Mercurial > repos > yufei-luo > s_mart
diff SMART/galaxy/restrictTranscriptList.xml @ 38:2c0c0a89fad7
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| author | m-zytnicki |
|---|---|
| date | Thu, 02 May 2013 09:56:47 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SMART/galaxy/restrictTranscriptList.xml Thu May 02 09:56:47 2013 -0400 @@ -0,0 +1,124 @@ +<tool id="restrictTranscriptList" name="restrict transcript list"> + <description>Select the features which are located in a given locus.</description> + <requirements> + <requirement type="set_environment">PYTHONPATH</requirement> + </requirements> + <command interpreter="python"> ../Java/Python/restrictTranscriptList.py -i $formatType.inputFileName + #if $formatType.FormatInputFileName == 'bed': + -f bed + #elif $formatType.FormatInputFileName == 'gff': + -f gff + #elif $formatType.FormatInputFileName == 'gff2': + -f gff2 + #elif $formatType.FormatInputFileName == 'gff3': + -f gff3 + #elif $formatType.FormatInputFileName == 'sam': + -f sam + #elif $formatType.FormatInputFileName == 'gtf': + -f gtf + #end if + + #if $OptionChrom.Chrom == "Yes": + -c $OptionChrom.ChromName + #end if + + #if $OptionStart.start == "Yes": + -s $OptionStart.startValue + #end if + + #if $OptionEnd.end == "Yes": + -e $OptionEnd.endValue + #end if + + -o $outputFile + + </command> + + + <inputs> + <conditional name="formatType"> + <param name="FormatInputFileName" type="select" label="Input File Format"> + <option value="bed">bed</option> + <option value="gff">gff</option> + <option value="gff2">gff2</option> + <option value="gff3">gff3</option> + <option value="sam">sam</option> + <option value="gtf">gtf</option> + </param> + <when value="bed"> + <param name="inputFileName" format="bed" type="data" label="Input File"/> + </when> + <when value="gff"> + <param name="inputFileName" format="gff" type="data" label="Input File"/> + </when> + <when value="gff2"> + <param name="inputFileName" format="gff2" type="data" label="Input File"/> + </when> + <when value="gff3"> + <param name="inputFileName" format="gff3" type="data" label="Input File"/> + </when> + <when value="sam"> + <param name="inputFileName" format="sam" type="data" label="Input File"/> + </when> + <when value="gtf"> + <param name="inputFileName" format="gtf" type="data" label="Input File"/> + </when> + </conditional> + + <conditional name="OptionChrom"> + <param name="Chrom" type="select" label="chromosome name"> + <option value="Yes">Yes</option> + <option value="No" selected="true">No</option> + </param> + <when value="Yes"> + <param name="ChromName" type="text" value="None"/> + </when> + <when value="No"> + </when> + </conditional> + + <conditional name="OptionStart"> + <param name="start" type="select" label="start region of the locus"> + <option value="Yes">Yes</option> + <option value="No" selected="true">No</option> + </param> + <when value="Yes"> + <param name="startValue" type="integer" value="0"/> + </when> + <when value="No"> + </when> + </conditional> + + <conditional name="OptionEnd"> + <param name="end" type="select" label="end region of the locus"> + <option value="Yes">Yes</option> + <option value="No" selected="true">No</option> + </param> + <when value="Yes"> + <param name="endValue" type="integer" value="0"/> + </when> + <when value="No"> + </when> + </conditional> + </inputs> + + <outputs> + <data format="gff3" name="outputFile" label="[restrict transcript list] output file"/> + </outputs> + + <help> +Reads a list of genomic coordinates and outputs those which on a given chromosome and / or between two given positions. + </help> +<tests> + <test> + <param name="FormatInputFileName" value="gtf" /> + <param name="inputFileName" value="genes.gtf" /> + <param name="Chrom" value="Yes"/> + <param name="ChromName" value="I"/> + <param name="start" value="No" /> +<param name="end" value="No" /> + <output name="outputFile" file="exp_restrictTranscriptList.gff3" /> + </test> + </tests> + +</tool>