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comparison cloudmap.xml @ 0:17ea8fd2ca18 draft

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Imported from capsule None
author wolma
date Sat, 13 Dec 2014 17:20:01 -0500
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1 <tool id="cloudmap_prepare" name="Prepare variant data for mapping">
2 <description>with the CloudMap series of tools.</description>
3 <requirements>
4 <requirement type="package" version="0.1.5">mimodd</requirement>
5 </requirements>
6 <version_command>mimodd version -q</version_command>
7 <command>
8 mimodd cloudmap "$ifile" ${run.mode}
9
10 #if $str($run.mode) != "EMS":
11 "${run.refsample}"
12 #end if
13
14 "$sample" -o $ofile
15
16 #if $seqdict:
17 -s $dictfile
18 #end if
19 </command>
20
21 <inputs>
22 <param name="ifile" type="data" format="vcf" label="vcf input file" />
23 <conditional name="run">
24 <param name="mode" type="select" label="CloudMap analysis to prepare data for">
25 <option value="EMS">EMS Variant Density Mapping</option>
26 <option value="VARIANT">Variant Discovery Mapping</option>
27 <option value="HAWAIIAN">Hawaiian Variant Mapping</option>
28 </param>
29 <when value="EMS">
30 <param name="refsample" type="hidden" value="None" />
31 </when>
32 <when value="VARIANT">
33 <param name="refsample" type="text" label="name of the reference sample" help="the sample that provides crossing strain variants to be EXCLUDED from the analysis" />
34 </when>
35 <when value="HAWAIIAN">
36 <param name="refsample" type="text" label="name of the reference sample" help="the sample that provides crossing strain variants to be INCLUDED in the analysis" />
37 </when>
38 </conditional>
39 <param name="sample" type="text" label="subject sample name" help="the sample to perform CloudMap mapping for" />
40 <param name="seqdict" type="boolean" checked="true" label="Generate species configuration file for CloudMap" />
41
42 </inputs>
43
44 <outputs>
45 <data name="ofile" format="vcf" label="CloudMap ${run.mode} Mapping-ready VCF File from ${on_string}" />
46 <data name="dictfile" format="tabular" label="Species Configuration File for CloudMap from ${on_string}">
47 <filter>seqdict</filter>
48 </data>
49 </outputs>
50
51 <help>
52 .. class:: infomark
53
54 **What it does**
55
56 The purpose of this tool is to provide compatibility of the MiModD analysis workflow with the external `CloudMap`_ *EMS Variant Density Mapping*, *Variant Discovery Mapping* and *Hawaiian Variant Mapping* tools.
57
58 These tools complement MiModD by providing easily interpreted visualizations of mapping-by-sequencing analysis workflows.
59
60 The tool converts a VCF file as generated by the *Extract Variant Sites* or *VCF Filter* tools to the format expected by the *CloudMap* series of tools.
61
62 Optionally, it also extracts the chromosome names and sizes and reports them in the *CloudMap* *species configuration file* format.
63 Such a file is required as input to the current versions of the *CloudMap* *Hawaiian* and *Variant Density* mapping tools, if you are working with a species other than the natively supported ones (i.e., other than *C. elegans* or *A. thaliana*).
64
65 To use the output datasets of the tool with *CloudMap*, you only have to upload them to any public Galaxy server that hosts *CloudMap* like, e.g., the main Galaxy server at https://usegalaxy.org .
66
67 .. class:: warningmark
68
69 EMS Variant Density Mapping is currently limited to *C. elegans* and other species with six chromosomes on the *CloudMap* side.
70
71 .. _CloudMap: https://usegalaxy.org/u/gm2123/p/cloudmap
72
73 </help>
74 </tool>