# HG changeset patch
# User wolma
# Date 1418509201 18000
# Node ID 17ea8fd2ca18629a0dddc689f0211e53e0b9c5c2
Imported from capsule None
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
@@ -0,0 +1,74 @@
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+ with the CloudMap series of tools.
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+ mimodd
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+ mimodd version -q
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+ mimodd cloudmap "$ifile" ${run.mode}
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+ #if $str($run.mode) != "EMS":
+ "${run.refsample}"
+ #end if
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+ "$sample" -o $ofile
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+ #if $seqdict:
+ -s $dictfile
+ #end if
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+ seqdict
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+.. class:: infomark
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+ **What it does**
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+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.
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+These tools complement MiModD by providing easily interpreted visualizations of mapping-by-sequencing analysis workflows.
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+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.
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+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*).
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+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 .
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+.. class:: warningmark
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+ EMS Variant Density Mapping is currently limited to *C. elegans* and other species with six chromosomes on the *CloudMap* side.
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+.. _CloudMap: https://usegalaxy.org/u/gm2123/p/cloudmap
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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
@@ -0,0 +1,6 @@
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