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comparison bedToIgv.xml @ 27:a39035fe5180 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5
author iuc
date Fri, 28 Oct 2016 12:54:27 -0400
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26:c0fbce5dc84a 27:a39035fe5180
1 <tool id="bedtools_bedtoigv" name="BED to IGV" version="@WRAPPER_VERSION@.0">
2 <description>create batch script for taking IGV screenshots</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <expand macro="stdio" />
8 <command>
9 <![CDATA[
10 bedToIgv
11 -i '$input'
12 #if $sort:
13 -sort $sort
14 #end if
15 $clps
16 $name
17 -slop $slop
18 -img $img
19 > '$output'
20 ]]>
21 </command>
22 <inputs>
23 <param format="bed,gff,gff3,vcf" name="input" type="data" label="Create IGV batch script the following BED file"/>
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.">
25 <option value="">No sorting at all (default)</option>
26 <option value="base">base</option>
27 <option value="position">position</option>
28 <option value="strand">strand</option>
29 <option value="quality">quality</option>
30 <option value="sample">sample</option>
31 <option value="readGroup">readGroup</option>
32 </param>
33 <param name="clps" type="boolean" truevalue="-clps" falsevalue="" label="Collapse the aligned reads prior to taking a snapshot?"/>
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."/>
35 <param name="slop" type="integer" min="0" value="0" label="Number of flanking base pairs on the left and right of the image."/>
36 <param name="img" type="select" label="Select the type of image to be created.">
37 <option value="png">png</option>
38 <option value="eps">eps</option>
39 <option value="svg">svg</option>
40 </param>
41 </inputs>
42 <outputs>
43 <data format="txt" name="output" metadata_source="input" label="BED to IGV on ${input.name}"/>
44 </outputs>
45 <tests>
46 <test>
47 <param name="input" value="bed12.bed" ftype="bed" />
48 <output name="output" file="igv_bed_script.txt" ftype="txt" />
49 </test>
50 </tests>
51 <help>
52 <![CDATA[
53 **What it does**
54
55 Creates a batch script to create IGV images at each interval defined in a BED/GFF/VCF file.
56
57 **Notes**
58
59 (1) The resulting script is meant to be run from within IGV.
60 (2) It is assumed that prior to running the script, you've loaded the proper genome and tracks.
61
62 @REFERENCES@
63 ]]>
64 </help>
65 <expand macro="citations" />
66 </tool>