Mercurial > repos > nanettec > qtlmap_15

diff qtlmap_15/qtlmap7_15nodes.xml @ 0:fa0693cf076b draft

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author nanettec
date Fri, 18 Mar 2016 05:51:39 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qtlmap_15/qtlmap7_15nodes.xml	Fri Mar 18 05:51:39 2016 -0400
@@ -0,0 +1,40 @@
+<tool id="qtlmap7_15nodes" name="Run QTL Cartographer" version="7.0.0">
+	<description> and parse the results</description>
+	<command interpreter="python">
+            qtlmap7_15nodes.py --input1 $input1 --input2 $input2 --input3 $input3 --output1 $output1
+        </command>
+        <inputs>
+            <param label="Phenotype-genotype (.inp) file" name="input1" type="data" format="txt" help="A .inp file with all genotype and phenotype information"></param>
+	    <param label="QTL Cartographer map file" name="input2" type="data" format="txt" help="A .inp file with all genotype and phenotype information"></param>
+	    <param label="Parameters file" name="input3" type="data" format="txt" help="Parameters file with the values of all the parameters for QTL mapping"></param>
+        </inputs>
+	<outputs>
+                <data format="tabular" name="output1" />
+	</outputs>
+	<requirements>
+	</requirements>
+	<tests>
+          <test>
+          </test>
+	</tests>
+	<help>
+		
+**What it does**
+
+Runs QTL Cartographer for QTL/eQTL mapping. Parse the results.  
+
+**Example output file**
+
+eQTL results file, each row correspond to an eQTL (21 columns; only a part of the file is shown)::
+
+ trait_name	trait_number	eQTL_number	chr	peak_marker	peak_position	peak_LR	peak_LOD	R2	TR2	S	additive 	dominance	LOD1_L_m	LOD1_L_pos	LOD1_R_m	LOD1_R_pos	LOD2_L_m	LOD2_L_pos	LOD2_R_m	LOD2_R_pos
+ geneA		4		2		3	15		79.31		14.576	3.162992	0.1093	0.1915	5.2649	-0.0602		0		12		0.6318		15		0.8678		11		0.5984		15		0.8941
+ geneB		5		1		6	7		54.41		12.0029	2.6046293	0.0833	0.1621	5.0323	0.0516		0		6		0.4803		7		0.6296		5		0.4237		7		0.6509
+ geneC		6		1		1	12		81.5		13.2053	2.8655501	0.082	0.2517	154.622	-0.0513		0		11		0.7835		12		0.815		10		0.6549		12		0.815
+ geneC		6		2		5	6		33.92		12.4418	2.6998706	0.0881	0.2653	161.127	0.0546		0		4		0.2652		6		0.4058		2		0.1031		7		0.4629
+ geneF		11		1		9	4		11.74		14.4418	3.1338706	0.0937	0.252	72.2489	-0.0562		0		1		0.0014		4		0.1995		1		0.0001		4		0.2035
+ geneH		12		2		1	9		43.66		16.9545	3.6791265	0.092	0.3558	0.1466	0.0544		0		8		0.4159		9		0.5408		5		0.3295		9		0.5987
+ geneJ		13		1		7	11		66.41		15.6251	3.3906467	0.0965	0.2625	8.2335	-0.0558		0		9		0.5515		11		0.7408		9		0.5464		12		0.7631
+
+        </help>
+</tool>