Mercurial > repos > bgruening > deeptools_bigwig_compare
diff bigwigCompare.xml @ 0:49a569aecb22 draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
author | bgruening |
---|---|
date | Mon, 25 Jan 2016 20:14:59 -0500 |
parents | |
children | 48f35873bbb1 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bigwigCompare.xml Mon Jan 25 20:14:59 2016 -0500 @@ -0,0 +1,139 @@ +<tool id="deeptools_bigwig_compare" name="bigwigCompare" version="@WRAPPER_VERSION@.0"> + <description>normalizes and compares two bigWig files to obtain the ratio, log2ratio or difference between them</description> + <macros> + <token name="@BINARY@">bigwigCompare</token> + <import>deepTools_macros.xml</import> + </macros> + <expand macro="requirements"/> + <command> +<![CDATA[ + @BINARY@ + @THREADS@ + --bigwig1 '$bigwigFile1' + --bigwig2 '$bigwigFile2' + + --outFileName '$outFileName' + --outFileFormat '$outFileFormat' + + --ratio $comparison.comparison_select + + #if $comparison.comparison_select in ['ratio','log2']: + --pseudocount $comparison.pseudocount + #end if + + #if str($region).strip() != '': + --region '$region' + #end if + + #if $advancedOpt.showAdvancedOpt == "yes": + + $advancedOpt.skipNAs + --scaleFactors '$advancedOpt.scaleFactor1:$advancedOpt.scaleFactor2' + --binSize $advancedOpt.binSize + + #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "": + --plotTitle '$advancedOpt.plotTitle' + #end if + + #end if +]]> + </command> + <inputs> + <param name="bigwigFile1" format="bigwig" type="data" label="Treatment bigwig file" /> + <param name="bigwigFile2" format="bigwig" type="data" label="bigWig file" /> + + <conditional name="comparison"> + <param name="comparison_select" type="select" + label="How to compare the two files" + help="The default is to output the log2ratio between the two samples. + The reciprocal ratio returns the negative of the inverse of the ratio if + the ratio is less than 0. The resulting values are interpreted as negative fold changes. (--ratio)"> + <option value="log2" selected="true">compute log2 of the number of reads ratio</option> + <option value="ratio">compute the ratio of the number of reads</option> + <option value="subtract">compute difference (subtract input from treatment) of the number of reads</option> + <option value="add">compute the sum over all reads</option> + <option value="reciprocal_ratio">Computes the fold change. If the fold change is less than 1, the negative of the inverse is reported. E.g. A fold change of 10 to 5 would be reported not as 0.5 but as -2</option> + </param> + <when value="log2"> + <expand macro="pseudocount" /> + </when> + <when value="ratio"> + <expand macro="pseudocount" /> + </when> + <when value="subtract" /> + <when value="add" /> + <when value="reciprocal_ratio"> + <expand macro="pseudocount" /> + </when> + </conditional> + + <param name="outFileFormat" type="select" label="Coverage file format"> + <option value="bigwig" selected="true">bigwig</option> + <option value="bedgraph">bedgraph</option> + </param> + + <expand macro="region_limit_operation" /> + + <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="--binSize" type="integer" value="50" min="1" + label="Length, in bases, of the non-overlapping bins used for averaging the score over the regions length" + help="Size of the bins in bases for the output of the bigwig/bedgraph file."/> + + <expand macro="skipNAs" /> + <expand macro="scaleFactors" /> + <expand macro="plotTitle" /> + </when> + </conditional> + </inputs> + <outputs> + <data format="bigwig" name="outFileName"> + <change_format> + <when input="outFileFormat" value="bigwig" format="bigwig" /> + <when input="outFileFormat" value="bedgraph" format="bedgraph" /> + </change_format> + </data> + </outputs> + <tests> + <test> + <param name="bigwigFile1" value="test.bw" ftype="bigwig" /> + <param name="bigwigFile2" value="test.bw" ftype="bigwig" /> + <param name="showAdvancedOpt" value="no" /> + <param name="outFileFormat" value="bigwig" /> + <param name="binSize" value="5" /> + <param name="comparison_select" value="ratio" /> + <output name="outFileName" file="bigwigCompare_result1.bw" ftype="bigwig" /> + </test> + <test> + <param name="bigwigFile1" value="test.bw" ftype="bigwig" /> + <param name="bigwigFile2" value="test.bw" ftype="bigwig" /> + <param name="showAdvancedOpt" value="no" /> + <param name="outFileFormat" value="bedgraph" /> + <param name="binSize" value="10" /> + <param name="comparison_select" value="ratio" /> + <output name="outFileName" file="bigwigCompare_result2.bg" ftype="bedgraph" /> + </test> + </tests> + <help> +<![CDATA[ + +**What it does** + +This tool compares two bigWig files based on the number of mapped reads. To +compare the bigwig files, the genome is partitioned into bins of equal size, +then the number of reads found in each bigWig file are counted for such bins and +finally a summary value reported. This value can be the ratio of the +number of reads per bin, the log2 of the ratio, the sum or the difference. + +----- + +@REFERENCES@ +]]> + </help> + <expand macro="citations" /> +</tool>