Mercurial > repos > simon-gladman > trimmomatic_032
changeset 13:476184b9b2f7 draft
Uploaded
| author | simon-gladman |
|---|---|
| date | Thu, 10 Jul 2014 14:38:25 -0400 |
| parents | e99104027742 |
| children | cb56fdcbe0a5 |
| files | trimmomatic.xml |
| diffstat | 1 files changed, 23 insertions(+), 8 deletions(-) [+] |
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--- a/trimmomatic.xml Thu Jul 10 14:06:31 2014 -0400 +++ b/trimmomatic.xml Thu Jul 10 14:38:25 2014 -0400 @@ -8,10 +8,17 @@ <command interpreter="perl"> trimmomatic_wrapper.pl paired ${paired.is_paired} - fwdfile ${paired.forwards_file} - #if $paired.is_paired: + #if $paired.is_paired == "single": + fwdfile ${paired.forwards_file} + #end if + #if $paired.is_paired == "paired": + fwdfile ${paired.forwards_file} revfile ${paired.reverse_file} #end if + #if $paired.is_paired == "collection": + fwdfile ${paired.collection_data.forward} + revfile ${paired.collection_data.reverse} + #end if phred $phred cutadapt ${adapt.adapters} #if $adapt.adapters: @@ -59,7 +66,12 @@ <inputs> <conditional name="paired"> - <param name="is_paired" type="boolean" checked="true" truevalue="paired" falsevalue="single" label="Paired end reads?" help="Do you have 2 separate paired end read files?"/> +<!-- <param name="is_paired" type="boolean" checked="true" truevalue="paired" falsevalue="single" label="Paired end reads?" help="Do you have 2 separate paired end read files?"/> --> + <param name="is_paired" type="select" label="Read type selector" help="single file (not pair aware), two files (paired reads) or a dataset collection of pairs"> + <option value="single" selected="true">Single File</option> + <option value="paired">Two Files</option> + <option value="collection">Single dataset collection pair</option> + </param> <when value="paired"> <param name="forwards_file" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Direction 1 fastq reads to trim"/> <param name="reverse_file" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Direction 2 fastq reads to trim"/> @@ -67,6 +79,9 @@ <when value="single"> <param name="forwards_file" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Fastq reads to trim"/> </when> + <when value="collection"> + <param name="collection_data" type="data_collection" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Paired end dataset collection" collection_type="paired"/> + </when> </conditional> <param name="phred" type="select" label="Quality encoding." help="Phred33 or Phred 64, probably Phred64"> <option value="phred64">phred64</option> @@ -139,13 +154,13 @@ <outputs> <data name="log" format="tabular" label="${tool.name} on ${on_string}: Trimmomatic Log" hidden="True"> </data> - <data name="fwdpairs" format="fastq" label="${tool.name} on ${on_string}: Dir1 trimmed pairs"> - <filter>(paired['is_paired'])</filter> + <data name="fwdpairs" format="input" label="${tool.name} on ${on_string}: Dir1 trimmed pairs"> + <filter>(paired['is_paired']=="single")</filter> </data> - <data name="revpairs" format="fastq" label="${tool.name} on ${on_string}: Dir2 trimmed pairs"> - <filter>(paired['is_paired'])</filter> + <data name="revpairs" format="input" label="${tool.name} on ${on_string}: Dir2 trimmed pairs"> + <filter>(paired['is_paired'] == "paired" or paired['is_paired'] == "collection")</filter> </data> - <data name="singles" format="fastq" label="${tool.name} on ${on_string}: trimmed reads"/> + <data name="singles" format="input" label="${tool.name} on ${on_string}: trimmed reads"/> <data name="dummy_out" format="tabular" label="${tool.name} on ${on_string}: DEBUG OUTPUT" hidden="True"/> </outputs>