--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gemini_set_somatic.xml	Tue Feb 16 05:57:15 2016 -0500
@@ -0,0 +1,94 @@
+<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
+    <description>Tag somatic mutations in a GEMINI database</description>
+    <macros>
+        <import>gemini_macros.xml</import>
+        <token name="@BINARY@">set_somatic</token>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version_command" />
+    <command>
+<![CDATA[
+        cp "${ infile }" "${ outfile }" &&
+
+        gemini @BINARY@
+
+        #if float($min_depth) >= 0:
+            --min-depth $min_depth
+        #end if
+        
+        #if float($min_quality) >= 0:
+            --min-qual $min_quality
+        #end if
+
+        #if float($min_somatic_score) >= 0:
+            --min-somatic-score $min_somatic_score
+        #end if
+
+        #if float($max_norm_alt_freq) >= 0:
+            --max-norm-alt-freq $max_norm_alt_freq
+        #end if
+
+        #if int($max_norm_alt_count) >= 0:
+            --max-norm-alt-count $max_norm_alt_count
+        #end if
+
+        #if int($min_norm_depth) >= 0:
+            --min-norm-depth $min_norm_depth
+        #end if
+
+        #if float($min_tumor_alt_freq) >= 0:
+            --min-tumor-alt-freq $min_tumor_alt_freq
+        #end if
+
+        #if int($min_tumor_alt_count) >= 0:
+            --min-tumor-alt-count $min_tumor_alt_count
+        #end if
+
+        #if int($min_tumor_depth) >= 0:
+            --min-tumor-depth $min_tumor_depth
+        #end if
+
+        #if str($chrom).strip():
+            --chrom "$chrom"
+        #end if 
+        "${ outfile }"
+]]>
+    </command>
+    <inputs>
+
+        <expand macro="infile" />
+        <param name="min_depth" type="float" value="-1" label="The min combined depth for tumor + normal" help="default: -1 (not set) (--min-depth)"/>
+        <param name="min_quality" type="float" value="-1" label="The min variant quality (VCF QUAL)" help="default: -1 (not set) (--min-qual)"/>
+        <param name="min_somatic_score" type="float" value="-1" label="The min somatic score (SSC)" help="default: -1 (not set) (--min-somatic-score)"/>
+        <param name="max_norm_alt_freq" type="float" value="-1" label="The max frequency of the alternative allele in the normal sample" help="default: -1 (not set) (--max-norm-alt-freq)"/>
+        <param name="max_norm_alt_count" type="integer" value="-1" min="-1" label="The max count of the alternative allele in the normal sample" help="default: -1 (not set) (--max-norm-alt-count)"/>
+        <param name="min_norm_depth" type="integer" value="-1" min="-1" label="The minimum depth allowed in the normal sample to believe somatic" help="default: -1 (not set) (--min-norm-depth)"/>
+        <param name="min_tumor_alt_freq" type="float" value="-1" label="The minimum frequency of the alternative allele in the tumor sample" help="default: -1 (not set) (--min-tumor-alt-freq)"/>
+        <param name="min_tumor_alt_count" type="integer" value="-1" min="-1" label="The minimum count of the alternative allele in the tumor sample" help="default: -1 (not set) (--min-tumor-alt-count)"/>
+        <param name="min_tumor_depth" type="integer" value="-1" min="-1" label="The minimum depth allowed in the tumor sample to believe somatic" help="default: -1 (not set) (--min-tumor-depth)"/>
+        <param name="chrom" type="text" label="A specific chromosome on which to tag somatic mutations" help="e.g. chrom12 (--chrom)" />
+
+    </inputs>
+    <outputs>
+        <data name="outfile" format="gemini.sqlite" />
+    </outputs>
+    <tests>
+        <test>
+            <!-- A very basic test with a nonsensical input db. The example 
+                databases that would produce something meaningful are >100 Mbyte -->
+            <param name="infile" value="gemini_amend_input.db" ftype="gemini.sqlite" />
+            <param name="min_somatic_score" value="5.65"  />
+            <output name="outfile" file="gemini_is_somatic_result.db" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**What it does**
+
+Gemini set_somatic sets the flag "is_somatic" by comparing tumor/normal pairs in an already loaded Gemini database. 
+
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>