| Previous changeset 7:bf7478987a6d (2015-11-23) Next changeset 9:f6f61b363467 (2015-11-23) |
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Commit message:
planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty |
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modified:
align_families.xml duplex.xml |
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| diff -r bf7478987a6d -r e504cc1d5a76 align_families.xml --- a/align_families.xml Mon Nov 23 19:05:48 2015 -0500 +++ b/align_families.xml Mon Nov 23 19:11:52 2015 -0500 |
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| @@ -4,8 +4,9 @@ <requirements> <requirement type="package" version="7.221">mafft</requirement> <requirement type="package" version="0.1">duplex</requirement> + <requirement type="set_environment">DUPLEX_DIR</requirement> </requirements> - <command interpreter="python" detect_errors="exit_code">align_families.py $input > $output + <command interpreter="python" detect_errors="exit_code">\$DUPLEX_DIR/align_families.py $input > $output </command> <inputs> <param name="input" type="data" format="tabular" label="Input reads" help="with barcodes, grouped by family"/> |
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| diff -r bf7478987a6d -r e504cc1d5a76 duplex.xml --- a/duplex.xml Mon Nov 23 19:05:48 2015 -0500 +++ b/duplex.xml Mon Nov 23 19:11:52 2015 -0500 |
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| @@ -3,15 +3,16 @@ <description>from duplex sequencing data</description> <requirements> <requirement type="package" version="0.1">duplex</requirement> + <requirement type="set_environment">DUPLEX_DIR</requirement> </requirements> <command interpreter="python" detect_errors="exit_code"><![CDATA[ - duplex.py -r $min_reads -q $qual_thres -F $qual_format $input + \$DUPLEX_DIR/duplex.py -r $min_reads -q $qual_thres -F $qual_format $input #if $keep_sscs: --sscs-file $sscs #end if > duplex.fa - && awk -f $__tool_directory__/utils/outconv.awk -v target=1 duplex.fa > $output1 - && awk -f $__tool_directory__/utils/outconv.awk -v target=2 duplex.fa > $output2 + && awk -f \$DUPLEX_DIR/utils/outconv.awk -v target=1 duplex.fa > $output1 + && awk -f \$DUPLEX_DIR/utils/outconv.awk -v target=2 duplex.fa > $output2 ]]> </command> <inputs> |