Mercurial > repos > sanbi-uwc > novo_align
changeset 19:94ae1dd64bca draft
planemo upload for repository https://github.com/zipho/novo_align commit 124365491ed2f8e1d9a600f21db23f7f5236bdf4
| author | sanbi-uwc |
|---|---|
| date | Fri, 20 Jan 2017 08:45:45 -0500 |
| parents | b8fd92de9062 |
| children | 77814664cb3f |
| files | novo_align.py novo_align.xml test-data/sample_r1.fastq.gz test-data/sample_r2.fastq.gz |
| diffstat | 4 files changed, 33 insertions(+), 16 deletions(-) [+] |
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--- a/novo_align.py Mon Jan 09 09:03:39 2017 -0500 +++ b/novo_align.py Fri Jan 20 08:45:45 2017 -0500 @@ -39,7 +39,7 @@ args = parser.parse_args() # a dirty way of referencing the file - index_file_path = args.index_filename # not sure of the logic here: + "/" + args.index_filename.split("/")[-1] + 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)
--- a/novo_align.xml Mon Jan 09 09:03:39 2017 -0500 +++ b/novo_align.xml Fri Jan 20 08:45:45 2017 -0500 @@ -1,9 +1,10 @@ <?xml version="1.0" encoding="utf-8" ?> -<tool id="novo_align" name="NOVO ALIGN" version="0.0.7"> +<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> <requirement type="package" version="3.04.04">novoalign</requirement> + <requirement type="package" version="04.2016">novoalign-license</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ #set $paired_input_type = $paired_end.paired_input_type_conditional.paired_input_type @@ -13,23 +14,27 @@ ln -s "${$paired_end.paired_input_type_conditional.fastq_r1_in}" ./input_mate1.gz && ln -s "${$paired_end.paired_input_type_conditional.fastq_r2_in}" ./input_mate2.gz && #else - ln -s "${$paired_end.paired_input_type_conditional.fastq_r1_in}" ./input_mate1 && - ln -s "${$paired_end.paired_input_type_conditional.fastq_r2_in}" ./input_mate2 && + #set $r1_ext = $paired_end.paired_input_type_conditional.fastq_r1_in.ext + #set $r2_ext = $paired_end.paired_input_type_conditional.fastq_r2_in.ext + ln -s "${$paired_end.paired_input_type_conditional.fastq_r1_in}" ./input_mate1.$r1_ext && + ln -s "${$paired_end.paired_input_type_conditional.fastq_r2_in}" ./input_mate2.$r2_ext && #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 && + #set $r1_ext = $paired_end.paired_input_type_conditional.fastq_pair.forward.ext + #set $r2_ext = $paired_end.paired_input_type_conditional.fastq_pair.reverse.ext + ln -s "${paired_end.paired_input_type_conditional.fastq_pair.forward}" ./input_mate1.$r1_ext && + ln -s "${paired_end.paired_input_type_conditional.fastq_pair.reverse}" ./input_mate2.$r2_ext && #end if #end if #else #if $fastq_in.metadata.is_gzipped ln -s "${fastq_in}" ./input_singles.gz && #else - ln -s "${fastq_in}" ./input_singles && + ln -s "${fastq_in}" ./input_singles.${fastq_in.ext} && #end if #end if @@ -51,27 +56,28 @@ --forward_file ./input_mate1.gz --reverse_file ./input_mate2.gz #else - --forward_file ./input_mate1 - --reverse_file ./input_mate2 + --forward_file ./input_mate1.$r1_ext + --reverse_file ./input_mate2.$r2_ext #end if #else #if $paired_end.paired_input_type_conditional.fastq_pair.forward.metadata.is_gzipped: --forward_file ./input_mate1.gz --reverse_file ./input_mate2.gz #else - --forward_file ./input_mate1 - --reverse_file ./input_mate2 + --forward_file ./input_mate1.$r1_ext + --reverse_file ./input_mate2.$r2_ext #end if #end if #else - --forward_file ${fastq_in} --reverse_file ${fastq_in} + --forward_file ${fastq_in}.${fastq_in.ext} --reverse_file ${fastq_in}.${fastq_in.ext} #end if + ]]></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" 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"> @@ -80,11 +86,11 @@ <option value="collection">Dataset collection pair</option> </param> <when value="pair_of_files"> - <param name="fastq_r1_in" type="data" format="fastqsanger" 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)" /> + <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" 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> @@ -128,6 +134,17 @@ <has_text text="# Fragment Length Distribution" /> </assert_stderr> </test> + <test> + <param name="is_paired_end" value="yes" /> + <param name="paired_input_type" value="pair_of_files" /> + <param name="fastq_r1_in" ftype="fastqsanger.gz" value="sample_r1.fastq.gz" /> + <param name="fastq_r2_in" ftype="fastqsanger.gz" value="sample_r2.fastq.gz" /> + <param name="source" value="history" /> + <param name="reference" ftype="fasta" value="reference.fasta" /> + <assert_stderr> + <has_text text="# Fragment Length Distribution" /> + </assert_stderr> + </test> </tests> <help><![CDATA[ `Novoalign`_ is a powerful tool designed for mapping of short reads onto a reference genome from Illumina,