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comparison cloudmap.xml @ 0:6231ae8f87b8

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author wolma
date Wed, 11 Feb 2015 08:29:02 -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 <version_command>mimodd version -q</version_command>
4 <command>
5 mimodd cloudmap "$ifile" ${run.mode}
6
7 #if $str($run.mode) != "SVD":
8 "${run.refsample}"
9 #end if
10
11 "$sample" -o "$ofile"
12
13 #if $seqdict:
14 -s "$dictfile"
15 #end if
16 </command>
17
18 <inputs>
19 <param name="ifile" type="data" format="vcf" label="vcf input file" />
20 <conditional name="run">
21 <param name="mode" type="select" label="CloudMap analysis to prepare data for">
22 <option value="SVD">EMS Variant Density Mapping</option>
23 <option value="VAF">Variant Discovery / Hawaiian Variant Mapping</option>
24 </param>
25 <when value="SVD">
26 <param name="refsample" type="hidden" value="None" />
27 </when>
28 <when value="VAF">
29 <param name="refsample" type="text" label="name of the reference sample" help="the sample that provides mapping strain variants" />
30 </when>
31 </conditional>
32 <param name="sample" type="text" label="subject sample name" help="the sample to perform CloudMap mapping for" />
33 <param name="seqdict" type="boolean" checked="true" label="Generate species configuration file for CloudMap" />
34
35 </inputs>
36
37 <outputs>
38 <data name="ofile" format="vcf" label="CloudMap-ready ${run.mode} File from ${on_string}" />
39 <data name="dictfile" format="tabular" label="Species Configuration File for CloudMap from ${on_string}">
40 <filter>seqdict</filter>
41 </data>
42 </outputs>
43
44 <help>
45 .. class:: infomark
46
47 **What it does**
48
49 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.
50
51 These tools complement MiModD by providing easily interpreted visualizations of mapping-by-sequencing analysis workflows.
52
53 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.
54
55 Optionally, it also extracts the chromosome names and sizes and reports them in the *CloudMap* *species configuration file* format.
56 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*).
57
58 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 .
59
60 .. class:: warningmark
61
62 EMS Variant Density Mapping is currently limited to *C. elegans* and other species with six chromosomes on the *CloudMap* side.
63
64 More information on combining MiModD and CloudMap in mapping-by-sequencing analyses can be found in the `corresponding section of the MiModD User Guide`_.
65
66 .. _CloudMap: https://usegalaxy.org/u/gm2123/p/cloudmap
67 .. _corresponding section of the MiModD User Guide: http://mimodd.readthedocs.org/en/latest/cloudmap.html
68
69 </help>
70 </tool>