Mercurial > repos > sanbi-uwc > novo_align
changeset 20:77814664cb3f draft
planemo upload for repository https://github.com/zipho/novo_align commit 5bc8cfdb572731dea908d62f22b080b1534ddedb
| author | sanbi-uwc |
|---|---|
| date | Tue, 27 Jun 2017 05:40:46 -0400 |
| parents | 94ae1dd64bca |
| children | 119cb8e503d0 |
| files | novo_align.xml |
| diffstat | 1 files changed, 6 insertions(+), 6 deletions(-) [+] |
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--- a/novo_align.xml Fri Jan 20 08:45:45 2017 -0500 +++ b/novo_align.xml Tue Jun 27 05:40:46 2017 -0400 @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="utf-8" ?> -<tool id="novo_align" name="NOVO ALIGN" version="0.0.8"> +<tool id="novo_align" name="NOVO ALIGN" version="0.0.9"> <description>Tool to run the Novo Align mapping tool</description> <requirements> <requirement type="package" version="1.2">samtools</requirement> @@ -46,7 +46,7 @@ '${out_file}' --index #if str($index.source) == 'builtin': - '${index.index1}' + '${index.index1.fields.path}' #else reference.nix #end if @@ -77,7 +77,7 @@ <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"> @@ -86,11 +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>