Mercurial > repos > bgruening > bedtools_test_bag

comparison BedToBam.xml @ 12:c782e0edc4f1 draft default tip

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author bgruening
date Thu, 19 Jun 2014 10:12:00 -0400
parents e526617a6bb9
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11:e526617a6bb9 12:c782e0edc4f1
1 <tool id="bedtools_bedtobam" name="Convert from BED to BAM" version="0.1.0"> 1 <tool id="bedtools_bedtobam" name="Convert from BED to BAM" version="@WRAPPER_VERSION@.0">
2 <description></description> 2 <description></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" />
10 $ubam 10 $ubam
11 $bed12 11 $bed12
12 -mapq $mapq 12 -mapq $mapq
13 -i '$input' 13 -i '$input'
14 &gt; '$output' 14 &gt; '$output'
15
16 </command> 15 </command>
17 <inputs> 16 <inputs>
18 <param format="bed" name="input" type="data" label="Convert the following BED file to BAM"/> 17 <param format="bed" name="input" type="data" label="Convert the following BED file to BAM"/>
19 <param name="bed12" type="boolean" label="Indicate that the input BED file is in BED12 (a.k.a “blocked” BED) format" truevalue="-bed12" falsevalue="" checked="false" help="If Selected, bedToBam will convert blocked BED features (e.g., gene annotaions) into “spliced” BAM alignments by creating an appropriate CIGAR string.."/> 18 <param name="bed12" type="boolean" label="Indicate that the input BED file is in BED12 (a.k.a “blocked” BED) format" truevalue="-bed12" falsevalue="" checked="false" help="If Selected, bedToBam will convert blocked BED features (e.g., gene annotaions) into “spliced” BAM alignments by creating an appropriate CIGAR string.."/>
20 <param name="mapq" type="integer" label="Set a mapping quality (SAM MAPQ field) value for all BED entries" value="255" /> 19 <param name="mapq" type="integer" label="Set a mapping quality (SAM MAPQ field) value for all BED entries" value="255" />
21 <param name="ubam" type="boolean" label="Write uncompressed BAM output." truevalue="-ubam" falsevalue="" checked="false"/> 20 <param name="ubam" type="boolean" label="Write uncompressed BAM output." truevalue="-ubam" falsevalue="" checked="false"/>
22
23 </inputs> 21 </inputs>
24 <outputs> 22 <outputs>
25 <data format="bam" name="output" metadata_source="input" label="${input.name} (as BAM)"/> 23 <data format="bam" name="output" metadata_source="input" label="${input.name} (as BAM)"/>
26 </outputs> 24 </outputs>
27 <help> 25 <help>