Mercurial > repos > yufei-luo > s_mart
view SMART/galaxy/SelectByTag.xml @ 12:5a054da77808
Updated CompareOverlappingSmallRef.xml
author | m-zytnicki |
---|---|
date | Thu, 14 Mar 2013 05:37:35 -0400 |
parents | 769e306b7933 |
children | 440ceca58672 |
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<tool id="SelectByTag" name="select by tag"> <description>Keeps the genomic coordinates such that a value of a given tag.</description> <command interpreter="python"> ../Java/Python/SelectByTag.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 -g $Tag #if $OptionValue.Value == "Yes": -a $OptionValue.valeur #end if #if $OptionMax.maximum == "Yes": -M $OptionMax.max #end if #if $OptionMin.minimum == "Yes": -m $OptionMin.min #end if #if $OptionDefault.default == "Yes": -d $OptionDefault.defaultValue #end if -o $outputFileGff </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> <param name="Tag" type="text" value="None" label="tag option" help="A given tag, you must choose a tag."/> <conditional name="OptionValue"> <param name="Value" type="select" label="value of tag"> <option value="Yes">Yes</option> <option value="No" selected="true">No</option> </param> <when value="Yes"> <param name="valeur" type="integer" value="1" help="Be Careful! The value must be upper than 0"/> </when> <when value="No"> </when> </conditional> <conditional name="OptionMax"> <param name="maximum" type="select" label="maximum value of tag"> <option value="Yes">Yes</option> <option value="No" selected="true">No</option> </param> <when value="Yes"> <param name="max" type="integer" value="1" help="Be Careful! The value must be upper than 0"/> </when> <when value="No"> </when> </conditional> <conditional name="OptionMin"> <param name="minimum" type="select" label="minimum value of tag"> <option value="Yes">Yes</option> <option value="No" selected="true">No</option> </param> <when value="Yes"> <param name="min" type="integer" value="1" help="Be Careful! The value must be upper than 0"/> </when> <when value="No"> </when> </conditional> <conditional name="OptionDefault"> <param name="default" type="select" label="gives this value if tag is not present"> <option value="Yes">Yes</option> <option value="No" selected="true">No</option> </param> <when value="Yes"> <param name="defaultValue" type="float" value="0" /> </when> <when value="No"> </when> </conditional> </inputs> <outputs> <data name="outputFileGff" format="gff3" label="[SelectByTag] Output File"/> </outputs> </tool>