Mercurial > repos > bgruening > deeptools
changeset 9:c53a73b8eef9 draft
Uploaded
| author | bgruening |
|---|---|
| date | Tue, 10 Dec 2013 12:13:18 -0500 |
| parents | 1c5ed9126db6 |
| children | 135f3bae5c56 |
| files | bamCompare.xml bamCoverage.xml bigwigCompare.xml computeGCBias.xml computeMatrix.xml correctGCBias.xml deepTools_macros.xml tool_dependencies.xml |
| diffstat | 8 files changed, 61 insertions(+), 34 deletions(-) [+] |
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--- a/bamCompare.xml Wed Dec 04 05:50:46 2013 -0500 +++ b/bamCompare.xml Tue Dec 10 12:13:18 2013 -0500 @@ -70,7 +70,7 @@ <param name="bamFile1" format="bam" type="data" label="Treatment BAM file" help="The BAM file must be sorted."/> - <param name="bamFile2" format="bam" type="data" label="Input BAM file" + <param name="bamFile2" format="bam" type="data" label="BAM file" help="The BAM file must be sorted."/> <param name="fragmentLength" type="integer" value="300" min="1"
--- a/bamCoverage.xml Wed Dec 04 05:50:46 2013 -0500 +++ b/bamCoverage.xml Tue Dec 10 12:13:18 2013 -0500 @@ -48,7 +48,7 @@ </command> <inputs> - <param name="bamInput" format="bam" type="data" label="Input BAM file" + <param name="bamInput" format="bam" type="data" label="BAM file" help="The BAM file must be sorted."/> <param name="fragmentLength" type="integer" value="300" min="1"
--- a/bigwigCompare.xml Wed Dec 04 05:50:46 2013 -0500 +++ b/bigwigCompare.xml Tue Dec 10 12:13:18 2013 -0500 @@ -35,7 +35,7 @@ </stdio> <inputs> <param name="bigwigFile1" format="bigwig" type="data" label="Treatment bigwig file" /> - <param name="bigwigFile2" format="bigwig" type="data" label="Input bigwig file" /> + <param name="bigwigFile2" format="bigwig" type="data" label="bigWig file" /> <param name="comparison_type" type="select" label="How to compare the two files"
--- a/computeGCBias.xml Wed Dec 04 05:50:46 2013 -0500 +++ b/computeGCBias.xml Tue Dec 10 12:13:18 2013 -0500 @@ -58,7 +58,7 @@ </command> <inputs> - <param name="bamInput" format="bam" type="data" label="Input BAM file" + <param name="bamInput" format="bam" type="data" label="BAM file" help="The BAM file must be sorted."/> <expand macro="reference_genome_source" />
--- a/computeMatrix.xml Wed Dec 04 05:50:46 2013 -0500 +++ b/computeMatrix.xml Tue Dec 10 12:13:18 2013 -0500 @@ -115,10 +115,11 @@ <when value="reference-point"> <param name="referencePoint" type="select" label="The reference point for the plotting"> - <option value="TSS" selected="true">region start (TSS)</option> - <option value="TES" selected="true">region end (TES)</option> - <option value="center" selected="true">center of the region</option> + <option value="TSS" selected="true">beginning of region (e.g. TSS)</option> + <option value="TES">end of region (e.g. TES)</option> + <option value="center">center of region</option> </param> + <param name="nanAfterEnd" type="boolean" truevalue="--nanAfterEnd" falsevalue="" label="Discard any values after the region end" help="This is useful to visualize the region end when not using the scale-regions mode and when the reference-point is set to the TSS."/> <param name="beforeRegionStartLength" type="integer" value="1000" min="1" label="Distance upstream of the start site of the regions defined in the region file" help="If the regions are genes, this would be the distance upstream of the transcription start site."/> @@ -128,15 +129,15 @@ <conditional name="output" > <param name="showOutputSettings" type="select" label="Show additional output options" > - <option value="no" selected="true">no</option> - <option value="yes">yes</option> - </param> - <when value="no" /> - <when value="yes"> - <param name="saveData" type="boolean" label="Save the averages per matrix column into a text file" help="This corresponds to the underlying data used to plot a summary profile."/> - <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap" help="This matrix can easily be loaded into R or other programs."/> - <param name="saveSortedRegions" type="boolean" label="Save the regions after skiping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/> - </when> + <option value="no" selected="true">no</option> + <option value="yes">yes</option> + </param> + <when value="no" /> + <when value="yes"> + <param name="saveData" type="boolean" label="Save the averages per matrix column into a text file" help="This corresponds to the underlying data used to plot a summary profile."/> + <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap" help="This matrix can easily be loaded into R or other programs."/> + <param name="saveSortedRegions" type="boolean" label="Save the regions after skiping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/> + </when> </conditional> <conditional name="advancedOpt" > @@ -182,17 +183,32 @@ </inputs> <outputs> - <data format="bgzip" name="outFileName" label="${tool.name} on ${on_string}: matrix"> + <data format="bgzip" name="outFileName" label="${tool.name} on ${on_string}: Matrix"> </data> - <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: raw data"> - <filter>(output['showOutputSettings'] == 'yes' and output['saveData'] == True)</filter> + <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column"> + <filter> + (( + output['showOutputSettings'] == 'yes' and + output['saveData'] is True + )) + </filter> </data> - <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: matrix of values"> - <filter>(output['showOutputSettings'] == 'yes' and output['saveMatrix'] == True)</filter> + <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values"> + <filter> + (( + output['showOutputSettings'] == 'yes' and + output['saveMatrix'] is True + )) + </filter> </data> <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions"> - <filter>(output['showOutputSettings'] == 'yes' and output['saveSortedRegions'] == True)</filter> - </data> + <filter> + (( + output['showOutputSettings'] == 'yes' and + output['saveSortedRegions'] is True + )) + </filter> + </data> </outputs> <!-- computeMatrix -S test.bw -R test2.bed -a 100 -b 100 -bs 1
--- a/correctGCBias.xml Wed Dec 04 05:50:46 2013 -0500 +++ b/correctGCBias.xml Tue Dec 10 12:13:18 2013 -0500 @@ -50,7 +50,7 @@ <param name="GCbiasFrequenciesFile" type="data" format="tabular" label="Output of computeGCBias" /> - <param name="bamInput" format="bam" type="data" label="Input BAM file" help="This should be same file that was used for computeGCbias. The BAM file must be sorted."/> + <param name="bamInput" format="bam" type="data" label="BAM file" help="This should be same file that was used for computeGCbias. The BAM file must be sorted."/> <expand macro="reference_genome_source" /> <expand macro="effectiveGenomeSize" />
--- a/deepTools_macros.xml Wed Dec 04 05:50:46 2013 -0500 +++ b/deepTools_macros.xml Tue Dec 10 12:13:18 2013 -0500 @@ -43,11 +43,13 @@ <requirement type="package" >samtools</requirement> <requirement type="package" >deepTools</requirement> <requirement type="package" >ucsc_tools</requirement> - <requirement type="package" version="1.5.1_323fa6bf083c9d40e5092a6364a4ab8fee57507a">deepTools</requirement> + <requirement type="package" version="1.5.4_fada41ab04f78c4c78d10c7a216e5c3160e8c36e">deepTools</requirement> <requirement type="package" version="0.1">ucsc_tools</requirement> <requirement type="package" version="1.7.1">numpy</requirement> <requirement type="package" version="0.7.7">pysam</requirement> + <requirement type="package" version="1.2.1">matplotlib</requirement> <requirement type="package" version="0.1.19">samtools</requirement> + <requirement type="package" version="12-2013">bx-python</requirement> <yield /> </requirements> </macro> @@ -68,7 +70,7 @@ </token> <macro name="multiple_input_bams"> - <repeat name="input_files" title="Input files" min="2"> + <repeat name="input_files" title="BAM files" min="2"> <param name="bamfile" type="data" format="bam" label="Bam file" help="The BAM file must be sorted."/>
--- a/tool_dependencies.xml Wed Dec 04 05:50:46 2013 -0500 +++ b/tool_dependencies.xml Tue Dec 10 12:13:18 2013 -0500 @@ -1,19 +1,22 @@ <?xml version="1.0"?> <tool_dependency> <package name="samtools" version="0.1.19"> - <repository changeset_revision="00e17a794a2e" name="package_samtools_0_1_19" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="00e17a794a2e" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> <package name="numpy" version="1.7.1"> - <repository changeset_revision="796c0081adad" name="package_numpy_1_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="796c0081adad" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> <package name="matplotlib" version="1.2.1"> - <repository changeset_revision="9d164359606b" name="package_matplotlib_1_2" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="9d164359606b" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> <package name="scipy" version="0.12.0"> - <repository changeset_revision="d277bf006c3e" name="package_scipy_0_12" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="d277bf006c3e" name="package_scipy_0_12" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> <package name="pysam" version="0.7.7"> - <repository changeset_revision="b62538c8c664" name="package_pysam_0_7_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="b62538c8c664" name="package_pysam_0_7_7" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + <package name="bx-python" version="12-2013"> + <repository changeset_revision="f938170835cc" name="package_bx_python_12_2013" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> <package name="ucsc_tools" version="0.1"> @@ -54,7 +57,7 @@ <readme>The tools downloaded by this dependency definition are free for academic use. TODO: UCSC tools are only available with their latest version. That is not good for reproducibility.</readme> </package> - <package name="deepTools" version="1.5.1_323fa6bf083c9d40e5092a6364a4ab8fee57507a"> + <package name="deepTools" version="1.5.4_fada41ab04f78c4c78d10c7a216e5c3160e8c36e"> <install version="1.0"> <actions> <action type="shell_command">git clone --recursive https://github.com/fidelram/deepTools.git</action> @@ -63,8 +66,11 @@ <repository changeset_revision="b62538c8c664" name="package_pysam_0_7_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu"> <package name="pysam" version="0.7.7" /> </repository> + <repository changeset_revision="f938170835cc" name="package_bx_python_12_2013" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu"> + <package name="bx-python" version="12-2013" /> + </repository> </action> - <action type="shell_command">git reset --hard 323fa6bf083c9d40e5092a6364a4ab8fee57507a</action> + <action type="shell_command">git reset --hard fada41ab04f78c4c78d10c7a216e5c3160e8c36e</action> <action type="make_directory">$INSTALL_DIR/lib/python</action> <action type="shell_command"> export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && @@ -78,6 +84,9 @@ </action> </actions> </install> - <readme>Installation of deepTools from Fidel Ramirez.</readme> + <readme> + Installation of deepTools from Fidel Ramirez. + https://github.com/fidelram/deepTools + </readme> </package> </tool_dependency>