# HG changeset patch
# User kpbioteam
# Date 1529327720 14400
# Node ID fc230fb2244cf80e47ccf66d8a8a6a0987dd6226
# Parent  30a95c57b9ea635a8898004118b26b0c6ed35a9c
planemo upload for repository https://github.com/kpbioteam/minfi_dmr commit b3aa56ab9ae9a3338c32dbe32c417a673e3ec99f

diff -r 30a95c57b9ea -r fc230fb2244c dmr.bedgraph
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dmr.bedgraph	Mon Jun 18 09:15:20 2018 -0400
@@ -0,0 +1,16719 @@
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+chr1	100715098	100715098	1	0.5
+chr1	100817839	100817839	1	0.5
+chr1	101362002	101362002	1	0.5
+chr1	109642671	109642671	1	0.5
+chr1	109825675	109825675	1	0.5
+chr1	111991531	111991531	1	0.5
+chr1	112162932	112162932	1	0.5
+chr1	114355299	114355299	1	0.5
+chr1	115259226	115259226	1	0.5
+chr1	120612404	120612404	1	0.5
+chr1	120837955	120837955	1	0.5
+chr1	145507220	145507220	1	0.5
+chr1	146643471	146643471	1	0.5
+chr1	146644430	146644430	1	0.5
+chr1	146714493	146714493	1	0.5
+chr1	149859104	149859104	1	0.5
+chr1	149859629	149859629	1	0.5
+chr1	149982400	149982400	1	0.5
+chr1	150039920	150039920	1	0.5
+chr1	150336129	150336129	1	0.5
+chr1	150534252	150534252	1	0.5
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+chr1	154973402	154973402	1	0.5
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+chr1	160001439	160001439	1	0.5
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+chr1	229694604	229694604	1	0.5
+chr1	231113872	231113872	1	0.5
+chr1	231376624	231376624	1	0.5
+chr1	231376895	231376895	1	0.5
+chr1	234509775	234509775	1	0.5
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+chr1	234748618	234748618	1	0.5
+chr1	235530811	235530811	1	0.5
+chr1	243418761	243418761	1	0.5
+chr1	244999141	244999141	1	0.5
+chr1	245025960	245025960	1	0.5
+chr1	245028075	245028075	1	0.5
+chr1	247094386	247094386	1	0.5
+chr1	247495250	247495250	1	0.5
+chr1	249120451	249120451	1	0.5
+chrX	15872521	15872521	1	0.5
+chrX	24167821	24167821	1	0.5
+chrX	34181023	34181023	1	0.5
+chrX	70680473	70680473	1	0.5
+chrX	79141321	79141321	1	0.5
+chrX	88308360	88308360	1	0.5
+chrX	90336867	90336867	1	0.5
+chrX	92657204	92657204	1	0.5
+chrX	94164453	94164453	1	0.5
+chrX	108410752	108410752	1	0.5
diff -r 30a95c57b9ea -r fc230fb2244c minfi_dmr.R
--- a/minfi_dmr.R	Sun Jun 17 06:34:32 2018 -0400
+++ b/minfi_dmr.R	Mon Jun 18 09:15:20 2018 -0400
@@ -62,4 +62,8 @@
 
 colnames(dmrGR) <- c("seqnames","start","end","width","strand","area","value")
 
-write.table(dmrGR, file= output1, quote = FALSE, row.names = FALSE, sep = "\t")
+dmrGR$strand <- NULL
+
+dmrGR$area <- NULL
+
+write.table(dmrGR, file= output1, quote = FALSE,col.names = FALSE, row.names = FALSE, sep = "\t")
diff -r 30a95c57b9ea -r fc230fb2244c minfi_dmr.xml
--- a/minfi_dmr.xml	Sun Jun 17 06:34:32 2018 -0400
+++ b/minfi_dmr.xml	Mon Jun 18 09:15:20 2018 -0400
@@ -19,13 +19,13 @@
 			<option value="bootstrap">bootstrap</option>
                     </param>
 
-        <param name="input9" type="select" label="verbose" help="logical value. If TRUE, it writes out some messages indicating progress. If FALSE nothing should be printed.">
+        <param name="input9" type="select" label="verbose" help="If TRUE, it writes out some messages indicating progress If FALSE nothing should be printed">
                         <option value="TRUE">TRUE</option>
                         <option value="FALSE">FALSE</option>
                     </param>
  </inputs>
     <outputs>
-        <data name="output1" format="bedgraph" label="Differentially Methylated Regions" /> 
+        <data name="output1" format="bedgraph" label="Differentially Methylated Regions"/> 
    </outputs>
     <tests>
         <test>
@@ -42,8 +42,7 @@
         </test>
     </tests>
     <help><![CDATA[
-        This tool is a version of the bump hunting algorithm (Andrew E Jaffe et al. 2012) adapted to the 450k array finding find differentially methylated regions (DMRs)
-    ]]></help>
+ This tool is a version of the bump hunting algorithm (Andrew E Jaffe et al. 2012) adapted to the 450k array finding find differentially methylated regions DMR: seqnames start end width area value]]></help>
     <citations>
         <citation type="doi">10.1093/bioinformatics/btu049</citation>
     </citations>
diff -r 30a95c57b9ea -r fc230fb2244c test-data/dmr.bedgraph
--- a/test-data/dmr.bedgraph	Sun Jun 17 06:34:32 2018 -0400
+++ b/test-data/dmr.bedgraph	Mon Jun 18 09:15:20 2018 -0400
@@ -1,16720 +1,16719 @@
-seqnames	start	end	width	strand	area	value
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-chrX	48754982	48755797	816	*	10.9187994853289	0.519942832634712
-chrX	47004051	47005131	1081	*	9.30496950054223	0.516942750030124
-chrX	110038886	110039604	719	*	9.15166255544827	0.538333091496957
-chrX	7895031	7896360	1330	*	9.0186963859978	0.530511552117518
-chrX	153775262	153776107	846	*	8.8961832017677	0.523304894221629
-chrX	48768632	48769670	1039	*	8.86784774515986	0.521638102656463
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-chrX	100603351	100604329	979	*	8.75747172801691	0.5151453957657
-chrX	152938698	152940274	1577	*	8.06615661246139	0.576154043747242
-chrX	128977299	128978347	1049	*	7.83078878535237	0.522052585690158
-chrX	133680249	133680974	726	*	7.81500163973275	0.651250136644396
-chrX	103267926	103268686	761	*	7.80954902010755	0.600734540008273
-chrX	118986581	118987328	748	*	7.79865165352476	0.519910110234984
-chrX	153602509	153603503	995	*	7.77220517127964	0.55515751223426
-chrX	16730344	16731095	752	*	7.66653370950929	0.511102247300619
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-chrX	8769269	8769701	433	*	7.64680236312294	0.637233530260245
-chrX	103499335	103500137	803	*	7.51528226846813	0.536805876319152
-chrX	3264341	3265404	1064	*	7.33685696316178	0.524061211654413
-chrX	149106299	149107029	731	*	7.28614833596923	0.520439166854945
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-chrX	152676586	152677554	969	*	5.47032083167345	0.547032083167345
-chrX	101967017	101967643	627	*	5.46400855518512	0.546400855518512
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-chrY	21728952	21729665	714	*	5.38568043211166	0.538568043211166
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+chrX	24167821	24167821	1	0.5
+chrX	34181023	34181023	1	0.5
+chrX	70680473	70680473	1	0.5
+chrX	79141321	79141321	1	0.5
+chrX	88308360	88308360	1	0.5
+chrX	90336867	90336867	1	0.5
+chrX	92657204	92657204	1	0.5
+chrX	94164453	94164453	1	0.5
+chrX	108410752	108410752	1	0.5