Mercurial > repos > yufei-luo > s_mart
comparison SMART/galaxy/getReadDistribution.xml @ 38:2c0c0a89fad7
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| author | m-zytnicki |
|---|---|
| date | Thu, 02 May 2013 09:56:47 -0400 |
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| children |
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| 37:d22fadc825e3 | 38:2c0c0a89fad7 |
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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 <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> |