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comparison bamToBed.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 bedtools bamtobed 9 <![CDATA[
10 $option 10 bedtools bamtobed
11 $option
11 $ed_score 12 $ed_score
12 -i '$input' 13 $split
13 &gt; '$output' 14 #if $tag and str($tag).strip():
14 #if str($tag): 15 -tag "${tag}"
15 -tag $tag
16 #end if 16 #end if
17 -i "${input}"
18 > "${output}"
19 ]]>
17 </command> 20 </command>
18 <inputs> 21 <inputs>
19 <param format="bam" name="input" type="data" label="Convert the following BAM file to BED"/> 22 <param format="bam" name="input" type="data" label="Convert the following BAM file to BED"/>
20 <param name="option" type="select" label="What type of BED output would you like"> 23 <param name="option" type="select" label="What type of BED output would you like">
21 <option value="">Create a 6-column BED file.</option> 24 <option value="">Create a 6-column BED file.</option>
22 <option value="-bed12">Create a full, 12-column "blocked" BED file.</option> 25 <option value="-bed12">Create a full, 12-column "blocked" BED file.</option>
23 <option value="-bedpe">Create a paired-end, BEDPE format.</option> 26 <option value="-bedpe">Create a paired-end, BEDPE format.</option>
24 </param> 27 </param>
25 <param name="split" type="boolean" label="Report each portion of a split BAM alignment" truevalue="-split" falsevalue="" checked="false" help="(i.e., having an 'N' CIGAR operation) as a distinct BED intervals."/> 28 <expand macro="split" />
26 <param name="ed_score" type="boolean" label="Use alignment's edit-distance for BED score" truevalue="-ed" falsevalue="" checked="false"/> 29 <param name="ed_score" type="boolean" truevalue="-ed" falsevalue="" checked="false"
27 <param name="tag" type="text" optional="true" label="Use other NUMERIC BAM alignment tag as the BED score"/> 30 label="Use alignment's edit-distance for BED score" />
31 <param name="tag" type="text" optional="true" label="Use other NUMERIC BAM alignment tag as the BED score"
32 help="(-tag)"/>
28 </inputs> 33 </inputs>
29 <outputs> 34 <outputs>
30 <data format="bed" name="output" metadata_source="input" label="${input.name} (as BED)"/> 35 <data format="bed" name="output" metadata_source="input" label="${input.name} (as BED)"/>
31 </outputs> 36 </outputs>
32 <help> 37 <tests>
33 38 <test>
39 <param name="input" value="srma_in3.bam" ftype="bam" />
40 <param name="option" value="" />
41 <param name="tag" value="" />
42 <output name="output" file="bamToBed_result1.bed" ftype="bed" />
43 </test>
44 <test>
45 <param name="input" value="srma_in3.bam" ftype="bam" />
46 <param name="option" value="" />
47 <param name="tag" value="NM" />
48 <output name="output" file="bamToBed_result2.bed" ftype="bed" />
49 </test>
50 </tests>
51 <help>
52 <![CDATA[
34 **What it does** 53 **What it does**
35 54
36 bedtools bamtobed is a conversion utility that converts sequence alignments in BAM format into BED, BED12, and/or BEDPE records. 55 bedtools bamtobed is a conversion utility that converts sequence alignments in BAM format into BED, BED12, and/or BEDPE records.
37 56
38 .. class:: infomark 57 .. class:: infomark
47 .. class:: warningmark 66 .. class:: warningmark
48 67
49 If creating a BEDPE output (see output formatting options), the BAM file should be sorted by query name. 68 If creating a BEDPE output (see output formatting options), the BAM file should be sorted by query name.
50 69
51 @REFERENCES@ 70 @REFERENCES@
52 71 ]]>
53 </help> 72 </help>
54 <expand macro="citations" /> 73 <expand macro="citations" />
55 </tool> 74 </tool>