Mercurial > repos > bgruening > deeptools_plot_pca
changeset 3:1f9a7501bd38 draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f
| author | bgruening |
|---|---|
| date | Mon, 21 Dec 2015 07:25:04 -0500 |
| parents | 828ecc09ca38 |
| children | cc4f39428bdf |
| files | deepTools_macros.xml plotPCA.xml test-data/plotCorrelation_result2.png |
| diffstat | 3 files changed, 51 insertions(+), 35 deletions(-) [+] |
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--- a/deepTools_macros.xml Fri Dec 18 12:28:44 2015 -0500 +++ b/deepTools_macros.xml Mon Dec 21 07:25:04 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>
--- a/plotPCA.xml Fri Dec 18 12:28:44 2015 -0500 +++ b/plotPCA.xml Mon Dec 21 07:25:04 2015 -0500 @@ -16,18 +16,18 @@ </command> <inputs> <param name="corData" format="deeptools_coverage_matrix" type="data" label="Matrix file from the bamCorrelate tool"/> - <expand macro="image_file_format" /> + <expand macro="input_image_file_format" /> <expand macro="plotTitle" /> </inputs> <outputs> - <expand macro="output_image_file_format" /> + <expand macro="output_image_file_format_not_nested" /> </outputs> <tests> <test> <param name="corData" value="bamCorrelate_result2.npz" ftype="deeptools_coverage_matrix" /> <param name="plotTitle" value="Test Plot" /> <param name="outFileFormat" value="png" /> - <output name="outFileName" file="plotPCA_result1.png" compare="sim_size" delta="100" /> + <output name="outFileName" file="plotPCA_result1.png" ftpye="png" compare="sim_size" delta="100" /> </test> </tests> <help>