diff gemini_qc.xml @ 0:a875f940d8fd draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gemini_qc.xml	Thu Feb 18 08:54:08 2016 -0500
@@ -0,0 +1,70 @@
+<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
+    <description>Quality control tool</description>
+    <macros>
+        <import>gemini_macros.xml</import>
+        <token name="@BINARY@">qc</token>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version_command" />
+    <command>
+<![CDATA[
+        gemini @BINARY@
+        --mode sex
+        --chrom "$chrom"
+
+        "${ infile }"
+        > "${ outfile }"
+]]>
+    </command>
+    <inputs>
+        <expand macro="infile" />
+        <param name="chrom" type="text" value="chrX" label="Which chromosome should the sex test be applied to?" help="(--chrom)"/>
+
+    </inputs>
+    <outputs>
+        <data name="outfile" format="tabular" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" value="gemini_amend_input.db" ftype="gemini.sqlite" />
+            <param name="chrom" value="chrX" ftype="gemini.sqlite" />
+            <output name="outfile" file="gemini_qc_result.tabular" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**What it does**
+
+Checks whether the given sex of the samples are probable. It issues the query::
+
+    SELECT gt_types
+    FROM   variants
+    WHERE  chrom = '$chrom'
+    AND start > 2699520 and start < 154931044
+    AND call_rate > 0.90
+    AND depth > 1000
+    AND filter is NULL
+    ORDER BY random()
+    LIMIT 10000
+
+and returns the called variants on that region of the given chromosome in a table::
+
+ sample  sex     X_homref  X_het  X_homalt  het_homref_ratio
+ SMS173  male    7265      1975   8010      0.271851342051
+ SMS254  male    5440      1316   3846      0.241911764706
+ SMS255  female  6275      3188   5423      0.508047808765
+ SMS253  male    5536      1355   3582      0.244761560694
+ SMS243  male    6181      1506   4479      0.243649894839
+ SMS242  male    6365      1437   4200      0.225765907306
+ SMS193  male    6667      1864   5829      0.279586020699
+ SMS238  male    6263      1638   4891      0.261536005109
+ SMS239  female  6755      3669   7618      0.543153219837
+ SMS244  female  6489      2953   5140      0.45507782401
+ SMS230  male    7209      1784   7146      0.247468442225
+ SMS231  female  7306      4659   9332      0.637695045168
+]]>
+
+    </help>
+    <expand macro="citations"/>
+</tool>