# HG changeset patch
# User wolma
# Date 1418509166 18000
# Node ID fe2ff108038dace605f222348c97e29c0f2623bc
Imported from capsule None
diff -r 000000000000 -r fe2ff108038d annotate_variants.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/annotate_variants.xml Sat Dec 13 17:19:26 2014 -0500
@@ -0,0 +1,169 @@
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+ Predict the effects of SNPs and indels on known genes in the reference genome using SnpEff
+
+ mimodd
+
+ mimodd version -q
+
+ mimodd annotate
+
+ $inputfile
+
+ #if $str($annotool.name)=='snpeff':
+ --genome "${annotool.genomeVersion}"
+ #if $annotool.ori_output:
+ --snpeff-out $snpeff_file
+ #end if
+ #if $annotool.stats:
+ --stats $summary_file
+ #end if
+ ${annotool.snpeff_settings.chr} ${annotool.snpeff_settings.no_us} ${annotool.snpeff_settings.no_ds} ${annotool.snpeff_settings.no_intron} ${annotool.snpeff_settings.no_intergenic} ${annotool.snpeff_settings.no_utr}
+ #if $annotool.snpeff_settings.min_cov:
+ --minC ${annotool.snpeff_settings.min_cov}
+ #end if
+ #if $annotool.snpeff_settings.min_qual:
+ --minQ ${annotool.snpeff_settings.min_qual}
+ #end if
+ #if $annotool.snpeff_settings.ud:
+ --ud ${annotool.snpeff_settings.ud}
+ #end if
+ #end if
+
+ --ofile $outputfile
+ #if $str($formatting.oformat) == "text":
+ --oformat text
+ #end if
+ #if $str($formatting.oformat) == "html":
+ #if $formatting.formatter_file:
+ --link ${formatting.formatter_file}
+ #end if
+ #if $formatting.species
+ --species "${formatting.species}"
+ #end if
+ #end if
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+ #if $str($grouping):
+ --grouping $grouping
+ #end if
+ --verbose
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+ ## default settings for SnpEff
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+ (annotool['name']=="snpeff" and annotool['ori_output'])
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+ (annotool['name']=="snpeff" and annotool['stats'])
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+.. class:: infomark
+
+ **What it does**
+
+The tool turns a variant list in VCF format into a more readable summary table listing variant sites and effects.
+
+If installed, the variant annotation tool SnpEff can be used transparently to determine the genomic features, e.g., genes or transcripts, affected by the variants.
+
+Use of this feature requires that you have an appropriate SnpEff genome file installed on the host machine. You can use the *List installed SnpEff genomes* tool to generate a list of all available SnpEff genomes.
+This list can then be used (by selecting the dataset as the *genome list*) to populate the *genome* dropdown menu, from which you can select the SnpEff genome file to be used for the annotation.
+
+As output file formats HTML or plain text are supported.
+In HTML mode, variant positions and/or affected genomic features can be turned into hyperlinks to corresponding views in web-based genome browsers and databases.
+
+The behavior of this feature depends on:
+
+1) Recognition of the species that is analyzed
+
+ You can declare the species you are working with using the *Species* text field.
+ If you are not declaring the species explicitly, but are choosing SnpEff for effect annotation, the tool will usually be able to auto-detect the species from the SnpEff genome you are using.
+ If no species gets assigned in either way, no hyperlinks will be generated and the html output will look essentially like plain text.
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+2) Available hyperlink formatting rules for this species
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+ When the species has been recognized, the tool checks if you have selected an *optional file with hyperlink formatting instructions*.
+ If you did and that file contains an entry matching the recognized species, that entry will be used as a template to construct the hyperlinks.
+ If no matching entry is found in the file, an error will be raised.
+
+ If you did not supply a hyperlink formatting instruction file, the tool will consult an internal lookup table to see if it finds default rules for the construction of the hyperlinks for the species.
+ If not, no hyperlinks will be generated and the html output will look essentially like plain text.
+
+ **TIP:**
+ MiModD's internal hyperlink formatting lookup tables are maintained and growing with every new version, but since weblinks are changing frequently as well, it is possible that you will encounter broken hyperlinks for your species of interest. In such a case, you can resort to two things: `tell us about the problem`_ to make sure it gets fixed in the next release and, in the meantime, use a custom file with hyperlink formatting instructions to overwrite the default entry for your species.
+
+.. _tell us about the problem: mailto:mimodd@googlegroups.com
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diff -r 000000000000 -r fe2ff108038d tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Sat Dec 13 17:19:26 2014 -0500
@@ -0,0 +1,6 @@
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