Mercurial > repos > sanbi-uwc > novo_align
changeset 22:482aef16b6f5 draft
planemo upload for repository https://github.com/zipho/novo_align commit 3aa343058f631ac4117c9bc86989dc449f84135f
| author | sanbi-uwc |
|---|---|
| date | Thu, 25 Jan 2018 03:37:56 -0500 |
| parents | 119cb8e503d0 |
| children | 80e0ad163783 |
| files | novo_align.py novo_align.xml |
| diffstat | 2 files changed, 66 insertions(+), 20 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/novo_align.py Thu Jan 25 03:37:56 2018 -0500 @@ -0,0 +1,47 @@ +#!/usr/bin/env python +from __future__ import print_function +import argparse +import shlex +import os +import sys +import logging +log = logging.getLogger( __name__ ) + + +def novo_align(output_filename, index_filename, fwd_file, rev_file ): + param = r'@RG\tID:RG\tSM:$i\tPL:ILLUMINA' + cmdline_str = "novoalign -c 8 -k -d {} -f {} {} -i PE 250, 100 -o SAM '{}' | samtools view -bS - > {}".format( + index_filename, + fwd_file, + rev_file, + param, + output_filename) + try: + os.system(cmdline_str) + except: + print("Error running the nova-align", file=sys.stderr) + + +def newSplit(value): + lex = shlex.shlex(value) + lex.quotes = '"' + lex.whitespace_split = True + lex.commenters = '' + return list(lex) + + +def main(): + parser = argparse.ArgumentParser(description="Generate a BAM file from the Novo Align tool") + parser.add_argument('output_filename') + parser.add_argument('--index_filename') + parser.add_argument('--forward_filename') + parser.add_argument('--reverse_filename') + args = parser.parse_args() + + # a dirty way of referencing the file + index_file_path = args.index_filename # removed old logic here: + "/" + args.index_filename.split("/")[-1] + novo_align(args.output_filename, index_file_path, args.forward_filename, args.reverse_filename) + + +if __name__ == "__main__": + main()
--- a/novo_align.xml Tue Jun 27 10:18:49 2017 -0400 +++ b/novo_align.xml Thu Jan 25 03:37:56 2018 -0500 @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="utf-8" ?> -<tool id="novo_align" name="novoalign" version="0.0.10"> +<tool id="novo_align" name="NOVO ALIGN" version="0.0.8"> <description>Tool to run the Novo Align mapping tool</description> <requirements> <requirement type="package" version="1.2">samtools</requirement> @@ -42,43 +42,42 @@ ln -s '${index.reference}' reference.fasta && novoindex -m reference.nix reference.fasta && #end if - novoalign -c \${GALAXY_SLOTS:-8} -k -d + python $__tool_directory__/novo_align.py + '${out_file}' + --index #if str($index.source) == 'builtin': '${index.index1.fields.path}' #else reference.nix #end if - -f #if $paired_end.is_paired_end #if $paired_input_type == "pair_of_files" #if $paired_end.paired_input_type_conditional.fastq_r1_in.metadata.is_gzipped - ./input_mate1.gz - ./input_mate2.gz + --forward_file ./input_mate1.gz + --reverse_file ./input_mate2.gz #else - ./input_mate1.$r1_ext - ./input_mate2.$r2_ext + --forward_file ./input_mate1.$r1_ext + --reverse_file ./input_mate2.$r2_ext #end if #else #if $paired_end.paired_input_type_conditional.fastq_pair.forward.metadata.is_gzipped: - ./input_mate1.gz - ./input_mate2.gz + --forward_file ./input_mate1.gz + --reverse_file ./input_mate2.gz #else - ./input_mate1.$r1_ext - ./input_mate2.$r2_ext + --forward_file ./input_mate1.$r1_ext + --reverse_file ./input_mate2.$r2_ext #end if #end if #else - '${fastq_in}.${fastq_in.ext}' '${fastq_in}.${fastq_in.ext}' + --forward_file ${fastq_in}.${fastq_in.ext} --reverse_file ${fastq_in}.${fastq_in.ext} #end if - -i PE 250, 100 - -o SAM '@RG\tID:RG\tSM:\$i\tPL:ILLUMINA' | samtools view -bS - | novosort -c \${GALAXY_SLOTS:-8} -m 8G -s -f - > '${out_file}' ]]></command> <inputs> <conditional name="paired_end"> <param name="is_paired_end" type="boolean" label="Paired end data?" truevalue="yes" falsevalue="no" checked="yes" /> <when value="no"> - <param name="fastq_in" type="data" format="fastqsanger,fastqsanger.gz" label="Input FASTQ file" /> + <param name="fastq_in" type="data" format="fastqsanger|fastqsanger.gz" label="Input FASTQ file" /> </when> <when value="yes"> <conditional name="paired_input_type_conditional"> @@ -87,11 +86,11 @@ <option value="collection">Dataset collection pair</option> </param> <when value="pair_of_files"> - <param name="fastq_r1_in" type="data" format="fastqsanger,fastqsanger.gz" label="Input FASTQ file (R1/first of pair)" /> - <param name="fastq_r2_in" type="data" format="fastqsanger,fastqsanger.gz" label="Input FASTQ file (R2/second of pair)" /> + <param name="fastq_r1_in" type="data" format="fastqsanger|fastqsanger.gz" label="Input FASTQ file (R1/first of pair)" /> + <param name="fastq_r2_in" type="data" format="fastqsanger|fastqsanger.gz" label="Input FASTQ file (R2/second of pair)" /> </when> <when value="collection"> - <param name="fastq_pair" format="fastqsanger,fastqsanger.gz" type="data_collection" + <param name="fastq_pair" format="fastqsanger|fastqsanger.gz" type="data_collection" collection_type="paired" label="Select FASTQ dataset collection with R1/R2 pair" /> </when> @@ -105,7 +104,7 @@ </param> <when value="builtin"> <param name="index1" type="select" label="Novo-Align Index(FASTA format)"> - <options from_data_table="novocraft_index"/> + <options from_data_table="all_fasta"/> </param> </when> <when value="history"> @@ -117,7 +116,7 @@ <param name="fastq_input1" type="data" format="fastqsanger" label="Select first set of reads" help="Specify dataset with forward reads"/> <param name="fastq_input2" type="data" format="fastqsanger" label="Select second set of reads" help="Specify dataset with reverse reads"/> <param name="index1" type="select" label="Novo-Align Index(FASTA format)"> - <options from_data_table="novocraft_index"/> + <options from_data_table="all_fasta"/> </param> </inputs>--> <outputs>