Mercurial > repos > bgruening > deeptools_plot_coverage
diff plotCoverage.xml @ 12:94b05ea80203 draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
| author | bgruening |
|---|---|
| date | Fri, 31 Mar 2017 09:26:58 -0400 |
| parents | 6fc072c36dc9 |
| children | d4fdd10516f6 |
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--- a/plotCoverage.xml Tue Jan 24 04:56:34 2017 -0500 +++ b/plotCoverage.xml Fri Mar 31 09:26:58 2017 -0400 @@ -1,124 +1,124 @@ -<tool id="deeptools_plot_coverage" name="plotCoverage" version="@WRAPPER_VERSION@.0"> - <description>assesses the sequencing depth of BAM files </description> - <macros> - <token name="@BINARY@">plotCoverage</token> - <import>deepTools_macros.xml</import> - </macros> - <expand macro="requirements"/> - <command> -<![CDATA[ - #set files=[] - #set labels=[] - - @multiple_input_bams@ - - @BINARY@ - - @THREADS@ - - --plotFile '$outFileName' - --bamfiles #echo " ".join($files)# - --labels #echo " ".join($labels)# - --plotFileFormat "$outFileFormat" - - #if $outRawCounts: - --outRawCounts '$outFileRawCounts' - #end if - - #if $advancedOpt.showAdvancedOpt == "yes": - --numberOfSamples '$advancedOpt.numberOfSamples' - $advancedOpt.skipZeros - - #if str($advancedOpt.region).strip() != '': - --region '$advancedOpt.region' - #end if - --numberOfSamples $advancedOpt.numberOfSamples - - #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "": - --plotTitle '$advancedOpt.plotTitle' - #end if - @ADVANCED_OPTS_READ_PROCESSING@ - @blacklist@ - #end if - -]]> - </command> - <inputs> - - <expand macro="multiple_input_bams" /> - - <conditional name="advancedOpt"> - <param name="showAdvancedOpt" type="select" label="Show advanced options" > - <option value="no" selected="true">no</option> - <option value="yes">yes</option> - </param> - <when value="no" /> - <when value="yes"> - <param argument="--numberOfSamples" type="integer" value="100000" min="1" - label="Number of samples" - help="Number of samples taken from the genome to compute the scaling factors."/> - <expand macro="region_limit_operation" /> - <expand macro="read_processing_options" /> - <expand macro="skipZeros" /> - <expand macro="plotTitle" /> - <expand macro="blacklist" /> - </when> - </conditional> - - <expand macro="input_image_file_format" /> - <param argument="--outRawCounts" type="boolean" label="Save raw counts (coverages) to a file" help=""/> - - - </inputs> - <outputs> - <expand macro="output_image_file_format_not_nested" /> - <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts"> - <filter>outRawCounts is True</filter> - </data> - </outputs> - <tests> - <test> - <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" /> - <!--param name="outFileFormat" value="png" /--> - <param name="showAdvancedOpt" value="yes" /> - <param name="plotTitle" value="Test Title from Galaxy" /> - <param name="outRawCounts" value="True" /> - <output name="outFileRawCounts" file="plotCoverage_result1.tabular" ftype="tabular" /> - <output name="outFileName" file="plotCoverage_result1.png" ftype="png" compare="sim_size" delta="2400" /> - </test> - </tests> - <help> -<![CDATA[ -What it does -------------- - -This tool is useful to **assess the sequencing depth** of a given sample. -It samples 1 million bp, counts the number of overlapping reads and reports -a coverage histogram that tells you how many bases are covered how many times. - -**Note:** Multiple BAM files are accepted but all should correspond to the same genome assembly. - -Output ---------- - -The default output is a **panel of two plots** (see below for an example): One is a density plot visualizing the frequencies of read coverages, the other one lets you estimate what fraction of the genome has a depth of sequencing of, for example, 2 overlapping reads or more. - -The optional output is a table where each row represents the number of reads overlapping with a sampled bp. - -.. image:: $PATH_TO_IMAGES/plotCoverage_output.png - :width: 600 - :height: 345 - -Example plot ------------------ - -.. image:: $PATH_TO_IMAGES/plotCoverage_annotated.png - :width: 600 - :height: 291 - - -@REFERENCES@ -]]> - </help> - <expand macro="citations" /> -</tool> +<tool id="deeptools_plot_coverage" name="plotCoverage" version="@WRAPPER_VERSION@.0"> + <description>assesses the sequencing depth of BAM files </description> + <macros> + <token name="@BINARY@">plotCoverage</token> + <import>deepTools_macros.xml</import> + </macros> + <expand macro="requirements"/> + <command> +<![CDATA[ + #set files=[] + #set labels=[] + + @multiple_input_bams@ + + @BINARY@ + + @THREADS@ + + --plotFile '$outFileName' + --bamfiles #echo " ".join($files)# + --labels #echo " ".join($labels)# + --plotFileFormat "$outFileFormat" + + #if $outRawCounts: + --outRawCounts '$outFileRawCounts' + #end if + + #if $advancedOpt.showAdvancedOpt == "yes": + --numberOfSamples '$advancedOpt.numberOfSamples' + $advancedOpt.skipZeros + + #if str($advancedOpt.region).strip() != '': + --region '$advancedOpt.region' + #end if + --numberOfSamples $advancedOpt.numberOfSamples + + #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "": + --plotTitle '$advancedOpt.plotTitle' + #end if + @ADVANCED_OPTS_READ_PROCESSING@ + @blacklist@ + #end if + +]]> + </command> + <inputs> + + <expand macro="multiple_input_bams" /> + + <conditional name="advancedOpt"> + <param name="showAdvancedOpt" type="select" label="Show advanced options" > + <option value="no" selected="true">no</option> + <option value="yes">yes</option> + </param> + <when value="no" /> + <when value="yes"> + <param argument="--numberOfSamples" type="integer" value="100000" min="1" + label="Number of samples" + help="Number of samples taken from the genome to compute the scaling factors."/> + <expand macro="region_limit_operation" /> + <expand macro="read_processing_options" /> + <expand macro="skipZeros" /> + <expand macro="plotTitle" /> + <expand macro="blacklist" /> + </when> + </conditional> + + <expand macro="input_image_file_format" /> + <param argument="--outRawCounts" type="boolean" label="Save raw counts (coverages) to a file" help=""/> + + + </inputs> + <outputs> + <expand macro="output_image_file_format_not_nested" /> + <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts"> + <filter>outRawCounts is True</filter> + </data> + </outputs> + <tests> + <test> + <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" /> + <!--param name="outFileFormat" value="png" /--> + <param name="showAdvancedOpt" value="yes" /> + <param name="plotTitle" value="Test Title from Galaxy" /> + <param name="outRawCounts" value="True" /> + <output name="outFileRawCounts" file="plotCoverage_result1.tabular" ftype="tabular" /> + <output name="outFileName" file="plotCoverage_result1.png" ftype="png" compare="sim_size" delta="2400" /> + </test> + </tests> + <help> +<![CDATA[ +What it does +------------- + +This tool is useful to **assess the sequencing depth** of a given sample. +It samples 1 million bp, counts the number of overlapping reads and reports +a coverage histogram that tells you how many bases are covered how many times. + +**Note:** Multiple BAM files are accepted but all should correspond to the same genome assembly. + +Output +--------- + +The default output is a **panel of two plots** (see below for an example): One is a density plot visualizing the frequencies of read coverages, the other one lets you estimate what fraction of the genome has a depth of sequencing of, for example, 2 overlapping reads or more. + +The optional output is a table where each row represents the number of reads overlapping with a sampled bp. + +.. image:: $PATH_TO_IMAGES/plotCoverage_output.png + :width: 600 + :height: 345 + +Example plot +----------------- + +.. image:: $PATH_TO_IMAGES/plotCoverage_annotated.png + :width: 600 + :height: 291 + + +@REFERENCES@ +]]> + </help> + <expand macro="citations" /> +</tool>