Mercurial > repos > iuc > bedtools
comparison bedpeToBam.xml @ 1:82aac94b06c3 draft
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author | iuc |
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date | Thu, 08 Jan 2015 14:25:51 -0500 |
parents | b8348686a0b9 |
children | 607c0576c6ab |
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0:b8348686a0b9 | 1:82aac94b06c3 |
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4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
5 </macros> | 5 </macros> |
6 <expand macro="requirements" /> | 6 <expand macro="requirements" /> |
7 <expand macro="stdio" /> | 7 <expand macro="stdio" /> |
8 <command> | 8 <command> |
9 <![CDATA[ | |
9 bedtools bedpetobam | 10 bedtools bedpetobam |
10 $ubam | 11 -mapq $mapq |
11 -mapq $mapq | 12 -i '$input' |
12 -i '$input' | 13 -g $genome |
13 -g $genome | 14 > '$output' |
14 > '$output' | 15 ]]> |
15 </command> | 16 </command> |
16 <inputs> | 17 <inputs> |
17 <param format="bed,gff,vcf" name="input" type="data" label="BED/VCF/GFF file"/> | 18 <param name="input" format="bed,gff,vcf" type="data" label="BED/VCF/GFF file"/> |
18 <expand macro="genome" /> | 19 <expand macro="genome" /> |
19 <param name="mapq" type="integer" label="Set a mapping quality (SAM MAPQ field) value for all BED entries" value="255" /> | 20 <param name="mapq" type="integer" value="255" |
20 <param name="ubam" type="boolean" label="Write uncompressed BAM output." truevalue="-ubam" falsevalue="" checked="false"/> | 21 label="Set a mapping quality (SAM MAPQ field) value for all BED entries" |
22 help="(-mapq)" /> | |
21 </inputs> | 23 </inputs> |
22 <outputs> | 24 <outputs> |
23 <data format="bam" name="output" metadata_source="input" label="${input.name} (as BAM)"/> | 25 <data format="bam" name="output" metadata_source="input"/> |
24 </outputs> | 26 </outputs> |
27 <tests> | |
28 <test> | |
29 <param name="input" value="bedpeToBamBed1.bed" ftype="bed" /> | |
30 <param name="genome" value="mm9.len"/> | |
31 <output name="output" file="bedpeToBam_result1.bam" lines_diff="72" ftype="bam" /> | |
32 </test> | |
33 </tests> | |
25 <help> | 34 <help> |
26 | 35 <![CDATA[ |
27 **What it does** | 36 **What it does** |
28 | 37 |
29 Converts feature records to BAM format. | 38 Converts feature records to BAM format. |
30 | 39 |
31 .. class:: warningmark | 40 .. class:: warningmark |
32 | 41 |
33 BED files must be at least BED4 to create BAM (needs name field). | 42 BED files must be at least BED4 to create BAM (needs name field). |
34 | 43 |
35 @REFERENCES@ | 44 @REFERENCES@ |
45 ]]> | |
36 </help> | 46 </help> |
37 <expand macro="citations" /> | 47 <expand macro="citations" /> |
38 </tool> | 48 </tool> |