Mercurial > repos > iuc > bedtools
diff unionBedGraphs.xml @ 17:44867b59dbf2 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
author | iuc |
---|---|
date | Tue, 05 Sep 2017 15:40:14 -0400 |
parents | 7308cc546a36 |
children | a8eabd2838f6 |
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--- a/unionBedGraphs.xml Fri Aug 18 15:33:08 2017 -0400 +++ b/unionBedGraphs.xml Tue Sep 05 15:40:14 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="bedtools_unionbedgraph" name="Merge BedGraph files" version="@WRAPPER_VERSION@.0"> +<tool id="bedtools_unionbedgraph" name="Merge BedGraph files" version="@WRAPPER_VERSION@.1"> <description>combines coverage intervals from multiple BEDGRAPH files</description> <macros> <import>macros.xml</import> @@ -10,10 +10,8 @@ unionBedGraphs $header -filler "${filler}" - #if $zero.value == True: - -empty - -g $genome - #end if + $empty.empty_selector + @GENOME_FILE_UNION@ #if str($tag.tag_select) == "tag": #set files = '" "'.join( [ str( $file ) for $file in $tag.inputs ] ) @@ -43,14 +41,20 @@ <when value="custom"> <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"/> + <param name="custom_name" type="text" area="false" label="Custom sample name" /> </repeat> </when> </conditional> - <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" /> + <conditional name="empty"> + <param name="empty_selector" argument="-empty" type="select" label="Report empty regions" help="Include regions that have zero coverage in all BedGraph datasets"> + <option value="-empty">Yes</option> + <option value="">No</option> + </param> + <when value="-empty"> + <expand macro="input_conditional_genome_file" /> + </when> + <when value="" /> + </conditional> <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)" /> @@ -61,27 +65,28 @@ </outputs> <tests> <test> - <param name="tag_select" value="tag"/> + <param name="tag_select" value="tag" /> <param name="inputs" value="unionBedGraphs1.bg,unionBedGraphs2.bg,unionBedGraphs3.bg" ftype="bedgraph" /> - <param name="zero" value="False"/> + <param name="empty_selector" value="" /> <output name="output" file="unionBedGraphs_result1.bg" ftype="bedgraph" /> </test> <test> - <param name="tag_select" value="tag"/> + <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"/> + <param name="header" value="True" /> + <param name="empty_selector" value="" /> <output name="output" file="unionBedGraphs_result2.bg" ftype="bedgraph" /> </test> <test> - <param name="tag_select" value="tag"/> + <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"/> + <param name="empty_selector" value="-empty" /> + <param name="genome_file_opts_selector" value="hist" /> + <param name="genome" value="unionBedGraphs1.len" /> <output name="output" file="unionBedGraphs_result3.bg" ftype="bedgraph" /> </test> <test> - <param name="tag_select" value="custom"/> + <param name="tag_select" value="custom" /> <repeat name="bedgraphs"> <param name="input" value="unionBedGraphs1.bg" /> <param name="custom_name" value="first" /> @@ -94,8 +99,9 @@ <param name="input" value="unionBedGraphs3.bg" /> <param name="custom_name" value="third" /> </repeat> - <param name="zero" value="True"/> - <param name="genome" value="unionBedGraphs1.len"/> + <param name="empty_selector" value="-empty" /> + <param name="genome_file_opts_selector" value="hist" /> + <param name="genome" value="unionBedGraphs1.len" /> <output name="output" file="unionBedGraphs_result4.bg" ftype="bedgraph" /> </test> </tests>