Mercurial > repos > iuc > bedtools
annotate bamToBed.xml @ 17:a2d4c30ba2f9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
| author | iuc |
|---|---|
| date | Sun, 21 Jun 2015 22:49:46 -0400 |
| parents | 0d3aa592ce27 |
| children | 5efc48568d8d |
| rev | line source |
|---|---|
|
17
a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
8
diff
changeset
|
1 <tool id="bedtools_bamtobed" name="BAM to BED" version="@WRAPPER_VERSION@.0"> |
|
a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
8
diff
changeset
|
2 <description>converter</description> |
| 8 | 3 <macros> |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <expand macro="stdio" /> | |
| 8 <command> | |
| 9 <![CDATA[ | |
| 10 bedtools bamtobed | |
| 11 $option | |
| 12 $ed_score | |
| 13 $split | |
| 14 #if $tag and str($tag).strip(): | |
| 15 -tag "${tag}" | |
| 16 #end if | |
| 17 -i "${input}" | |
| 18 > "${output}" | |
| 19 ]]> | |
| 20 </command> | |
| 21 <inputs> | |
| 22 <param format="bam" name="input" type="data" label="Convert the following BAM file to BED"/> | |
| 23 <param name="option" type="select" label="What type of BED output would you like"> | |
| 24 <option value="">Create a 6-column BED file.</option> | |
| 25 <option value="-bed12">Create a full, 12-column "blocked" BED file.</option> | |
| 26 <option value="-bedpe">Create a paired-end, BEDPE format.</option> | |
| 27 </param> | |
| 28 <expand macro="split" /> | |
| 29 <param name="ed_score" type="boolean" truevalue="-ed" falsevalue="" checked="false" | |
| 30 label="Use alignment's edit-distance for BED score" /> | |
| 31 <param name="tag" type="text" optional="true" label="Use other NUMERIC BAM alignment tag as the BED score" | |
| 32 help="(-tag)"/> | |
| 33 </inputs> | |
| 34 <outputs> | |
| 35 <data format="bed" name="output" metadata_source="input" label="${input.name} (as BED)"/> | |
| 36 </outputs> | |
| 37 <tests> | |
| 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[ | |
| 53 **What it does** | |
| 54 | |
| 55 bedtools bamtobed is a conversion utility that converts sequence alignments in BAM format into BED, BED12, and/or BEDPE records. | |
| 56 | |
| 57 .. class:: infomark | |
| 58 | |
| 59 The "Report spliced BAM alignment..." option breaks BAM alignments with the "N" (splice) operator into distinct BED entries. For example, using this option on a CIGAR such as 50M1000N50M would, by default, produce a single BED record that spans 1100bp. However, using this option, it would create two separate BED records that are each 50bp in size and are separated by 1000bp (the size of the N operation). This is important for RNA-seq and structural variation experiments. | |
| 60 | |
| 61 | |
| 62 .. class:: warningmark | |
| 63 | |
| 64 If using a custom BAM alignment TAG as the BED score, note that this must be a numeric tag (e.g., type "i" as in NM:i:0). | |
| 65 | |
| 66 .. class:: warningmark | |
| 67 | |
| 68 If creating a BEDPE output (see output formatting options), the BAM file should be sorted by query name. | |
| 69 | |
| 70 @REFERENCES@ | |
| 71 ]]> | |
| 72 </help> | |
| 73 <expand macro="citations" /> | |
| 74 </tool> |