Mercurial > repos > nick > duplex
annotate dunovo.xml @ 5:4bc49a5769ee draft
Version 0.5: Split interleaved SSCS output file into two paired files.
| author | nick |
|---|---|
| date | Thu, 01 Dec 2016 23:22:52 -0500 |
| parents | 7f513b9b1b1e |
| children | 9a0bee12b583 |
| rev | line source |
|---|---|
| 4 | 1 <?xml version="1.0"?> |
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Version 0.5: Split interleaved SSCS output file into two paired files.
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2 <tool id="duplex" name="Du Novo: Make consensus reads" version="0.5"> |
| 4 | 3 <description>from duplex sequencing alignments</description> |
| 4 <requirements> | |
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Version 0.5: Split interleaved SSCS output file into two paired files.
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5 <requirement type="package" version="0.5">duplex</requirement> |
| 4 | 6 <requirement type="set_environment">DUPLEX_DIR</requirement> |
| 7 <!-- TODO: require Python 2.7 --> | |
| 8 </requirements> | |
| 9 <command detect_errors="exit_code"><![CDATA[ | |
| 10 python \$DUPLEX_DIR/dunovo.py -r $min_reads -q $qual_thres -F $qual_format $input | |
| 11 #if $keep_sscs: | |
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Version 0.5: Split interleaved SSCS output file into two paired files.
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12 --sscs-file sscs.fa |
| 4 | 13 #end if |
| 14 > duplex.fa | |
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Version 0.5: Split interleaved SSCS output file into two paired files.
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15 && python \$DUPLEX_DIR/utils/outconv.py duplex.fa -1 $dcs1 -2 $dcs2 |
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4bc49a5769ee
Version 0.5: Split interleaved SSCS output file into two paired files.
nick
parents:
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diff
changeset
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16 #if $keep_sscs: |
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4bc49a5769ee
Version 0.5: Split interleaved SSCS output file into two paired files.
nick
parents:
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17 && python \$DUPLEX_DIR/utils/outconv.py sscs.fa -1 $sscs1 -2 $sscs2 |
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4bc49a5769ee
Version 0.5: Split interleaved SSCS output file into two paired files.
nick
parents:
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changeset
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18 #end if |
| 4 | 19 ]]> |
| 20 </command> | |
| 21 <inputs> | |
| 22 <param name="input" type="data" format="tabular" label="Aligned input reads" /> | |
| 23 <param name="min_reads" type="integer" value="3" min="1" label="Minimum reads per family" help="Single-strand families with fewer than this many reads will be skipped."/> | |
| 24 <param name="qual_thres" type="integer" value="25" min="1" label="Minimum base quality" help="Bases with a PHRED score less than this will not be counted in the consensus making."/> | |
| 25 <param name="qual_format" type="select" label="FASTQ format" help="Solexa should also work for Illumina 1.3+ and 1.5+, and Sanger should work for Illumina 1.8+"> | |
| 26 <option value="sanger" selected="true">Sanger (PHRED 0 = "!")</option> | |
| 27 <option value="solexa">Solexa (PHRED 0 = "@")</option> | |
| 28 </param> | |
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29 <param name="keep_sscs" type="boolean" truevalue="true" falsevalue="" label="Output single-strand consensus sequences as well" /> |
| 4 | 30 </inputs> |
| 31 <outputs> | |
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Version 0.5: Split interleaved SSCS output file into two paired files.
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32 <data name="dcs1" format="fasta" label="$tool.name on $on_string (mate 1)"/> |
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4bc49a5769ee
Version 0.5: Split interleaved SSCS output file into two paired files.
nick
parents:
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diff
changeset
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33 <data name="dcs2" format="fasta" label="$tool.name on $on_string (mate 2)"/> |
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4bc49a5769ee
Version 0.5: Split interleaved SSCS output file into two paired files.
nick
parents:
4
diff
changeset
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34 <data name="sscs1" format="fasta" label="$tool.name on $on_string (SSCS mate 1)"> |
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4bc49a5769ee
Version 0.5: Split interleaved SSCS output file into two paired files.
nick
parents:
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diff
changeset
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35 <filter>keep_sscs</filter> |
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4bc49a5769ee
Version 0.5: Split interleaved SSCS output file into two paired files.
nick
parents:
4
diff
changeset
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36 </data> |
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4bc49a5769ee
Version 0.5: Split interleaved SSCS output file into two paired files.
nick
parents:
4
diff
changeset
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37 <data name="sscs2" format="fasta" label="$tool.name on $on_string (SSCS mate 2)"> |
| 4 | 38 <filter>keep_sscs</filter> |
| 39 </data> | |
| 40 </outputs> | |
| 41 <tests> | |
| 42 <test> | |
| 43 <param name="input" value="families.msa.tsv"/> | |
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4bc49a5769ee
Version 0.5: Split interleaved SSCS output file into two paired files.
nick
parents:
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diff
changeset
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44 <output name="dcs1" file="families.cons_1.fa"/> |
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4bc49a5769ee
Version 0.5: Split interleaved SSCS output file into two paired files.
nick
parents:
4
diff
changeset
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45 <output name="dcs2" file="families.cons_2.fa"/> |
| 4 | 46 </test> |
| 47 </tests> | |
| 48 <help> | |
| 49 | |
| 50 **What it does** | |
| 51 | |
| 52 This is for processing duplex sequencing data. It creates single-strand and duplex consensus reads from aligned read families. | |
| 53 | |
| 54 ----- | |
| 55 | |
| 56 **Input** | |
| 57 | |
| 58 This expects the output format of the "Align families" tool. | |
| 59 | |
| 60 ----- | |
| 61 | |
| 62 **Output** | |
| 63 | |
| 64 This will output final, duplex consensus reads in two FASTA files (first and second reads in the pairs). Optionally, you can save the single-strand reads too, in a separate FASTA file. | |
| 65 | |
| 66 </help> | |
| 67 </tool> |