Mercurial > repos > yufei-luo > s_mart
view SMART/galaxy/getReadDistribution.xml @ 45:e454402ba9d9
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author | m-zytnicki |
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date | Wed, 18 Sep 2013 08:51:22 -0400 |
parents | 2c0c0a89fad7 |
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<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>