Mercurial > repos > iuc > bedtools
comparison bamToBed.xml @ 1:82aac94b06c3 draft
Uploaded
author | iuc |
---|---|
date | Thu, 08 Jan 2015 14:25:51 -0500 |
parents | b8348686a0b9 |
children | 607c0576c6ab |
comparison
equal
deleted
inserted
replaced
0:b8348686a0b9 | 1:82aac94b06c3 |
---|---|
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 $split |
13 > '$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> |