Mercurial > repos > yufei-luo > s_mart
view SMART/galaxy/SelectByTag.xml @ 45:e454402ba9d9
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author | m-zytnicki |
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date | Wed, 18 Sep 2013 08:51:22 -0400 |
parents | 2c0c0a89fad7 |
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<tool id="SelectByTag" name="select by tag"> <description>Keep the genomic coordinates such that a value of a given tag.</description> <requirements> <requirement type="set_environment">PYTHONPATH</requirement> </requirements> <command interpreter="python"> ../Java/Python/SelectByTag.py -i $formatType.inputFileName #if $formatType.FormatInputFileName == 'gff': -f gff #elif $formatType.FormatInputFileName == 'gff2': -f gff2 #elif $formatType.FormatInputFileName == 'gff3': -f gff3 #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="gff">gff</option> <option value="gff2">gff2</option> <option value="gff3">gff3</option> <option value="gtf">gtf</option> </param> <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="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="given value for the tag"> <option value="Yes">Yes</option> <option value="No" selected="true">No</option> </param> <when value="Yes"> <param name="valeur" type="integer" value="1"/> </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"/> </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"/> </when> <when value="No"> </when> </conditional> <conditional name="OptionDefault"> <param name="default" type="select" label="give 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="[select by tag] output file"/> </outputs> <help> The script reads a list of genomic coordinates and output all the features with specific tag values. If you want to know more about tags, please consult the GFF format page: http://www.sequenceontology.org/gff3.shtml The tools reads the input file, and more specifically the tag that you specified. You can mention a lower and a upper bound for its value, or a specific value, and the tool will print all the features such that the tags are between the specified bounds or matches the string. A tag has to be present for each feature. If not, you can specify a default value which will be used if the tag is absent. This tool can be used to select the clusters with a minimum number of elements (the tag **nbElements** counts the number of elements per clusters) or to select the reads which have mapped less than *n* times (the tag **nbOccurrences** counts the number of mappings per read). </help> </tool>