38
+ − 1 <tool id="getReadDistribution" name="get read distribution">
+ − 2 <description>Get Read Distribution v1.0.1: Plot the number of identical reads and give the most represented.</description>
+ − 3 <requirements>
+ − 4 <requirement type="set_environment">PYTHONPATH</requirement>
+ − 5 </requirements>
+ − 6 <command interpreter="python">
+ − 7 ../Java/Python/WrappGetReadDistribution.py -i $formatType.inputFileName
+ − 8 #if $formatType.FormatInputFileName == 'fasta':
+ − 9 -f fasta
+ − 10 #elif $formatType.FormatInputFileName == 'fastq':
+ − 11 -f fastq
+ − 12 #end if
+ − 13
+ − 14 #if $optionnumber.number == 'Yes':
+ − 15 -n $optionnumber.bestNumber
+ − 16 #end if
+ − 17 #if $optionpercent.percent == 'Yes':
+ − 18 -p $optionpercent.percentage
+ − 19 #end if
+ − 20 -o $outputFile
+ − 21 </command>
+ − 22
+ − 23 <inputs>
+ − 24 <conditional name="formatType">
+ − 25 <param name="FormatInputFileName" type="select" label="Sequence input File Format ">
+ − 26 <option value="fasta">fasta</option>
+ − 27 <option value="fastq">fastq</option>
+ − 28 </param>
+ − 29 <when value="fasta">
+ − 30 <param name="inputFileName" format="fasta" type="data" label="Sequence input File"/>
+ − 31 </when>
+ − 32 <when value="fastq">
+ − 33 <param name="inputFileName" format="fastq" type="data" label="Sequence input File"/>
+ − 34 </when>
+ − 35 </conditional>
+ − 36
+ − 37 <conditional name="optionnumber">
+ − 38 <param name="number" type="select" label="keep the best n">
+ − 39 <option value="Yes">Yes</option>
+ − 40 <option value="No" selected="true">No</option>
+ − 41 </param>
+ − 42 <when value="Yes">
+ − 43 <param name="bestNumber" type="integer" value="0" />
+ − 44 </when>
+ − 45 <when value="No">
+ − 46 </when>
+ − 47 </conditional>
+ − 48
+ − 49 <conditional name="optionpercent">
+ − 50 <param name="percent" type="select" label="keep the best n percentage">
+ − 51 <option value="Yes">Yes</option>
+ − 52 <option value="No" selected="true">No</option>
+ − 53 </param>
+ − 54 <when value="Yes">
+ − 55 <param name="percentage" type="integer" value="0" />
+ − 56 </when>
+ − 57 <when value="No">
+ − 58 </when>
+ − 59 </conditional>
+ − 60
+ − 61 </inputs>
+ − 62
+ − 63 <outputs>
+ − 64 <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."/>
+ − 65 </outputs>
+ − 66
+ − 67 <help>
+ − 68 This script gives a .tar out file, if you want to take look at the results, you have to download it.
+ − 69 </help>
+ − 70 </tool>
