Mercurial > repos > nick > dunovo
changeset 12:b4d7ec92b30f draft
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'b133d7a65a2371efa097a11ccf123587007e1662\n'-dirty
| author | nick |
|---|---|
| date | Thu, 24 Aug 2017 02:01:11 -0400 |
| parents | 134117de3cd0 |
| children | ffbdaa57d4c6 |
| files | align_families.xml correct_barcodes.xml dunovo.xml |
| diffstat | 3 files changed, 3 insertions(+), 3 deletions(-) [+] |
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--- a/align_families.xml Thu Aug 24 01:59:13 2017 -0400 +++ b/align_families.xml Thu Aug 24 02:01:11 2017 -0400 @@ -6,7 +6,7 @@ <requirement type="package" version="0.7.6">dunovo</requirement> <!-- TODO: require Python 2.7 --> </requirements> - <command detect_errors="exit_code">align_families.py --galaxy $phone -p \${GALAXY_SLOTS:-1} '$input' > '$output' + <command detect_errors="exit_code">align_families.py --test --galaxy $phone -p \${GALAXY_SLOTS:-1} '$input' > '$output' </command> <inputs> <param name="input" type="data" format="tabular" label="Input reads" help="with barcodes, grouped by family"/>
--- a/correct_barcodes.xml Thu Aug 24 01:59:13 2017 -0400 +++ b/correct_barcodes.xml Thu Aug 24 02:01:11 2017 -0400 @@ -11,7 +11,7 @@ <command detect_errors="exit_code"><![CDATA[ baralign.sh '$input' refdir barcodes.bam && samtools view -f 256 barcodes.bam - | correct.py --galaxy $phone -d $dist -m $mapq -p $pos '$input' refdir/barcodes.fa + | correct.py --test --galaxy $phone -d $dist -m $mapq -p $pos '$input' refdir/barcodes.fa | sort > '$output' ]]>
--- a/dunovo.xml Thu Aug 24 01:59:13 2017 -0400 +++ b/dunovo.xml Thu Aug 24 02:01:11 2017 -0400 @@ -6,7 +6,7 @@ <!-- TODO: require Python 2.7 --> </requirements> <command detect_errors="exit_code"><![CDATA[ - dunovo.py --galaxy $phone -r $min_reads -q $qual_thres -F $qual_format '$input' + dunovo.py --test --galaxy $phone -r $min_reads -q $qual_thres -F $qual_format '$input' #if $keep_sscs: --sscs-file sscs.fa #end if