Mercurial > repos > iuc > bedtools

annotate bedToIgv.xml @ 16:e0cec48a4695 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ea1ac33f3337ac44f43150f585c9ccd38e08da0c
author iuc
date Fri, 18 Aug 2017 15:33:08 -0400
parents 7b3aaff0d78c
children 95a3b2c25bd1
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
12
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
1 <tool id="bedtools_bedtoigv" name="BED to IGV" version="@WRAPPER_VERSION@.0">
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
2 <description>create batch script for taking IGV screenshots</description>
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
3 <macros>
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
4 <import>macros.xml</import>
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
5 </macros>
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
6 <expand macro="requirements" />
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
7 <expand macro="stdio" />
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
8 <command>
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
9 <![CDATA[
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
10 bedToIgv
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
11 -i '$input'
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
12 #if $sort:
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
13 -sort $sort
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
14 #end if
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
15 $clps
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
16 $name
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
17 -slop $slop
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
18 -img $img
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
19 > '$output'
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
20 ]]>
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
21 </command>
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
22 <inputs>
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
23 <param format="bed,gff,gff3,vcf" name="input" type="data" label="Create IGV batch script the following BED file"/>
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
24 <param name="sort" type="select" label="Sort BAM file by" help="The type of BAM sorting you would like to apply to each image.">
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
25 <option value="">No sorting at all (default)</option>
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
26 <option value="base">base</option>
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
27 <option value="position">position</option>
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
28 <option value="strand">strand</option>
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
29 <option value="quality">quality</option>
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
30 <option value="sample">sample</option>
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
31 <option value="readGroup">readGroup</option>
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
32 </param>
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
33 <param name="clps" type="boolean" truevalue="-clps" falsevalue="" label="Collapse the aligned reads prior to taking a snapshot?"/>
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
34 <param name="name" type="boolean" truevalue="-name" falsevalue="" label="Use the name field (column 4) for each image's filename." help="Default is to use chr:start-pos."/>
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
35 <param name="slop" type="integer" min="0" value="0" label="Number of flanking base pairs on the left and right of the image."/>
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
36 <param name="img" type="select" label="Select the type of image to be created.">
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
37 <option value="png">png</option>
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
38 <option value="eps">eps</option>
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
39 <option value="svg">svg</option>
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
40 </param>
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
41 </inputs>
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
42 <outputs>
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
43 <data format="txt" name="output" metadata_source="input" label="BED to IGV on ${input.name}"/>
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
44 </outputs>
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
45 <tests>
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
46 <test>
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
47 <param name="input" value="bed12.bed" ftype="bed" />
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
48 <output name="output" file="igv_bed_script.txt" ftype="txt" />
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
49 </test>
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
50 </tests>
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
51 <help>
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
52 <![CDATA[
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
53 **What it does**
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
54
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
55 Creates a batch script to create IGV images at each interval defined in a BED/GFF/VCF file.
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
56
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
57 **Notes**
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
58
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
59 (1) The resulting script is meant to be run from within IGV.
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
60 (2) It is assumed that prior to running the script, you've loaded the proper genome and tracks.
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
61
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
62 @REFERENCES@
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
63 ]]>
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
64 </help>
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
65 <expand macro="citations" />
7b3aaff0d78c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
iuc
parents:
diff changeset
66 </tool>