6
+ − 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 <command interpreter="python">
+ − 4 ../Java/Python/WrappGetReadDistribution.py -i $formatType.inputFileName
+ − 5 #if $formatType.FormatInputFileName == 'fasta':
+ − 6 -f fasta
+ − 7 #elif $formatType.FormatInputFileName == 'fastq':
+ − 8 -f fastq
+ − 9 #end if
+ − 10
+ − 11 #if $optionnumber.number == 'Yes':
+ − 12 -n $optionnumber.bestNumber
+ − 13 #end if
+ − 14 #if $optionpercent.percent == 'Yes':
+ − 15 -p $optionpercent.percentage
+ − 16 #end if
+ − 17 -o $outputFile
+ − 18 </command>
+ − 19
+ − 20 <inputs>
+ − 21 <conditional name="formatType">
+ − 22 <param name="FormatInputFileName" type="select" label="Sequence input File Format ">
+ − 23 <option value="fasta">fasta</option>
+ − 24 <option value="fastq">fastq</option>
+ − 25 </param>
+ − 26 <when value="fasta">
+ − 27 <param name="inputFileName" format="fasta" type="data" label="Sequence input File"/>
+ − 28 </when>
+ − 29 <when value="fastq">
+ − 30 <param name="inputFileName" format="fastq" type="data" label="Sequence input File"/>
+ − 31 </when>
+ − 32 </conditional>
+ − 33
+ − 34 <conditional name="optionnumber">
+ − 35 <param name="number" type="select" label="keep the best n">
+ − 36 <option value="Yes">Yes</option>
+ − 37 <option value="No" selected="true">No</option>
+ − 38 </param>
+ − 39 <when value="Yes">
+ − 40 <param name="bestNumber" type="integer" value="0" />
+ − 41 </when>
+ − 42 <when value="No">
+ − 43 </when>
+ − 44 </conditional>
+ − 45
+ − 46 <conditional name="optionpercent">
+ − 47 <param name="percent" type="select" label="keep the best n percentage">
+ − 48 <option value="Yes">Yes</option>
+ − 49 <option value="No" selected="true">No</option>
+ − 50 </param>
+ − 51 <when value="Yes">
+ − 52 <param name="percentage" type="integer" value="0" />
+ − 53 </when>
+ − 54 <when value="No">
+ − 55 </when>
+ − 56 </conditional>
+ − 57
+ − 58 </inputs>
+ − 59
+ − 60 <outputs>
+ − 61 <data name="outputFile" format="tar" label="[getReadDistribution] tar out file" help="You can not see the results directly from galaxy, but you can download this tar output file."/>
+ − 62 </outputs>
+ − 63
+ − 64 <help>
+ − 65 This script gives a .tar out file, if you want to take look at the results, you have to download it.
+ − 66 </help>
+ − 67 </tool>
