Mercurial > repos > bgruening > deeptools_plot_heatmap
changeset 38:375e7508e571 draft
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d
| author | bgruening |
|---|---|
| date | Tue, 19 Feb 2019 04:34:43 -0500 |
| parents | 7d1521817494 |
| children | d2865b310365 |
| files | deepTools_macros.xml plotHeatmap.xml repository_dependencies.xml |
| diffstat | 3 files changed, 68 insertions(+), 11 deletions(-) [+] |
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--- a/deepTools_macros.xml Thu Aug 23 04:03:11 2018 -0400 +++ b/deepTools_macros.xml Tue Feb 19 04:34:43 2019 -0500 @@ -1,11 +1,11 @@ <macros> <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token> - <token name="@WRAPPER_VERSION@">3.1.2.0</token> + <token name="@WRAPPER_VERSION@">3.2.0.0</token> <xml name="requirements"> <requirements> - <requirement type="package" version="3.1.2">deeptools</requirement> - <requirement type="package" version="1.7">samtools</requirement> + <requirement type="package" version="3.2.0">deeptools</requirement> + <requirement type="package" version="1.9">samtools</requirement> </requirements> <expand macro="stdio" /> <version_command>@BINARY@ --version</version_command> @@ -359,7 +359,7 @@ </xml> <xml name="pseudocount"> - <param argument="--pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/> + <param argument="--pseudocount" type="text" value="1 1" label="Pseudocount" help="Small number to avoid dividing by zero. You can specify separate values for the pseudocount added to the numerator and denominator by providing two values separated by a space."/> </xml> <token name="@REFERENCES@"> @@ -423,12 +423,47 @@ </conditional> </xml> + <xml name="custom_sample_labels"> + <conditional name="custom_sample_labels_conditional"> + <param name="custom_labels_select" type="select" label="Would you like custom sample labels?" help="By default, the names of the samples in your history are used."> + <option value="No" selected="true">No, use sample names in the history</option> + <option value="Yes">Yes, I want to specify new labels</option> + </param> + <when value="No"> + </when> + <when value="Yes"> + <param argument="--labels" type="text" label="Sample Labels" help="Labels, separated by a space. If your labels themselves contain spaces then please enclose them in quotes (e.g., "sample 1" "sample 2")"> + <sanitizer> + <valid initial="string.printable"> + </valid> + </sanitizer> + </param> + </when> + </conditional> + </xml> + <xml name="plotTitle"> <param argument="--plotTitle" type="text" value="" size="30" optional="True" label="Title of the plot" help="Title of the plot, to be printed on top of the generated image." /> </xml> + <xml name="legendLocation"> + <param argument="--legendLocation" type="select" label="Legend location" help="Location for the legend in the summary plot. Note that none cannot be used in plotProfile."> + <option value="best" selected="true">Best (automatic)</option> + <option value="upper-right">upper-right</option> + <option value="upper-left">upper-left</option> + <option value="upper-center">upper-center</option> + <option value="lower-right">lower-right</option> + <option value="lower-left">lower-left</option> + <option value="lower-center">lower-center</option> + <option value="center-right">center-right</option> + <option value="center-left">center-left</option> + <option value="center">center</option> + <option value="none">none (only works for heatmaps</option> + </param> + </xml> + <xml name="labelRotation"> <param argument="--labelRotation" type="integer" value="0" label="Rotation of the X-axis labels (in degrees)" @@ -438,6 +473,9 @@ <token name="@multiple_input_bams@"> <![CDATA[ + #if $custom_sample_labels_conditional.custom_labels_select == "Yes": + #set custom_labels=labels + #end if #set files=[] #set labels=[] #import re @@ -466,11 +504,17 @@ #silent $labels.append("'%s'" % $identifier) #end for #end if + #if $custom_sample_labels_conditional.custom_labels_select == "Yes": + #set labels=custom_labels + #end if ]]> </token> <token name="@multiple_input_bigwigs@"> <![CDATA[ + #if $custom_labels_conditional.custom_labels_select == "Yes": + #set custom_labels=labels + #end if #set files=[] #set labels=[] #import re @@ -489,6 +533,9 @@ #silent $labels.append("'%s'" % $identifier) #end for #end if + #if $custom_labels_conditional.custom_labels_select == "Yes": + #set labels=custom_labels + #end if ]]> </token>
--- a/plotHeatmap.xml Thu Aug 23 04:03:11 2018 -0400 +++ b/plotHeatmap.xml Tue Feb 19 04:34:43 2019 -0500 @@ -1,4 +1,4 @@ -<tool id="deeptools_plot_heatmap" name="plotHeatmap" version="@WRAPPER_VERSION@.0" profile="18.01"> +<tool id="deeptools_plot_heatmap" name="plotHeatmap" version="@WRAPPER_VERSION@.1" profile="18.01"> <description>creates a heatmap for score distributions across genomic regions</description> <macros> <token name="@BINARY@">plotHeatmap</token> @@ -42,6 +42,8 @@ --averageTypeSummaryPlot '$advancedOpt.averageTypeSummaryPlot' #end if + --plotType '$advancedOpt.plotType' + #if str($advancedOpt.missingDataColor.value) != "None": --missingDataColor '$advancedOpt.missingDataColor' #end if @@ -87,17 +89,19 @@ --refPointLabel '$advancedOpt.referencePointLabel' #if $advancedOpt.samplesLabel and str($advancedOpt.samplesLabel).strip() != "": - --samplesLabel '$advancedOpt.samplesLabel' + --samplesLabel $advancedOpt.samplesLabel #end if #if $advancedOpt.regionsLabel and str($advancedOpt.regionsLabel).strip() != "": - --regionsLabel '$advancedOpt.regionsLabel' + --regionsLabel $advancedOpt.regionsLabel #end if #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "": --plotTitle '$advancedOpt.plotTitle' #end if + --legendLocation '$advancedOpt.legendLocation' + --labelRotation '$advancedOpt.labelRotation' $advancedOpt.perGroup @@ -136,7 +140,12 @@ <option value="sum">sum</option> <option value="std">std</option> </param> - + <param argument="--plotType" type="select" label="Type of summary plot"> + <option value="lines">plot the profile line based on the statistic selected above.</option> + <option value="fill">fills the region between zero and the profile.</option> + <option value="se">color the region between the profile and the standard error.</option> + <option value="std">color the region between the profile and the standard deviation.</option> + </param> <param argument="--missingDataColor" type="text" value="black" optional="true" label="Missing data color" help="If 'Represent missing data as zero' is not set, such cases will be colored in black by default. By using this parameter a different color can be set. A value between 0 and 1 will be used for a gray scale (black is 0). @@ -206,6 +215,7 @@ For example, label_1 "label 2"" /> <expand macro="plotTitle" /> + <expand macro="legendLocation" /> <expand macro="labelRotation" /> <param argument="--perGroup" type="boolean" truevalue="--perGroup" falsevalue="" label="Make one plot per group of regions"
--- a/repository_dependencies.xml Thu Aug 23 04:03:11 2018 -0400 +++ b/repository_dependencies.xml Tue Feb 19 04:34:43 2019 -0500 @@ -1,4 +1,4 @@ -<?xml version="1.0"?> +<?xml version="1.0" ?> <repositories> - <repository changeset_revision="fced964b054a" name="data_manager_twobit_builder" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" /> -</repositories> + <repository changeset_revision="fced964b054a" name="data_manager_twobit_builder" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu"/> +</repositories> \ No newline at end of file