Mercurial > repos > yufei-luo > s_mart
changeset 30:5677346472b5
Deleted selected files
| author | m-zytnicki |
|---|---|
| date | Mon, 29 Apr 2013 03:45:52 -0400 |
| parents | c78966712a57 |
| children | 0ab839023fe4 |
| files | SMART/galaxy/getReadDistribution.xml |
| diffstat | 1 files changed, 0 insertions(+), 70 deletions(-) [+] |
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--- a/SMART/galaxy/getReadDistribution.xml Mon Apr 29 03:44:49 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,70 +0,0 @@ -<tool id="getReadDistribution" name="get read distribution"> - <description>Get Read Distribution v1.0.1: Plot the number of identical reads and give the most represented.</description> - <requirements> - <requirement type="set_environment">PYTHONPATH</requirement> - </requirements> - <command interpreter="python"> - ../Java/Python/WrappGetReadDistribution.py -i $formatType.inputFileName - #if $formatType.FormatInputFileName == 'fasta': - -f fasta - #elif $formatType.FormatInputFileName == 'fastq': - -f fastq - #end if - - #if $optionnumber.number == 'Yes': - -n $optionnumber.bestNumber - #end if - #if $optionpercent.percent == 'Yes': - -p $optionpercent.percentage - #end if - -o $outputFile - </command> - - <inputs> - <conditional name="formatType"> - <param name="FormatInputFileName" type="select" label="Sequence input File Format "> - <option value="fasta">fasta</option> - <option value="fastq">fastq</option> - </param> - <when value="fasta"> - <param name="inputFileName" format="fasta" type="data" label="Sequence input File"/> - </when> - <when value="fastq"> - <param name="inputFileName" format="fastq" type="data" label="Sequence input File"/> - </when> - </conditional> - - <conditional name="optionnumber"> - <param name="number" type="select" label="keep the best n"> - <option value="Yes">Yes</option> - <option value="No" selected="true">No</option> - </param> - <when value="Yes"> - <param name="bestNumber" type="integer" value="0" /> - </when> - <when value="No"> - </when> - </conditional> - - <conditional name="optionpercent"> - <param name="percent" type="select" label="keep the best n percentage"> - <option value="Yes">Yes</option> - <option value="No" selected="true">No</option> - </param> - <when value="Yes"> - <param name="percentage" type="integer" value="0" /> - </when> - <when value="No"> - </when> - </conditional> - - </inputs> - - <outputs> - <data name="outputFile" format="tar" label="[get read distribution] tar out file" help="You can not see the results directly from galaxy, but you can download this tar output file."/> - </outputs> - - <help> - This script gives a .tar out file, if you want to take look at the results, you have to download it. - </help> -</tool>