Mercurial > repos > bgruening > deeptools_bigwig_correlate
changeset 4:40f1c9035551 draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f
| author | bgruening |
|---|---|
| date | Mon, 21 Dec 2015 07:23:17 -0500 |
| parents | 44389875efe3 |
| children | bdd6ace83c80 |
| files | bigwigCorrelate.xml deepTools_macros.xml test-data/plotCorrelation_result2.png |
| diffstat | 3 files changed, 49 insertions(+), 33 deletions(-) [+] |
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--- a/bigwigCorrelate.xml Fri Dec 18 12:22:46 2015 -0500 +++ b/bigwigCorrelate.xml Mon Dec 21 07:23:17 2015 -0500 @@ -46,7 +46,7 @@ help="In the bins mode, the correlation is computed based on equal length bins. In the BED file mode, as list of genomic regions in BED format has to be given. For each region in the BED file the number of overlapping reads is counted in - each of the BAM files. Then the correlation is computed."> + each of the BigWig files. Then the correlation is computed."> <option value="bins" selected="true">Bins</option> <option value="BED-file">Limit correlation to certain regions (BED file)</option> </param>
--- a/deepTools_macros.xml Fri Dec 18 12:22:46 2015 -0500 +++ b/deepTools_macros.xml Mon Dec 21 07:23:17 2015 -0500 @@ -14,7 +14,11 @@ </xml> <token name="@ADVANCED_OPTS_READ_PROCESSING@"> - --extendReads $advancedOpt.extendReads + #if $advancedOpt.doExtendCustom.doExtend == 'custom': + --extendReads $advancedOpt.doExtendCustom.extendReadsValue + #else if $advancedOpt.doExtendCustom.doExtend == 'yes': + --extendReads + #end if $advancedOpt.ignoreDuplicates $advancedOpt.centerReads #if $advancedOpt.minMappingQuality: @@ -36,15 +40,15 @@ </xml> <token name="@HEATMAP_OPTIONS@"> - #if $zMin: - --zMin $zMin + #if $plotting_type.zMin: + --zMin $plotting_type.zMin #end if - #if $zMax: - --zMax $zMax + #if $plotting_type.zMax: + --zMax $plotting_type.zMax #end if - --colorMap '$colorMap' - $plotNumbers - --plotTitle $plotTitle + --colorMap '$plotting_type.colorMap' + $plotting_type.plotNumbers + --plotTitle '$plotting_type.plotTitle' </token> @@ -55,9 +59,9 @@ </xml> <xml name="zMin_zMax"> - <param argument="--zMin" type="integer" value="" optional="true" label="Minimum value for the heatmap intensities" + <param argument="--zMin" type="float" value="" optional="true" label="Minimum value for the heatmap intensities" help="If not specified the value is set automatically."/> - <param argument="--zMax" type="integer" value="" optional="true" label="Maximum value for the heatmap intensities" + <param argument="--zMax" type="float" value="" optional="true" label="Maximum value for the heatmap intensities" help="If not specified the value is set automatically."/> </xml> @@ -146,14 +150,26 @@ </xml> <xml name="extendReads"> - <param argument="--extendReads" type="integer" value="" optional="True" - label="Extend reads to the given average fragment size" - help="(1) Single-end reads and singletons are extended to match this length. (2) Paired-end reads are extended to match the fragment size, regardless of what is set here. - By default *each* read mate is extended. - This can be modified using the SAM flags (see --samFlagInclude and --samFlagExclude options) to keep only the first or the second mate. - Unmated reads, mate reads that map on different chromosomes or too far apart are extended to the given value. - Reads are only extended if --extendReads is set to a value greater than the read length. *NOTE*: For spliced-read data, this option is not - recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data."/> + <conditional name="doExtendCustom"> + <param name="doExtend" type="select" label="Extend reads to the given average fragment size." + help="(1) Single-end reads and singletons are extended to match this length. (2) Paired-end reads are extended to match the fragment size, regardless of what is set here. + By default *each* read mate is extended. + This can be modified using the SAM flags (see --samFlagInclude and --samFlagExclude options) to keep only the first or the second mate. + Unmated reads, mate reads that map on different chromosomes or too far apart are extended to the given value. + Reads are only extended if --extendReads is set to a value greater than the read length. *NOTE*: For spliced-read data, this option is not + recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data."> + <option value="no" selected="True">No extension. The default value and most typically appropriate.</option> + <option value="yes">Paired-end extension. Suitable only for paired-end datasets.</option> + <option value="custom">A custom length, which will be applied to ALL reads.</option> + </param> + <when value="no" /> + <when value="yes" /> + <when value="custom"> + <param name="extendReadsValue" type="integer" value="300" min="1" + label="Extend reads to the given average fragment size" + help="Extend all reads to this length" /> + </when> + </conditional> </xml> <xml name="corMethod"> @@ -274,13 +290,13 @@ </xml> <xml name="multiple_input_bams"> - <param argument="--bamfiles" type="data" format="bam" + <param argument="--bamfiles" type="data" format="bam" min="2" label="Bam file" multiple="true" help="The BAM file must be sorted."/> </xml> <xml name="multiple_input_bigwigs"> - <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" + <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="2" label="Bigwig file" help="The Bigwig file must be sorted."/> </xml> @@ -366,15 +382,6 @@ </conditional> </xml> - <xml name="image_file_format"> - <param argument="--outFileFormat" type="select" label="Image file format"> - <option value="png" selected="true">png</option> - <option value="pdf">pdf</option> - <option value="svg">svg</option> - <option value="eps">eps</option> - </param> - </xml> - <xml name="skipNAs"> <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False" label="Ignore missing data?" @@ -407,13 +414,13 @@ </conditional> </xml> + <xml name="input_image_file_format"> - <param name="outFileFormat" type="select" label="Image file format"> + <param argument="--outFileFormat" type="select" label="Image file format"> <option value="png" selected="true">png</option> <option value="pdf">pdf</option> <option value="svg">svg</option> <option value="eps">eps</option> - <option value="emf">emf</option> </param> </xml> @@ -423,7 +430,16 @@ <when input="output.outFileFormat" value="pdf" format="pdf" /> <when input="output.outFileFormat" value="svg" format="svg" /> <when input="output.outFileFormat" value="eps" format="eps" /> - <when input="output.outFileFormat" value="emf" format="emf" /> + </change_format> + </data> + </xml> + + <xml name="output_image_file_format_not_nested"> + <data format="png" name="outFileName" label="${tool.name} image"> + <change_format> + <when input="outFileFormat" value="pdf" format="pdf" /> + <when input="outFileFormat" value="svg" format="svg" /> + <when input="outFileFormat" value="eps" format="eps" /> </change_format> </data> </xml>