| Previous changeset 16:6135c3075bc5 (2013-04-22) Next changeset 18:94ab73e8a190 (2013-04-29) |
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Commit message:
Deleted selected files |
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removed:
SMART/galaxy/cleanGff.xml SMART/galaxy/clusterize.xml SMART/galaxy/getSequence.xml |
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| diff -r 6135c3075bc5 -r b0e8584489e6 SMART/galaxy/cleanGff.xml --- a/SMART/galaxy/cleanGff.xml Mon Apr 22 11:09:41 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,21 +0,0 @@ -<tool id="cleanGff" name="clean Gff"> - <description>Clean a GFF file (e.g. as given by NCBI) and produces a new GFF3 file, understood by S-MART.</description> - <command interpreter="python"> ../Java/Python/cleanGff.py -i $inputFile - -t $type - -o $outputFile - </command> - - <inputs> - <param name="inputFile" type="data" label="Input File" format="gff"/> - <param name="type" type="text" value="tRNA,rRNA,ncRNA,CDS" label="Tags you keep" help="lists of comma separated types that you want to keep, e.g. ncRNA,tRNA,rRNA,CDS"/> - </inputs> - - <outputs> - <data format="gff3" name="outputFile" label="[cleanGff] Output File"/> - </outputs> - - <help> - A GFF file (please consult http://www.sequenceontology.org/gff3.shtml to know more about it) may contain different sources of information: chromosome size, genes, transcripts, etc. S-MART mostly works on transcripts. This scripts filters the input GFF3 to keep the information you really want, based on the feature (3rd column). - </help> -</tool> - |
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| diff -r 6135c3075bc5 -r b0e8584489e6 SMART/galaxy/clusterize.xml --- a/SMART/galaxy/clusterize.xml Mon Apr 22 11:09:41 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,57 +0,0 @@ -<tool id="MergingDataClusterize" name="Clusterize"> - <description>Clusterize features when their genomic intervals overlap.</description> - <command interpreter="python"> - ../Java/Python/clusterize.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 - #end if - -o $outputFileGff - $colinear - $normalize - -d $distance - $log $outputFileLog - </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> - </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> - </conditional> - - <param name="colinear" type="boolean" truevalue="-c" falsevalue="" checked="false" label="Only merge collinear data"/> - <param name="normalize" type="boolean" truevalue="-n" falsevalue="" checked="false" label="Normalize data." help="This only works if the tag nbOccurrences is set."/> - <param name="distance" type="integer" value="0" label="Merge features if their relative distance is withing N nt"/> - </inputs> - - <outputs> - <data name="outputFileGff" format="gff3" label="[clusterize]output file"/> - </outputs> -</tool> |
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| diff -r 6135c3075bc5 -r b0e8584489e6 SMART/galaxy/getSequence.xml --- a/SMART/galaxy/getSequence.xml Mon Apr 22 11:09:41 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,21 +0,0 @@ -<tool id="getSequence" name="get sequence"> - <description>Get a single sequence in a FASTA file.</description> - <command interpreter="python"> ../Java/Python/getSequence.py -i $inputFile - -n $name - -o $outputFile - - </command> - - - <inputs> - <param name="inputFile" type="data" label="Input fasta File" format="fasta"/> - <param name="name" type="text" value="None" label="name of the sequence [compulsory option]"/> - </inputs> - - <outputs> - <data format="fasta" name="outputFile" label="[getSequence] Output File"/> - </outputs> - - <help> - </help> -</tool> |