Mercurial > repos > pjbriggs > amplicon_analysis_pipeline
changeset 6:45db1f97795c draft
planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit e75f078692e313af3295d2d991fcd8d61270242f
| author | pjbriggs |
|---|---|
| date | Mon, 18 Jun 2018 05:41:05 -0400 |
| parents | bbfc9638ba84 |
| children | 1cd017d72920 |
| files | amplicon_analysis_pipeline.xml relabel_fasta.py tool_dependencies.xml |
| diffstat | 3 files changed, 21 insertions(+), 69 deletions(-) [+] |
line wrap: on
line diff
--- 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 @@ <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="3.2.0">R</requirement> + <requirement type="package" version="3.2.1">R</requirement> <requirement type="package" version="1.1.3">vsearch</requirement> <!-- microbiomeutil not available in bioconda --> <requirement type="package" version="2010-04-29">microbiomeutil</requirement>
--- 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 <PREFIX>1, <PREFIX>2, -<PREFIX>3 etc (where <PREFIX> 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 - -
--- /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 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="amplicon_analysis_pipeline" version="1.2.2"> + <install version="1.0"> + <actions> + <action type="download_by_url">https://github.com/MTutino/Amplicon_analysis/archive/v1.2.2.tar.gz</action> + <action type="move_directory_files"> + <source>.</source> + <destination>$INSTALL_DIR/Amplicon_analysis_pipeline</destination> + </action> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/Amplicon_analysis_pipeline</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>