Mercurial > repos > iuc > bedtools
changeset 38:fe5b4cb8356c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b822ff8f05f2396fc15bd95a71bc6878503081eb"
| author | iuc |
|---|---|
| date | Thu, 06 May 2021 14:16:19 +0000 |
| parents | ce3c7f062223 |
| children | 3e38c9b3214f |
| files | bamToBed.xml |
| diffstat | 1 files changed, 4 insertions(+), 4 deletions(-) [+] |
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--- a/bamToBed.xml Tue Mar 23 20:23:14 2021 +0000 +++ b/bamToBed.xml Thu May 06 14:16:19 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="bedtools_bamtobed" name="bedtools BAM to BED" version="@TOOL_VERSION@"> +<tool id="bedtools_bamtobed" name="bedtools BAM to BED" version="@TOOL_VERSION@+galaxy1"> <description>converter</description> <macros> <import>macros.xml</import> @@ -8,8 +8,8 @@ </expand> <expand macro="stdio" /> <command><![CDATA[ -#if $input.extension == 'bam' and $option == "-bedpe": - samtools sort -n -T "\${TMPDIR:-.}" '${input}' ./input && +#if $input.extension in ['bam', 'unsorted.bam', 'qname_input_sorted.bam'] and $option == "-bedpe": + samtools sort -n -@ "\${GALAXY_SLOTS:-4}" -T "\${TMPDIR:-.}" '${input}' ./input && #else ln -s '${input}' ./input.bam && #end if @@ -25,7 +25,7 @@ > '${output}' ]]></command> <inputs> - <param name="input" type="data" format="bam" label="Convert the following BAM file to BED"/> + <param name="input" type="data" format="unsorted.bam" label="Convert the following BAM file to BED"/> <param name="option" type="select" label="What type of BED output would you like"> <option value="">Create a 6-column BED file</option> <option value="-bed12">Create a full, 12-column "blocked" BED file</option>