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comparison bedToIgv.xml @ 42:d279800f4ff9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59
author iuc
date Thu, 26 Apr 2018 17:02:24 -0400
parents a39035fe5180
children 2f457890d8c8
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41:c96688f1746d 42:d279800f4ff9
18 -img $img 18 -img $img
19 > '$output' 19 > '$output'
20 ]]> 20 ]]>
21 </command> 21 </command>
22 <inputs> 22 <inputs>
23 <param format="bed,gff,gff3,vcf" name="input" type="data" label="Create IGV batch script the following BED file"/> 23 <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="Create IGV batch script for this @STD_BEDTOOLS_INPUT_LABEL@ 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."> 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> 25 <option value="">No sorting at all (default)</option>
26 <option value="base">base</option> 26 <option value="base">base</option>
27 <option value="position">position</option> 27 <option value="position">position</option>
28 <option value="strand">strand</option> 28 <option value="strand">strand</option>
50 </tests> 50 </tests>
51 <help> 51 <help>
52 <![CDATA[ 52 <![CDATA[
53 **What it does** 53 **What it does**
54 54
55 Creates a batch script to create IGV images at each interval defined in a BED/GFF/VCF file. 55 Creates a batch script to create IGV images at each interval defined in a @STD_BEDTOOLS_INPUT_LABEL@ file.
56 56
57 **Notes** 57 **Notes**
58 58
59 (1) The resulting script is meant to be run from within IGV. 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. 60 (2) It is assumed that prior to running the script, you've loaded the proper genome and tracks.