| Previous changeset 6:d25966c8ddeb (2016-05-22) Next changeset 8:0232cdab3664 (2016-09-05) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 964b3159deeade1c90d20cef92dc15a14195edb7 |
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modified:
genomeCoverageBed.xml |
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| diff -r d25966c8ddeb -r 8e6b7c3597a8 genomeCoverageBed.xml --- a/genomeCoverageBed.xml Sun May 22 12:33:32 2016 -0400 +++ b/genomeCoverageBed.xml Mon Jul 18 14:06:15 2016 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="bedtools_genomecoveragebed" name="Genome Coverage" version="@WRAPPER_VERSION@.0"> +<tool id="bedtools_genomecoveragebed" name="Genome Coverage" version="@WRAPPER_VERSION@.1"> <description>compute the coverage over an entire genome</description> <macros> <import>macros.xml</import> @@ -8,11 +8,11 @@ <command> <![CDATA[ bedtools genomecov - #if $input.ext == "bam" - -ibam '$input' + #if $input_type.input_type_select == 'bam' + -ibam '$input_type.input' #else - -i '$input' - -g $genome + -i '$input_type.input' + -g '$input_type.genome' #end if $split @@ -42,9 +42,19 @@ ]]> </command> <inputs> - <param format="bed,bam" name="input" type="data" label="The BAM or BED file from which coverage should be computed"> - <validator type="unspecified_build" /> - </param> + <conditional name="input_type"> + <param name="input_type_select" type="select" label="Input type"> + <option value="bed">BED/VCF/GFF</option> + <option value="bam">BAM</option> + </param> + <when value="bed"> + <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file" /> + <expand macro="genome" /> + </when> + <when value="bam"> + <param format="bam" name="input" type="data" label="BAM file" /> + </when> + </conditional> <conditional name="report"> <param name="report_select" type="select" label="Output type"> <option value="bg" selected="true">BedGraph coverage file</option> @@ -62,7 +72,6 @@ help="Combine all positions with a depth >= max into a single bin in the histogram. (-max)"/> </when> </conditional> - <expand macro="genome" /> <expand macro="split" /> <param name="strand" type="select" label="Calculate coverage based on" help="(-strand)"> <option value="">both strands combined</option> @@ -88,8 +97,9 @@ </outputs> <tests> <test> + <param name="input_type_select" value="bed" /> <param name="input" value="genomeCoverageBed1.bed" ftype="bed" /> - <param name="genome" value="genomeCoverageBed1.len" /> + <param name="genome" value="genomeCoverageBed1.len" ftype="tabular" /> <param name="report_select" value="hist" /> <output name="output" file="genomeCoverageBed_result1.bed" ftype="tabular" /> </test> |