Mercurial > repos > yufei-luo > s_mart
comparison smart_toolShed/SMART/galaxy/getReadDistribution.xml @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
| author | yufei-luo |
|---|---|
| date | Thu, 17 Jan 2013 10:52:14 -0500 |
| parents | |
| children |
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| -1:000000000000 | 0:e0f8dcca02ed |
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| 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> |