Mercurial > repos > sanbi-uwc > novo_align
changeset 12:bfe39c503a40 draft
planemo upload for repository https://github.com/zipho/novo_align commit 896a5a73f2a5f71a7b38dc0403f54afba1f27643
| author | sanbi-uwc |
|---|---|
| date | Tue, 29 Nov 2016 09:18:10 -0500 |
| parents | dbeac2baa4dc |
| children | bab35d33b28d |
| files | novo_align.py novo_align.xml |
| diffstat | 2 files changed, 90 insertions(+), 6 deletions(-) [+] |
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--- a/novo_align.py Thu Apr 07 09:55:31 2016 -0400 +++ b/novo_align.py Tue Nov 29 09:18:10 2016 -0500 @@ -3,9 +3,11 @@ 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:$i\tPL:ILLUMINA' cmdline_str = "novoalign -c 8 -k -d {} -f {} {} -i PE 250, 100 -o SAM '{}' | samtools view -bS - > {}".format( @@ -19,6 +21,7 @@ except: print("Error running the nova-align", file=sys.stderr) + def newSplit(value): lex = shlex.shlex(value) lex.quotes = '"' @@ -26,6 +29,7 @@ lex.commenters = '' return list(lex) + def main(): parser = argparse.ArgumentParser(description="Generate a BAM file from the Novo Align tool") parser.add_argument('output_filename') @@ -33,9 +37,10 @@ parser.add_argument('--forward_filename') parser.add_argument('--reverse_filename') args = parser.parse_args() - + # a dirty way of referencing the file index_file_path = args.index_filename + "/" + args.index_filename.split("/")[-1] novo_align(args.output_filename, index_file_path, args.forward_filename, args.reverse_filename) -if __name__ == "__main__": main() +if __name__ == "__main__": + main()
--- a/novo_align.xml Thu Apr 07 09:55:31 2016 -0400 +++ b/novo_align.xml Tue Nov 29 09:18:10 2016 -0500 @@ -9,16 +9,95 @@ <exit_code range=":-1" /> <exit_code range="1:" /> </stdio> - <command interpreter="python"> - novo_align.py '${out_file}' --index_file ${index1.fields.path} --forward_file ${fastq_input1} --reverse_file ${fastq_input2} - </command> + <command><![CDATA[ + #set $paired_input_type = $paired_end.paired_input_type_conditional.paired_input_type + #if $paired_end.is_paired_end + #if $paired_input_type == "pair_of_files" + #if $paired_end.paired_input_type_conditional.fastq_r1_in.metadata.is_gzipped + ln -s "${$paired_end.paired_input_type_conditional.fastq_r1_in}" ./input_mate1.gz; + ln -s "${$paired_end.paired_input_type_conditional.fastq_r2_in}" ./input_mate2.gz; + #else + ln -s "${$paired_end.paired_input_type_conditional.fastq_r1_in}" ./input_mate1; + ln -s "${$paired_end.paired_input_type_conditional.fastq_r2_in}" ./input_mate2; + #end if + #else: + #if $paired_end.paired_input_type_conditional.fastq_pair.forward.metadata.is_gzipped + ln -s "${paired_end.paired_input_type_conditional.fastq_pair.forward}" ./input_mate1.gz; + ln -s "${paired_end.paired_input_type_conditional.fastq_pair.reverse}" ./input_mate2.gz; + #else + ln -s "${paired_end.paired_input_type_conditional.fastq_pair.forward}" ./input_mate1; + ln -s "${paired_end.paired_input_type_conditional.fastq_pair.reverse}" ./input_mate2; + #end if + #end if + #else + #if $fastq_in.metadata.is_gzipped + ln -s "${fastq_in}" ./input_singles.gz; + #else + ln -s "${fastq_in}" ./input_singles; + #end if + #end if + + + $__tool_directory__/novo_align.py + '${out_file}' + --index_file ${index1.fields.path} + #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 + --forward_file ./input_mate1.gz + --reverse_file ./input_mate2.gz + #else + --forward_file ./input_mate1 + --reverse_file ./input_mate2 + #end if + #else + #if $paired_end.paired_input_type_conditional.fastq_pair.forward.metadata.is_gzipped: + --forward_file ./input_mate1.gz + --reverse_file ./input_mate2.gz + #else + --forward_file ./input_mate1 + --reverse_file ./input_mate2 + #end if + #end if + #else + --forward_file ${fastq_in} --reverse_file ${fastq_in} + #end if + ]]></command> <inputs> + <conditional name="paired_end"> + <param name="is_paired_end" type="boolean" label="Paired end data?" truevalue="yes" falsevalue="no" checked="on" /> + <when value="no"> + <param name="fastq_in" type="data" format="fastqsanger" label="Input FASTQ file" /> + </when> + <when value="yes"> + <conditional name="paired_input_type_conditional"> + <param name="paired_input_type" type="select" label="Input Type"> + <option value="pair_of_files" selected="true">Pair of datasets</option> + <option value="collection">Dataset collection pair</option> + </param> + <when value="pair_of_files"> + <param name="fastq_r1_in" type="data" format="fastqsanger" label="Input FASTQ file (R1/first of pair)" /> + <param name="fastq_r2_in" type="data" format="fastqsanger" label="Input FASTQ file (R2/second of pair)" /> + </when> + <when value="collection"> + <param name="fastq_pair" format="fastqsanger" type="data_collection" + collection_type="paired" + label="Select FASTQ dataset collection with R1/R2 pair" /> + </when> + </conditional> + </when> + </conditional> + <param name="index1" type="select" label="Novo-Align Index(FASTA format)"> + <options from_data_table="novocraft_index"/> + </param> + </inputs> + <!--<inputs> <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"/> </param> - </inputs> + </inputs>--> <outputs> <data format="bam" name="out_file" /> </outputs>