Mercurial > repos > yufei-luo > s_mart
diff SMART/galaxy/SelectByTag.xml @ 31:0ab839023fe4
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author | m-zytnicki |
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date | Tue, 30 Apr 2013 14:33:21 -0400 |
parents | 94ab73e8a190 |
children |
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--- a/SMART/galaxy/SelectByTag.xml Mon Apr 29 03:45:52 2013 -0400 +++ b/SMART/galaxy/SelectByTag.xml Tue Apr 30 14:33:21 2013 -0400 @@ -1,16 +1,17 @@ <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> + <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 @@ -36,11 +37,16 @@ <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> @@ -50,6 +56,9 @@ <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> @@ -58,12 +67,12 @@ <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"> + <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"/> + <param name="valeur" type="integer" value="1" help="Be Careful! The value must be upper than 0"/> </when> <when value="No"> </when> @@ -75,7 +84,7 @@ <option value="No" selected="true">No</option> </param> <when value="Yes"> - <param name="max" type="integer" value="1"/> + <param name="max" type="integer" value="1" help="Be Careful! The value must be upper than 0"/> </when> <when value="No"> </when> @@ -87,14 +96,14 @@ <option value="No" selected="true">No</option> </param> <when value="Yes"> - <param name="min" type="integer" value="1"/> + <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="give this value if tag is not present"> + <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> @@ -107,16 +116,7 @@ </inputs> <outputs> - <data name="outputFileGff" format="gff3" label="[select by tag] output file"/> + <data name="outputFileGff" format="gff3" label="[SelectByTag] 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>