diff gemini_burden.xml @ 0:720cbfb4190d draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gemini_burden.xml	Mon Aug 25 17:15:54 2014 -0400
@@ -0,0 +1,82 @@
+<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
+    <description>perform sample-wise gene-level burden calculations</description>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <macros>
+        <import>gemini_macros.xml</import>
+        <token name="@BINARY@">burden</token>
+    </macros>
+    <command>
+<![CDATA[
+        gemini @BINARY@
+          --cases $cases
+          --controls $controls
+            $save_tscores
+            $nonsynonymous
+            $calpha
+            --permutations $permutations
+            #if float( str($min_aaf) ) >= 0.0:
+                --min-aaf $min_aaf
+            #end if
+            #if float( str($max_aaf) ) >= 0.0:
+                --max-aaf $max_aaf
+            #end if
+            "${ infile }"
+            > "${ outfile }"
+]]>
+
+    </command>
+    <expand macro="stdio" />
+    <inputs>
+        <param name="infile" type="data" format="sqlite" label="GEMINI database" />
+
+        <param name="cases" size="30" type="text" value="" label="Space separated list of cases for association testing" help="(--cases)"/>
+        <param name="controls" size="30" type="text" value="" label="Space separated list of controls for association testing" help="(--controls)"/>
+
+        <param name="save_tscores" type="boolean" truevalue="--save_tscores" falsevalue="" checked="False" 
+            label="Save the permuted T-scores in the output file" help="(--save_tscores)"/>
+
+        <param name="nonsynonymous" type="boolean" truevalue="--nonsynonymous" falsevalue="" checked="False" 
+            label="Count all nonsynonymous variants as contributing burden" help="(--nonsynonymous)"/>
+        <param name="calpha" type="boolean" truevalue="--calpha" falsevalue="" checked="False" 
+            label="Run the C-alpha association test" help="(--calpha)"/>
+        <param name="min_aaf" type="float" value="-1" size="5" label="The min. alt. allele frequency for a variant to be included" 
+            help="(--min-aaf)">
+            <!--validator type="in_range" min="0.0"/-->
+        </param>
+        <param name="max_aaf" type="float" value="-1" size="5" label="The max. alt. allele frequency for a variant to be included" 
+            help="(--max-aaf)">
+            <!--validator type="in_range" min="0.0"/-->
+        </param>
+
+        <param name="permutations" type="integer" value="1000" size="10" label="Number of permutations to run for the C-alpha test" 
+            help="(--permutations)">
+            <validator type="in_range" min="0"/>
+        </param>
+
+    </inputs>
+    <outputs>
+        <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+The burden tool provides a set of utilities to perform burden summaries on a per-gene, per sample basis. 
+By default, it outputs a table of gene-wise counts of all high impact variants in coding regions for each sample.
+
+$ gemini burden test.burden.db
+gene    M10475  M10478  M10500  M128215
+WDR37   2       2       2       2
+CTBP2   0       0       0       1
+DHODH   1       0       0       0
+
+@CITATION@
+    </help>
+    <expand macro="citations">
+        <citation type="doi">10.1371/journal.pgen.1001322</citation><!-- c-alpha citation -->
+    </expand>
+</tool>