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comparison bedpeToBam.xml @ 4:315929597efb draft

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author iuc
date Wed, 07 Jan 2015 12:45:05 -0500
parents 7511823bdea1
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3:190a747ddaa8 4:315929597efb
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 &gt; '$output' 15 ]]>
15 </command> 16 </command>
16 <inputs> 17 <inputs>
17 <param format="bed,gff,vcf" name="input" type="data" label="BED/VCF/GFF file"/> 18 <param name="input" format="bed,gff,vcf" type="data" label="BED/VCF/GFF file"/>
18 <expand macro="genome" /> 19 <expand macro="genome" />
19 <param name="mapq" type="integer" label="Set a mapping quality (SAM MAPQ field) value for all BED entries" value="255" /> 20 <param name="mapq" type="integer" value="255"
20 <param name="ubam" type="boolean" label="Write uncompressed BAM output." truevalue="-ubam" falsevalue="" checked="false"/> 21 label="Set a mapping quality (SAM MAPQ field) value for all BED entries"
22 help="(-mapq)" />
21 </inputs> 23 </inputs>
22 <outputs> 24 <outputs>
23 <data format="bam" name="output" metadata_source="input" label="${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>