# HG changeset patch # User pjbriggs # Date 1529314865 14400 # Node ID 45db1f97795cefe81aa93b4bd1e444fa49e2bd4a # Parent bbfc9638ba8403df68f0a8d20177967a2d074b20 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit e75f078692e313af3295d2d991fcd8d61270242f diff -r bbfc9638ba84 -r 45db1f97795c amplicon_analysis_pipeline.xml --- a/amplicon_analysis_pipeline.xml Wed Jun 13 08:39:26 2018 -0400 +++ b/amplicon_analysis_pipeline.xml Mon Jun 18 05:41:05 2018 -0400 @@ -14,7 +14,7 @@ blast-legacy fasta-splitter rdp_classifier - R + R vsearch microbiomeutil diff -r bbfc9638ba84 -r 45db1f97795c relabel_fasta.py --- a/relabel_fasta.py Wed Jun 13 08:39:26 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,68 +0,0 @@ -#!/usr/bin/env python - -""" -Replace FASTA labels with new labels 1, 2, -3 etc (where is a user-provided argument). - -Can be used to label OTUs as OTU_1, OTU_2 etc. - -This is a reimplementation of the fasta_number.py script from -https://drive5.com/python/fasta_number_py.html -""" - -import argparse - -def relabel_fasta(fp,prefix,include_size=False): - """ - """ - # 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('>'): - # - nlabel += 1 - label = line[1:].strip() - if args.needsize: - # 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() - p.add_argument("--needsize",action="store_true") - p.add_argument("--nosize",action="store_true") - p.add_argument("fasta") - p.add_argument("prefix") - - # 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 bbfc9638ba84 -r 45db1f97795c tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Jun 18 05:41:05 2018 -0400 @@ -0,0 +1,20 @@ + + + + + + https://github.com/MTutino/Amplicon_analysis/archive/v1.2.2.tar.gz + + . + $INSTALL_DIR/Amplicon_analysis_pipeline + + + $INSTALL_DIR/Amplicon_analysis_pipeline + + + + + + + +