xml	Fri Sep 28 11:28:17 2018 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
-  <package name="amplicon_analysis_pipeline" version="1.2.2">
+  <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/v1.2.2.tar.gz</action>