Mercurial > repos > nick > dunovo
changeset 30:7ee4030173ea draft
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'230f018da2c0bc4eedc72e0f70eac0df1e85ebdb\n'-dirty
| author | nick |
|---|---|
| date | Fri, 01 Jun 2018 17:07:49 -0400 |
| parents | 9d28b4509c02 |
| children | 9dcdd56ca7a5 |
| files | trimmer.xml |
| diffstat | 1 files changed, 0 insertions(+), 84 deletions(-) [+] |
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--- a/trimmer.xml Fri Jun 01 16:51:02 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,84 +0,0 @@ -<tool id="sequence_content_trimmer" version="0.1" name="Sequence Content Trimmer"> - <description>trim reads based on certain bases</description> - <command interpreter="python"> - trimmer.py $input1 - #if $paired.is_paired: - $input2 $output1 $output2 - #if ('fasta' in $input1.extension and 'fastq' in $input2.extension) or ('fastq' in $input1.extension and 'fasta' in $input2.extension) - --error 'Both input files must be either fastq or fasta (no mixing the two).' - #end if - #end if - #if $input1.extension == 'fastq' or $input1.extension == 'fastqsanger' or $input1.extension == 'fastqillumina' or $input1.extension == 'fastqsolexa' - -f fastq - #elif $input1.extension == 'fasta' - -f fasta - #else - -f $input1.extension - #end if - -b $bases -t $thres -w $win_len $invert - #if $min_len.has_min_len: - -m $min_len.value - #end if - #if not $paired.is_paired: - > $output1 - #end if - </command> - <inputs> - <conditional name="paired"> - <param name="is_paired" type="select" label="Paired reads?"> - <option value="" selected="True">Unpaired</option> - <option value="true">Paired</option> - </param> - <when value="true"> - <param name="input1" type="data" format="fasta,fastq" label="Input reads (mate 1)"/> - <param name="input2" type="data" format="fasta,fastq" label="Input reads (mate 2)"/> - </when> - <when value=""> - <param name="input1" type="data" format="fasta,fastq" label="Input reads"/> - </when> - </conditional> - <param name="bases" type="text" value="N" label="Bases to filter on"/> - <param name="thres" type="float" value="0.5" min="0" max="1" label="Frequency threshold" help="Trim when the frequency of filter bases (or non-filter bases, if inverting) exceeds this value."/> - <param name="win_len" type="integer" value="10" min="1" label="Size of the window"/> - <param name="invert" type="boolean" truevalue="--invert" falsevalue="" checked="False" label="Invert filter bases" help="Trim when the frequency of bases NOT in the "filter bases" list exceeds the threshold."/> - <conditional name="min_len"> - <param name="has_min_len" type="boolean" truevalue="true" falsevalue="" checked="False" label="Set a minimum read length"/> - <when value="true"> - <param name="value" type="integer" value="10" min="0" label="Minimum read length" help="Reads trimmed to less than this length will be omitted from the output. Pairs will be preserved: both must exceed this threshold to be kept."/> - </when> - </conditional> - </inputs> - <outputs> - <data name="output1" format_source="input1"/> - <data name="output2" format_source="input2"> - <filter>paired['is_paired']</filter> - </data> - </outputs> - - <help> - -.. class:: infomark - -**What it does** - -This tool trims the 3' ends of reads based on the presence of the given bases. For instance, trim when N's are encountered or when the GC content exceeds a certain frequency. - - -.. class:: infomark - -**How it works** - -This will slide along the read with a window, and trim once the frequency of filter bases exceeds the frequency threshold (unless "Invert filter bases" is enabled, in which case it will trim once non-filter bases exceed the threshold). - -The trim point will be just before the first (leftmost) filter base in the final window (the one where the frequency exceeded the threshold). - - -.. class:: infomark - -**Input** - -The inputs can be in the following formats: fasta, fastq, fastqsanger, fastqillumina, and fastqsolexa. Both must be either a fasta or fastq type (no mixing fastq and fasta). - - </help> - -</tool>