Mercurial > repos > iuc > bedtools
diff unionBedGraphs.xml @ 1:82aac94b06c3 draft
Uploaded
author | iuc |
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date | Thu, 08 Jan 2015 14:25:51 -0500 |
parents | b8348686a0b9 |
children | 607c0576c6ab |
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--- a/unionBedGraphs.xml Tue Nov 04 01:45:04 2014 -0500 +++ b/unionBedGraphs.xml Thu Jan 08 14:25:51 2015 -0500 @@ -1,106 +1,106 @@ -<tool id="bedtools_mergebedgraph" name="Merge BedGraph files" version="@WRAPPER_VERSION@.0"> +<tool id="bedtools_unionbedgraph" name="Merge BedGraph files" version="@WRAPPER_VERSION@.0"> <description></description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <expand macro="stdio" /> - <command>unionBedGraphs + <command> +<![CDATA[ + unionBedGraphs $header - -filler '$filler' + -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}' + -g $genome #end if - #if $name2.choice == "tag": - '${input2.name}' - #else - '${name2.custom_name}' + #if str($tag.tag_select) == "tag": + #set files = '" "'.join( [ str( $file ) for $file in $tag.inputs ] ) + -i "${files}" + #else: + -i + #for $bg in $tag.bedgraphs: + "${bg.input}" + #end for + -names + #for $bg in $tag.bedgraphs: + "${bg.custom_name}" + #end for #end if - - #for $q in $bedgraphs - #if $q.name.choice == "tag": - '${q.input.name}' - #else - '${q.input.custom_name}' - #end if - #end for - > '$output' + > "${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"> + <conditional name="tag"> + <param name="tag_select" type="select" label="Sample name"> <option value="tag" selected="true">Use input's tag</option> - <option value="custom">Enter custom table name</option> + <option value="custom">Enter custom name per file</option> </param> <when value="tag"> + <param name="inputs" format="bedgraph" type="data" multiple="True" label="BedGraph files" /> </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"/> + <repeat name="bedgraphs" title="Add BedGraph files" min="2" > + <param name="input" format="bedgraph" type="data" multiple="True" label="BedGraph file" /> + <param name="custom_name" type="text" area="false" label="Custom sample name"/> + </repeat> </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." /> + <expand macro="genome" /> + <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="N/A" + label="Text to use for no-coverage value" + help="Can be 0.0, N/A, - or any other value. (-filler)" /> + <expand macro="print_header" /> </inputs> - <outputs> - <data format="tabular" name="output" metadata_source="input1" label="Merged BedGraphs of ${input1.name}, ${input2.name} and so on." /> + <data name="output" format="bedgraph" /> </outputs> + <tests> + <test> + <param name="tag_select" value="tag"/> + <param name="inputs" value="unionBedGraphs1.bg,unionBedGraphs2.bg,unionBedGraphs3.bg" ftype="bedgraph" /> + <param name="zero" value="False"/> + <output name="output" file="unionBedGraphs_result1.bg" ftype="bedgraph" /> + </test> + <test> + <param name="tag_select" value="tag"/> + <param name="inputs" value="unionBedGraphs1.bg,unionBedGraphs2.bg,unionBedGraphs3.bg" ftype="bedgraph" /> + <param name="header" value="True"/> + <param name="zero" value="False"/> + <output name="output" file="unionBedGraphs_result2.bg" ftype="bedgraph" /> + </test> + <test> + <param name="tag_select" value="tag"/> + <param name="inputs" value="unionBedGraphs1.bg,unionBedGraphs2.bg,unionBedGraphs3.bg" ftype="bedgraph" /> + <param name="zero" value="True"/> + <param name="genome" value="unionBedGraphs1.len"/> + <output name="output" file="unionBedGraphs_result3.bg" ftype="bedgraph" /> + </test> + <test> + <param name="tag_select" value="custom"/> + <repeat name="bedgraphs"> + <param name="input" value="unionBedGraphs1.bg" /> + <param name="custom_name" value="first" /> + </repeat> + <repeat name="bedgraphs"> + <param name="input" value="unionBedGraphs2.bg" /> + <param name="custom_name" value="second" /> + </repeat> + <repeat name="bedgraphs"> + <param name="input" value="unionBedGraphs3.bg" /> + <param name="custom_name" value="third" /> + </repeat> + <param name="zero" value="True"/> + <param name="genome" value="unionBedGraphs1.len"/> + <output name="output" file="unionBedGraphs_result4.bg" ftype="bedgraph" /> + </test> + </tests> <help> - +<![CDATA[ **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. @@ -226,7 +226,7 @@ chr1 600 700 0 0.43 @REFERENCES@ - +]]> </help> <expand macro="citations" /> </tool>