Mercurial > repos > bgruening > deeptools_bam_compare
changeset 22:59cbb059cd1e draft
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d
| author | bgruening |
|---|---|
| date | Tue, 19 Feb 2019 10:03:16 -0500 |
| parents | e4287c038599 |
| children | c09c23eaf116 |
| files | bamCompare.xml deepTools_macros.xml repository_dependencies.xml |
| diffstat | 3 files changed, 60 insertions(+), 7 deletions(-) [+] |
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--- a/bamCompare.xml Wed Aug 22 17:14:20 2018 -0400 +++ b/bamCompare.xml Tue Feb 19 10:03:16 2019 -0500 @@ -63,6 +63,7 @@ @ADVANCED_OPTS_READ_PROCESSING@ $advancedOpt.skipNAs + $advancedOpt.skipZeroOverZero #if str($advancedOpt.ignoreForNormalization).strip() != '': --ignoreForNormalization '$advancedOpt.ignoreForNormalization' @@ -163,6 +164,11 @@ <expand macro="read_processing_options" /> <expand macro="skipNAs" /> + <param argument="--skipZeroOverZero" type="select" label="Skip bins of no coverage" + help="Skip bins where BOTH files lack coverage."> + <option value="no" selected="true">No</option> + <option value="yes">Yes, skip them.</option> + </param> <param argument="--ignoreForNormalization" type="text" value="" size="50" label="regions that should be excluded for calculating the scaling factor"
--- a/deepTools_macros.xml Wed Aug 22 17:14:20 2018 -0400 +++ b/deepTools_macros.xml Tue Feb 19 10:03:16 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/repository_dependencies.xml Wed Aug 22 17:14:20 2018 -0400 +++ b/repository_dependencies.xml Tue Feb 19 10:03:16 2019 -0500 @@ -1,4 +1,4 @@ -<?xml version="1.0"?> +<?xml version="1.0" ?> <repositories> - <repository changeset_revision="9946bc39c834" name="data_manager_twobit_builder" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> -</repositories> + <repository changeset_revision="9946bc39c834" name="data_manager_twobit_builder" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu"/> +</repositories> \ No newline at end of file