Mercurial > repos > iuc > bedtools
diff mapBed.xml @ 43:07e8b80f278c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
author | iuc |
---|---|
date | Fri, 01 Apr 2022 19:02:51 +0000 |
parents | 7ab85ac5f64b |
children |
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--- a/mapBed.xml Wed Jan 12 19:22:14 2022 +0000 +++ b/mapBed.xml Fri Apr 01 19:02:51 2022 +0000 @@ -1,4 +1,4 @@ -<tool id="bedtools_map" name="bedtools MapBed" version="@TOOL_VERSION@.2" profile="@PROFILE@"> +<tool id="bedtools_map" name="bedtools MapBed" version="@TOOL_VERSION@.3" profile="@PROFILE@"> <description>apply a function to a column for each overlapping interval</description> <macros> <import>macros.xml</import> @@ -19,7 +19,7 @@ $reciprocal $split $header -@GENOME_FILE_MAPBED@ +@GENOME_FILE@ > '${output}' ]]></command> <inputs> @@ -36,7 +36,7 @@ </expand> <expand macro="split" /> <expand macro="print_header" /> - <expand macro="input_optional_genome_file" /> + <expand macro="input_conditional_genome_file" optional="true"/> </inputs> <outputs> <data name="output" format_source="inputA" metadata_source="inputA" label="Mapping of ${inputB.name} into ${inputA.name}" /> @@ -88,9 +88,24 @@ <param name="operation" value="collapse" /> </repeat> <param name="strand" value="-s" /> - <param name="genome_choose" value="-g" /> - <param name="genome_file_opts_selector" value="hist" /> - <param name="genome" value="mm9.len" ftype="bed" /> + <conditional name="genome_file_opts"> + <param name="genome_file_opts_selector" value="hist" /> + <param name="genome" value="mm9.len" ftype="bed" /> + </conditional> + <output name="output" file="mapBed_result5.bed" ftype="bed" /> + </test> + <test> + <param name="inputA" value="mapBed3.bed" ftype="bed" /> + <param name="inputB" value="mapBed4.bed" ftype="bed" /> + <repeat name="c_and_o_argument_repeat"> + <param name="col" value="5" /> + <param name="operation" value="collapse" /> + </repeat> + <param name="strand" value="-s" /> + <conditional name="genome_file_opts"> + <param name="genome_file_opts_selector" value="loc" /> + <param name="genome" value="mm9"/> + </conditional> <output name="output" file="mapBed_result5.bed" ftype="bed" /> </test> </tests>