| Previous changeset 0:17ea8fd2ca18 (2014-12-13) Next changeset 2:1fcb80c861c1 (2015-01-16) |
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Commit message:
upgrade to v0.1.5.1 |
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modified:
cloudmap.xml tool_dependencies.xml |
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| diff -r 17ea8fd2ca18 -r e81a2448d1fb cloudmap.xml --- a/cloudmap.xml Sat Dec 13 17:20:01 2014 -0500 +++ b/cloudmap.xml Fri Jan 16 10:42:08 2015 -0500 |
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| @@ -1,13 +1,10 @@ <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": + #if $str($run.mode) != "SVD": "${run.refsample}" #end if @@ -22,18 +19,14 @@ <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> + <option value="SVD">EMS Variant Density Mapping</option> + <option value="VAF">Variant Discovery / Hawaiian Variant Mapping</option> </param> - <when value="EMS"> + <when value="SVD"> <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 value="VAF"> + <param name="refsample" type="text" label="name of the reference sample" help="the sample that provides mapping strain variants" /> </when> </conditional> <param name="sample" type="text" label="subject sample name" help="the sample to perform CloudMap mapping for" /> @@ -42,7 +35,7 @@ </inputs> <outputs> - <data name="ofile" format="vcf" label="CloudMap ${run.mode} Mapping-ready VCF File from ${on_string}" /> + <data name="ofile" format="vcf" label="CloudMap-ready ${run.mode} File from ${on_string}" /> <data name="dictfile" format="tabular" label="Species Configuration File for CloudMap from ${on_string}"> <filter>seqdict</filter> </data> |
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| diff -r 17ea8fd2ca18 -r e81a2448d1fb tool_dependencies.xml --- a/tool_dependencies.xml Sat Dec 13 17:20:01 2014 -0500 +++ b/tool_dependencies.xml Fri Jan 16 10:42:08 2015 -0500 |
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| @@ -1,6 +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 name="mimodd" version="0.1.5"> + <repository changeset_revision="a1ed24182b03" name="package_mimodd_0_1_5" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |