| Next changeset 1:e81a2448d1fb (2015-01-16) |
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Commit message:
Imported from capsule None |
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added:
cloudmap.xml tool_dependencies.xml |
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| diff -r 000000000000 -r 17ea8fd2ca18 cloudmap.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cloudmap.xml Sat Dec 13 17:20:01 2014 -0500 |
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| @@ -0,0 +1,74 @@ +<tool id="cloudmap_prepare" name="Prepare variant data for mapping"> + <description>with the CloudMap series of tools.</description> + <requirements> + <requirement type="package" version="0.1.5">mimodd</requirement> + </requirements> + <version_command>mimodd version -q</version_command> + <command> + mimodd cloudmap "$ifile" ${run.mode} + + #if $str($run.mode) != "EMS": + "${run.refsample}" + #end if + + "$sample" -o $ofile + + #if $seqdict: + -s $dictfile + #end if + </command> + + <inputs> + <param name="ifile" type="data" format="vcf" label="vcf input file" /> + <conditional name="run"> + <param name="mode" type="select" label="CloudMap analysis to prepare data for"> + <option value="EMS">EMS Variant Density Mapping</option> + <option value="VARIANT">Variant Discovery Mapping</option> + <option value="HAWAIIAN">Hawaiian Variant Mapping</option> + </param> + <when value="EMS"> + <param name="refsample" type="hidden" value="None" /> + </when> + <when value="VARIANT"> + <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" /> + </when> + <when value="HAWAIIAN"> + <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" /> + </when> + </conditional> + <param name="sample" type="text" label="subject sample name" help="the sample to perform CloudMap mapping for" /> + <param name="seqdict" type="boolean" checked="true" label="Generate species configuration file for CloudMap" /> + + </inputs> + + <outputs> + <data name="ofile" format="vcf" label="CloudMap ${run.mode} Mapping-ready VCF File from ${on_string}" /> + <data name="dictfile" format="tabular" label="Species Configuration File for CloudMap from ${on_string}"> + <filter>seqdict</filter> + </data> + </outputs> + + <help> +.. class:: infomark + + **What it does** + +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. + +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. + +Optionally, it also extracts the chromosome names and sizes and reports them in the *CloudMap* *species configuration file* format. +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*). + +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 . + +.. class:: warningmark + + EMS Variant Density Mapping is currently limited to *C. elegans* and other species with six chromosomes on the *CloudMap* side. + +.. _CloudMap: https://usegalaxy.org/u/gm2123/p/cloudmap + + </help> +</tool> |
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| diff -r 000000000000 -r 17ea8fd2ca18 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Sat Dec 13 17:20:01 2014 -0500 |
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| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="mimodd" version="0.1.5"> + <repository changeset_revision="fbac402764d6" name="package_mimodd_0_1_5" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |