Mercurial > repos > iuc > bedtools
comparison bamToBed.xml @ 38:fe5b4cb8356c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b822ff8f05f2396fc15bd95a71bc6878503081eb"
author | iuc |
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date | Thu, 06 May 2021 14:16:19 +0000 |
parents | b28e0cfa7ba1 |
children | 3e38c9b3214f |
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37:ce3c7f062223 | 38:fe5b4cb8356c |
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1 <tool id="bedtools_bamtobed" name="bedtools BAM to BED" version="@TOOL_VERSION@"> | 1 <tool id="bedtools_bamtobed" name="bedtools BAM to BED" version="@TOOL_VERSION@+galaxy1"> |
2 <description>converter</description> | 2 <description>converter</description> |
3 <macros> | 3 <macros> |
4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
5 </macros> | 5 </macros> |
6 <expand macro="requirements"> | 6 <expand macro="requirements"> |
7 <requirement type="package" version="@SAMTOOLS_VERSION@">samtools</requirement> | 7 <requirement type="package" version="@SAMTOOLS_VERSION@">samtools</requirement> |
8 </expand> | 8 </expand> |
9 <expand macro="stdio" /> | 9 <expand macro="stdio" /> |
10 <command><![CDATA[ | 10 <command><![CDATA[ |
11 #if $input.extension == 'bam' and $option == "-bedpe": | 11 #if $input.extension in ['bam', 'unsorted.bam', 'qname_input_sorted.bam'] and $option == "-bedpe": |
12 samtools sort -n -T "\${TMPDIR:-.}" '${input}' ./input && | 12 samtools sort -n -@ "\${GALAXY_SLOTS:-4}" -T "\${TMPDIR:-.}" '${input}' ./input && |
13 #else | 13 #else |
14 ln -s '${input}' ./input.bam && | 14 ln -s '${input}' ./input.bam && |
15 #end if | 15 #end if |
16 | 16 |
17 bedtools bamtobed | 17 bedtools bamtobed |
23 #end if | 23 #end if |
24 -i ./input.bam | 24 -i ./input.bam |
25 > '${output}' | 25 > '${output}' |
26 ]]></command> | 26 ]]></command> |
27 <inputs> | 27 <inputs> |
28 <param name="input" type="data" format="bam" label="Convert the following BAM file to BED"/> | 28 <param name="input" type="data" format="unsorted.bam" label="Convert the following BAM file to BED"/> |
29 <param name="option" type="select" label="What type of BED output would you like"> | 29 <param name="option" type="select" label="What type of BED output would you like"> |
30 <option value="">Create a 6-column BED file</option> | 30 <option value="">Create a 6-column BED file</option> |
31 <option value="-bed12">Create a full, 12-column "blocked" BED file</option> | 31 <option value="-bed12">Create a full, 12-column "blocked" BED file</option> |
32 <option value="-bedpe">Create a paired-end, BEDPE format</option> | 32 <option value="-bedpe">Create a paired-end, BEDPE format</option> |
33 </param> | 33 </param> |