--- a/gemini_burden.xml	Fri Oct 16 13:55:09 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,82 +0,0 @@
-<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
-    <description>perform sample-wise gene-level burden calculations</description>
-    <macros>
-        <import>gemini_macros.xml</import>
-        <token name="@BINARY@">burden</token>
-    </macros>
-    <expand macro="requirements" />
-    <expand macro="stdio" />
-    <expand macro="version_command" />
-    <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>
-    <inputs>
-        <expand macro="infile" />
-
-        <param name="cases" type="text" value="" label="Space separated list of cases for association testing" help="(--cases)"/>
-        <param name="controls" 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" 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" 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" 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" />
-    </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>