Mercurial > repos > nick > duplex
comparison duplex.xml @ 8:e504cc1d5a76 draft
planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
| author | nick |
|---|---|
| date | Mon, 23 Nov 2015 19:11:52 -0500 |
| parents | 9d46c9ca7ceb |
| children | f6f61b363467 |
comparison
equal
deleted
inserted
replaced
| 7:bf7478987a6d | 8:e504cc1d5a76 |
|---|---|
| 1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
| 2 <tool id="duplex" name="Make consensus reads" version="0.1"> | 2 <tool id="duplex" name="Make consensus reads" version="0.1"> |
| 3 <description>from duplex sequencing data</description> | 3 <description>from duplex sequencing data</description> |
| 4 <requirements> | 4 <requirements> |
| 5 <requirement type="package" version="0.1">duplex</requirement> | 5 <requirement type="package" version="0.1">duplex</requirement> |
| 6 <requirement type="set_environment">DUPLEX_DIR</requirement> | |
| 6 </requirements> | 7 </requirements> |
| 7 <command interpreter="python" detect_errors="exit_code"><![CDATA[ | 8 <command interpreter="python" detect_errors="exit_code"><![CDATA[ |
| 8 duplex.py -r $min_reads -q $qual_thres -F $qual_format $input | 9 \$DUPLEX_DIR/duplex.py -r $min_reads -q $qual_thres -F $qual_format $input |
| 9 #if $keep_sscs: | 10 #if $keep_sscs: |
| 10 --sscs-file $sscs | 11 --sscs-file $sscs |
| 11 #end if | 12 #end if |
| 12 > duplex.fa | 13 > duplex.fa |
| 13 && awk -f $__tool_directory__/utils/outconv.awk -v target=1 duplex.fa > $output1 | 14 && awk -f \$DUPLEX_DIR/utils/outconv.awk -v target=1 duplex.fa > $output1 |
| 14 && awk -f $__tool_directory__/utils/outconv.awk -v target=2 duplex.fa > $output2 | 15 && awk -f \$DUPLEX_DIR/utils/outconv.awk -v target=2 duplex.fa > $output2 |
| 15 ]]> | 16 ]]> |
| 16 </command> | 17 </command> |
| 17 <inputs> | 18 <inputs> |
| 18 <param name="input" type="data" format="tabular" label="Aligned input reads" /> | 19 <param name="input" type="data" format="tabular" label="Aligned input reads" /> |
| 19 <param name="min_reads" type="integer" value="3" min="1" label="Minimum reads per family" help="Single-strand families with fewer than this many reads will be skipped."/> | 20 <param name="min_reads" type="integer" value="3" min="1" label="Minimum reads per family" help="Single-strand families with fewer than this many reads will be skipped."/> |