Mercurial > repos > yufei-luo > s_mart
comparison SMART/galaxy/trimAdaptor.xml @ 6:769e306b7933
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| author | yufei-luo |
|---|---|
| date | Fri, 18 Jan 2013 04:54:14 -0500 |
| parents | |
| children | 440ceca58672 |
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| 5:ea3082881bf8 | 6:769e306b7933 |
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| 1 <tool id="trimAdaptor" name="trim adaptors"> | |
| 2 <description>Remove the 3' adaptor of a list of reads.</description> | |
| 3 <command interpreter="python"> ../Java/Python/trimAdaptor.py -i $inputFile -f fastq | |
| 4 -a $adaptor | |
| 5 #if $OptionError.Error == "Yes": | |
| 6 -e $OptionError.ErrorVal | |
| 7 #end if | |
| 8 $noAdaptor $noAdaptorFile | |
| 9 -o $outputFile | |
| 10 </command> | |
| 11 | |
| 12 | |
| 13 <inputs> | |
| 14 <param name="inputFile" type="data" label="Input fastq File" format="fastq"/> | |
| 15 <param name="adaptor" type="text" value="None" label="adaptor [compulsory option]"/> | |
| 16 <conditional name="OptionError"> | |
| 17 <param name="Error" type="select" label="number of errors in percent"> | |
| 18 <option value="Yes">Yes</option> | |
| 19 <option value="No" selected="true">No</option> | |
| 20 </param> | |
| 21 <when value="Yes"> | |
| 22 <param name="ErrorVal" type="integer" value="0" /> | |
| 23 </when> | |
| 24 <when value="No"> | |
| 25 </when> | |
| 26 </conditional> | |
| 27 <param name="noAdaptor" type="boolean" truevalue="-n" falsevalue="" checked="false" label="log option" help="file name where to print sequences with no adaptor"/> | |
| 28 </inputs> | |
| 29 | |
| 30 <outputs> | |
| 31 <data format="fastq" name="outputFile" label="[trimAdaptor] Output File"/> | |
| 32 <data name="noAdaptorFile" format="fastq" label="[trimAdaptor] Log File"> | |
| 33 <filter>noAdaptor</filter> | |
| 34 </data> | |
| 35 </outputs> | |
| 36 | |
| 37 <help> | |
| 38 </help> | |
| 39 </tool> |