annotate cloudmap.xml @ 5:bdd1995c9e66

upgrade to mimodd version 0.1.6.1
author Wolfgang Maier
date Tue, 28 Jul 2015 23:21:11 +0200
parents ffee8534a5c4
children 85214e4428fd
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
bdd1995c9e66 upgrade to mimodd version 0.1.6.1
Wolfgang Maier
parents: 4
diff changeset
1 <tool id="cloudmap_prepare" name="Prepare variant data for mapping" version="0.1.6.1">
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
2 <description>with the CloudMap series of tools.</description>
2
72d20758ba2c final upload
wolma
parents: 1
diff changeset
3 <macros>
72d20758ba2c final upload
wolma
parents: 1
diff changeset
4 <import>toolshed_macros.xml</import>
72d20758ba2c final upload
wolma
parents: 1
diff changeset
5 </macros>
72d20758ba2c final upload
wolma
parents: 1
diff changeset
6 <expand macro="requirements"/>
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
7 <version_command>mimodd version -q</version_command>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
8 <command>
4
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
9 mimodd cloudmap "$ifile" ${run.mode} "$sample"
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
10
4
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
11 #if $str($run.related_parent_sample):
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
12 -r "${run.related_parent_sample}"
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
13 #end if
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
14 #if $str($run.unrelated_parent_sample):
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
15 -u "${run.unrelated_parent_sample}"
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
16 #end if
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
17
4
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
18 $run.infer_missing
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
19 -o "$ofile"
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
20
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
21 #if $seqdict:
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
22 -s "$dictfile"
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
23 #end if
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
24 </command>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
25
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
26 <inputs>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
27 <param name="ifile" type="data" format="vcf" label="vcf input file" />
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
28 <conditional name="run">
4
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
29 <param name="mode" type="select" label="Type of CloudMap analysis to prepare data for" help="select Simple Variant Density (SVD) Mapping to generate output for the CloudMap EMS Variant Density Mapping tool or Variant Allele Frequency (VAF) Mapping for output for the CloudMap Variant Discovery or Hawaiian Variant Mapping tools.">
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
30 <option value="SVD">Simple Variant Density Mapping</option>
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
31 <option value="VAF">Variant Allele Frequency Mapping</option>
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
32 </param>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
33 <when value="SVD">
4
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
34 <param name="related_parent_sample" type="hidden" value="" />
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
35 <param name="unrelated_parent_sample" type="hidden" value="" />
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
36 <param name="infer_missing" type="hidden" value="" />
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
37 </when>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
38 <when value="VAF">
4
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
39 <param name="related_parent_sample" type="text" label="name of the related parent sample" help="the sample that provides variants present in your original mutant strain or in an ancestor (like the pre-mutagenesis strain); leave blank if not available" />
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
40 <param name="unrelated_parent_sample" type="text" label="name of the unrelated parent sample" help="the sample that provides variants present in the unrelated mapping strain (or in an ancestor of it) used in the mapping cross; leave blank if not available" />
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
41 <param name="infer_missing" type="boolean" checked="false" truevalue="--infer-missing" falsevalue="" label="Infer alleles for missing parent" help="if variant data for either the related or the unrelated parent strain is not available, the tool can try to infer the alleles present in that parent from the allele spectrum found in the mapping sample. This is an experimental option that will give a benefit only in certain situations. Enable at your own risk." />
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
42 </when>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
43 </conditional>
4
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
44 <param name="sample" type="text" label="mapping sample name" help="the sample to perform mutation mapping for" />
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
45 <param name="seqdict" type="boolean" checked="true" label="Generate species configuration file for CloudMap" />
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
46 </inputs>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
47
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
48 <outputs>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
49 <data name="ofile" format="vcf" label="CloudMap-ready ${run.mode} File from ${on_string}" />
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
50 <data name="dictfile" format="tabular" label="Species Configuration File for CloudMap from ${on_string}">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
51 <filter>seqdict</filter>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
52 </data>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
53 </outputs>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
54
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
55 <help>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
56 .. class:: infomark
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
57
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
58 **What it does**
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
59
4
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
60 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. These tools complement MiModD by providing easily interpreted visualizations of mapping-by-sequencing analysis workflows.
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
61
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
62 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.
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
63
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
64 Optionally, it also extracts the chromosome names and sizes and reports them in the *CloudMap* *species configuration file* format.
4
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
65 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*, *A. thaliana* or *Brachypodium distachyon*).
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
66
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
67 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 .
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
68
4
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
69 **Notes:**
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
70
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
71 1) Simple Variant Density (SVD) Mapping mode generates output for use with the CloudMap EMS Variant Density Mapping tool. The aim of SVD analysis is to identify clusters of variants that appear linked to a mutant phenotype selected for during several rounds of outcrossing or backcrossing to a non-mutagenized strain. The "mapping sample" is the out-/backcrossed strain and only its variants are taken into account for the analysis.
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
72
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
73 .. class:: warningmark
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
74
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
75 EMS Variant Density Mapping is currently limited to *C. elegans* and other species with six chromosomes on the *CloudMap* side.
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
76
4
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
77 2) Variant Allele Frequency (VAF) Mapping mode generates output for use with the CloudMap Variant Discovery or Hawaiian Variant Mapping tools. The aim of VAF analysis is to identify clusters of variants with (near) homozygous inheritance in a F2 population obtained from a cross between a mutant strain of interest and an unrelated mapping strain. Here, the "mapping sample" is the pooled F2 population. To analyze inheritance patterns this mode **requires either** a list of variants that could have been inherited through the mapping strain, i.e. the "unrelated parent strain", or through the mutant parent, i.e. through the "related parent strain". If variants are available for both parents, they can be analyzed together for higher mapping accuracy.
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
78
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
79 3) More information on combining MiModD and CloudMap in mapping-by-sequencing analyses can be found in the `corresponding section of the MiModD User Guide`_.
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
80
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
81 .. _CloudMap: https://usegalaxy.org/u/gm2123/p/cloudmap
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
82 .. _corresponding section of the MiModD User Guide: http://mimodd.readthedocs.org/en/latest/cloudmap.html
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
83
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
84 </help>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
85 </tool>