Mercurial > repos > iuc > bedtools
diff unionBedGraphs.xml @ 0:b8348686a0b9 draft
Imported from capsule None
| author | iuc |
|---|---|
| date | Tue, 04 Nov 2014 01:45:04 -0500 |
| parents | |
| children | 82aac94b06c3 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/unionBedGraphs.xml Tue Nov 04 01:45:04 2014 -0500 @@ -0,0 +1,232 @@ +<tool id="bedtools_mergebedgraph" name="Merge BedGraph files" version="@WRAPPER_VERSION@.0"> + <description></description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <command>unionBedGraphs + $header + -filler '$filler' + #if $zero.value == True: + -empty + -g ${chromInfo} + #end if + + -i '$input1' + '$input2' + #for $q in $bedgraphs + '${q.input}' + #end for + + -names + #if $name1.choice == "tag": + '${input1.name}' + #else + '${name1.custom_name}' + #end if + + #if $name2.choice == "tag": + '${input2.name}' + #else + '${name2.custom_name}' + #end if + + #for $q in $bedgraphs + #if $q.name.choice == "tag": + '${q.input.name}' + #else + '${q.input.custom_name}' + #end if + #end for + > '$output' + </command> + <inputs> + <!-- Make it easy for the user, first two input files are always shown --> + <!-- INPUT 1 --> + <param name="input1" format="bedgraph" type="data" label="First BedGraph file" /> + + <conditional name="name1"> + <param name="choice" type="select" label="Sample name"> + <option value="tag" selected="true">Use input's tag</option> + <option value="custom">Enter custom table name</option> + </param> + <when value="tag"> + </when> + <when value="custom"> + <param name="custom_name" type="text" area="false" label="Custom sample name"/> + </when> + </conditional> + + <!-- INPUT 2 --> + <param name="input2" format="bedgraph" type="data" label="Second BedGraph file" /> + + <conditional name="name2"> + <param name="choice" type="select" label="Sample name"> + <option value="tag" selected="true">Use input's tag</option> + <option value="custom">Enter custom table name</option> + </param> + <when value="tag"> + </when> + <when value="custom"> + <param name="custom_name" type="text" area="false" label="Custom sample name"/> + </when> + </conditional> + + <!-- Additional files, if the user needs more --> + <repeat name="bedgraphs" title="Add'l BedGraph files" > + <param name="input" format="bedgraph" type="data" label="BedGraph file" /> + <conditional name="name"> + <param name="choice" type="select" label="Sample name"> + <option value="tag" selected="true">Use input's tag</option> + <option value="custom">Enter custom table name</option> + </param> + <when value="tag"> + </when> + <when value="custom"> + <param name="custom_name" type="text" area="false" label="Custom sample name"/> + </when> + </conditional> + </repeat> + + <param name="header" type="boolean" checked="true" truevalue="-header" falsevalue="" label="Print header line" help="The first line will include the name of each sample." /> + + <param name="zero" type="boolean" checked="true" label="Report regions with zero coverage" help="If set, regions without any coverage will also be reported. Requires a valid organism key for all input datasets" /> + + <param name="filler" type="text" value="0" label="Text to use for no-coverage value" help="Can be 0.0, N/A, - or any other value." /> + </inputs> + + <outputs> + <data format="tabular" name="output" metadata_source="input1" label="Merged BedGraphs of ${input1.name}, ${input2.name} and so on." /> + </outputs> + <help> + +**What it does** + +This tool merges multiple BedGraph files, allowing direct and fine-scale coverage comparisons among many samples/files. The BedGraph files need not represent the same intervals; the tool will identify both common and file-specific intervals. In addition, the BedGraph values need not be numeric: one can use any text as the BedGraph value and the tool will compare the values from multiple files. + +.. image:: http://people.virginia.edu/~arq5x/files/bedtools-galaxy/ubg.png + + +.. class:: warningmark + +This tool requires that each BedGraph file is reference-sorted (chrom, then start) and contains non-overlapping intervals (within a given file). + + +------ + +**Example input**:: + + # 1.bedgraph + chr1 1000 1500 10 + chr1 2000 2100 20 + + # 2.bedgraph + chr1 900 1600 60 + chr1 1700 2050 50 + + # 3.bedgraph + chr1 1980 2070 80 + chr1 2090 2100 20 + + +------ + +**Examples using the Zero Coverage checkbox** + +Output example (*without* checking "Report regions with zero coverage"):: + + chr1 900 1000 0 60 0 + chr1 1000 1500 10 60 0 + chr1 1500 1600 0 60 0 + chr1 1700 1980 0 50 0 + chr1 1980 2000 0 50 80 + chr1 2000 2050 20 50 80 + chr1 2050 2070 20 0 80 + chr1 2070 2090 20 0 0 + chr1 2090 2100 20 0 20 + + +Output example (*with* checking "Report regions with zero coverage"). The lines marked with (*) are not covered in any input file, but are still reported (The asterisk marking does not appear in the file).:: + + chr1 0 900 0 0 0 (*) + chr1 900 1000 0 60 0 + chr1 1000 1500 10 60 0 + chr1 1500 1600 0 60 0 + chr1 1600 1700 0 0 0 (*) + chr1 1700 1980 0 50 0 + chr1 1980 2000 0 50 80 + chr1 2000 2050 20 50 80 + chr1 2050 2070 20 0 80 + chr1 2070 2090 20 0 0 + chr1 2090 2100 20 0 20 + chr1 2100 247249719 0 0 0 (*) + + +------ + +**Examples adjusting the "Filler value" for no-covered intervals** + +The default value is '0', but you can use any other value. + +Output example with **filler = N/A**:: + + chr1 900 1000 N/A 60 N/A + chr1 1000 1500 10 60 N/A + chr1 1500 1600 N/A 60 N/A + chr1 1600 1700 N/A N/A N/A + chr1 1700 1980 N/A 50 N/A + chr1 1980 2000 N/A 50 80 + chr1 2000 2050 20 50 80 + chr1 2050 2070 20 N/A 80 + chr1 2070 2090 20 N/A N/A + chr1 2090 2100 20 N/A 20 + + +------ + +**Examples using the "sample name" labels**:: + + chrom start end WT-1 WT-2 KO-1 + chr1 900 1000 N/A 60 N/A + chr1 1000 1500 10 60 N/A + chr1 1500 1600 N/A 60 N/A + chr1 1600 1700 N/A N/A N/A + chr1 1700 1980 N/A 50 N/A + chr1 1980 2000 N/A 50 80 + chr1 2000 2050 20 50 80 + chr1 2050 2070 20 N/A 80 + chr1 2070 2090 20 N/A N/A + chr1 2090 2100 20 N/A 20 + + +------ + +**Non-numeric values** + +The input BedGraph files can contain any kind of value in the fourth column, not necessarily a numeric value. + +Input Example:: + + File-1 File-2 + chr1 200 300 Sample1 chr1 100 240 0.75 + chr1 400 450 Sample1 chr1 250 700 0.43 + chr1 530 600 Sample2 + +Output Example:: + + chr1 100 200 0 0.75 + chr1 200 240 Sample1 0.75 + chr1 240 250 Sample1 0 + chr1 250 300 Sample1 0.43 + chr1 300 400 0 0.43 + chr1 400 450 Sample1 0.43 + chr1 450 530 0 0.43 + chr1 530 600 Sample2 0.43 + chr1 600 700 0 0.43 + +@REFERENCES@ + + </help> + <expand macro="citations" /> +</tool>