Mercurial > repos > nick > dunovo
diff dunovo.xml @ 3:00dde366870a draft
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'a3ad9fbb3f010253808fc0c7329897a741ec9feb\n'
| author | nick |
|---|---|
| date | Mon, 11 Sep 2017 16:59:44 -0400 |
| parents | a9cb6fb9ea94 |
| children | 5fbeaa41b223 |
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--- a/dunovo.xml Thu Aug 24 02:13:33 2017 -0400 +++ b/dunovo.xml Mon Sep 11 16:59:44 2017 -0400 @@ -1,25 +1,21 @@ <?xml version="1.0"?> -<tool id="dunovo" name="Du Novo: Make consensus reads" version="0.7.6"> +<tool id="dunovo" name="Du Novo: Make consensus reads" version="0.8.1"> <description>from duplex sequencing alignments</description> <requirements> - <requirement type="package" version="0.7.6">dunovo</requirement> + <requirement type="package" version="0.8.1">dunovo</requirement> <!-- 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' + <command detect_errors="exit_code"> + dunovo.py --galaxy $phone --processes \${GALAXY_SLOTS:-1} --min-reads $min_reads --qual $qual_thres --qual-format $qual_format --cons-thres $cons_thres --min-cons-reads $min_cons_reads '$input' --dcs1 '$dcs1' --dcs2 '$dcs2' #if $keep_sscs: - --sscs-file sscs.fa + --sscs1 '$sscs1' --sscs2 '$sscs2' #end if - > duplex.fa - && outconv.py duplex.fa -1 '$dcs1' -2 '$dcs2' - #if $keep_sscs: - && outconv.py sscs.fa -1 '$sscs1' -2 '$sscs2' - #end if - ]]> </command> <inputs> <param name="input" type="data" format="tabular" label="Aligned input reads" /> <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."/> + <param name="cons_thres" type="float" value="0.5" min="0.5" max="1.0" label="The threshold to use when making consensus sequences. The consensus base must be present in more than this fraction of the reads, or "N" will be used."/> + <param name="min_cons_reads" type="integer" value="0" min="0" label="The minimum number of reads a base must appear in to be used as the consensus base. If no base at the position appears in at least this many reads, "N" will be used."/> <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."/> <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+"> <option value="sanger" selected="true">Sanger (PHRED 0 = "!")</option> @@ -41,8 +37,8 @@ <tests> <test> <param name="input" value="families.msa.tsv"/> - <output name="dcs1" file="families.cons_1.fa"/> - <output name="dcs2" file="families.cons_2.fa"/> + <output name="dcs1" file="families.dcs_1.fa"/> + <output name="dcs2" file="families.dcs_2.fa"/> </test> </tests> <citations>