Mercurial > repos > iuc > bedtools
comparison bamToBed.xml @ 41:7ab85ac5f64b draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 500a03281ea704abc7a16d9af63d67dbdcc5cd0b"
author | iuc |
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date | Thu, 04 Nov 2021 11:36:55 +0000 |
parents | 3e38c9b3214f |
children | 64e2edfe7a2c |
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40:a68aa6c1204a | 41:7ab85ac5f64b |
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1 <tool id="bedtools_bamtobed" name="bedtools BAM to BED" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> | 1 <tool id="bedtools_bamtobed" name="bedtools BAM to BED" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@"> |
2 <description>converter</description> | 2 <description>converter</description> |
3 <expand macro="bio_tools" /> | |
4 <macros> | 3 <macros> |
5 <import>macros.xml</import> | 4 <import>macros.xml</import> |
6 </macros> | 5 </macros> |
6 <expand macro="bio_tools" /> | |
7 <expand macro="requirements"> | 7 <expand macro="requirements"> |
8 <requirement type="package" version="@SAMTOOLS_VERSION@">samtools</requirement> | 8 <requirement type="package" version="@SAMTOOLS_VERSION@">samtools</requirement> |
9 </expand> | 9 </expand> |
10 <expand macro="stdio" /> | 10 <expand macro="stdio" /> |
11 <command><![CDATA[ | 11 <command><![CDATA[ |
12 #if $input.extension in ['bam', 'unsorted.bam', 'qname_input_sorted.bam'] and $option == "-bedpe": | 12 #if $input.extension in ['bam', 'unsorted.bam', 'qname_input_sorted.bam'] and $option == "-bedpe": |
13 samtools sort -n -@ "\${GALAXY_SLOTS:-4}" -T "\${TMPDIR:-.}" '${input}' ./input && | 13 samtools sort -n -@ "\${GALAXY_SLOTS:-4}" -T "\${TMPDIR:-.}" '${input}' > ./input.bam && |
14 #else | 14 #else |
15 ln -s '${input}' ./input.bam && | 15 ln -s '${input}' ./input.bam && |
16 #end if | 16 #end if |
17 | 17 |
18 bedtools bamtobed | 18 bedtools bamtobed |
52 <param name="input" value="srma_in3.bam" ftype="bam" /> | 52 <param name="input" value="srma_in3.bam" ftype="bam" /> |
53 <param name="option" value="" /> | 53 <param name="option" value="" /> |
54 <param name="tag" value="NM" /> | 54 <param name="tag" value="NM" /> |
55 <output name="output" file="bamToBed_result2.bed" ftype="bed" /> | 55 <output name="output" file="bamToBed_result2.bed" ftype="bed" /> |
56 </test> | 56 </test> |
57 <test> | |
58 <param name="input" value="bedpeToBam_result1.bam" ftype="bam" /> | |
59 <param name="option" value="-bedpe" /> | |
60 <param name="tag" value="" /> | |
61 <output name="output" file="bamToBed_result3.bed" ftype="bed" /> | |
62 </test> | |
57 </tests> | 63 </tests> |
58 <help><![CDATA[ | 64 <help><![CDATA[ |
59 **What it does** | 65 **What it does** |
60 | 66 |
61 bedtools bamtobed is a conversion utility that converts sequence alignments in BAM format into BED, BED12, and/or BEDPE records. | 67 bedtools bamtobed is a conversion utility that converts sequence alignments in BAM format into BED, BED12, and/or BEDPE records. |