# HG changeset patch
# User iuc
# Date 1528572880 14400
# Node ID d7a84a789c832504e3112d93974491258dcbb34a
# Parent  c886ddb8e122ef536a64c1a19d4626cfad429877
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2307743fd10f0babde52eec30289fe1682236287

diff -r c886ddb8e122 -r d7a84a789c83 hicPlotDistVsCounts.xml
--- a/hicPlotDistVsCounts.xml	Fri Apr 27 08:39:05 2018 -0400
+++ b/hicPlotDistVsCounts.xml	Sat Jun 09 15:34:40 2018 -0400
@@ -30,6 +30,10 @@
             #if $chromosomeExclude:
                 --chromosomeExclude '$chroms'
             #end if
+
+            #if $outFileData_Boolean:
+                $outFileData_Boolean ./outFileData
+            #end if
 ]]>
     </command>
     <inputs>
@@ -49,9 +53,14 @@
                 <validator type="empty_field" />
             </param>
         </repeat>
+        <param name='outFileData_Boolean' type='boolean' truevalue='--outFileData'  falsevalue="" checked="false" label="Save data underlying the plots as BAM"
+            help="A bam file containing all data underlying the plots is saved on this file."/>
     </inputs>
     <outputs>
         <data name="plotFile" from_work_dir="plot.png" format="png" label="${tool.name} on [${on_string}]: Plot"/>
+        <data name="outFileData" from_work_dir="outFileData" format="txt" label="${tool.name} data file on ${on_string}">
+            <filter>outFileData_Boolean</filter>
+        </data>
     </outputs>
     <tests>
         <test>
@@ -60,6 +69,13 @@
             <output name="plotFile" file="hicPlotDistVsCounts_result1.png" ftype="png" compare="sim_size"/>
         </test>
         <test>
+            <param name="matrices" ftype="h5" value="small_test_matrix_50kb_res.h5"/>
+            <param name="skipDiagonal" value="False"/>
+            <param name='outFileData_Boolean' value='True'/>
+            <output name="plotFile" file="hicPlotDistVsCounts_result1.png" ftype="png" compare="sim_size"/>
+            <output name="outFileData" file="distVsCounts.txt" ftype="txt" compare="sim_size" delta='600'/>
+        </test>
+        <test>
             <param name="matrices" ftype="h5" value="small_test_matrix_50kb_res.h5,small_test_matrix_50kb_res.h5"/>
             <param name="skipDiagonal" value="False"/>
             <param name="perchr" value="True" />
diff -r c886ddb8e122 -r d7a84a789c83 macros.xml
--- a/macros.xml	Fri Apr 27 08:39:05 2018 -0400
+++ b/macros.xml	Sat Jun 09 15:34:40 2018 -0400
@@ -1,6 +1,6 @@
 <macros>
     <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
-    <token name="@WRAPPER_VERSION@">2.1.2</token>
+    <token name="@WRAPPER_VERSION@">2.1.4</token>
     <token name="@USE_RANGE@">
         #if $use_range.select_use_range == "yes_use_range":
             --range $range_min:$range_max
diff -r c886ddb8e122 -r d7a84a789c83 test-data/Li_chrX30-35_cool.png
Binary file test-data/Li_chrX30-35_cool.png has changed
diff -r c886ddb8e122 -r d7a84a789c83 test-data/Li_et_al_2015.cool
Binary file test-data/Li_et_al_2015.cool has changed
diff -r c886ddb8e122 -r d7a84a789c83 test-data/distVsCounts.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/distVsCounts.txt	Sat Jun 09 15:34:40 2018 -0400
@@ -0,0 +1,62 @@
+	Chromosome	Contacts	Distance	Matrix
+0	all	2.673662429796039	0	small_test_matrix_50kb_res.h5
+1	all	1.6689429928741093	50000	small_test_matrix_50kb_res.h5
+2	all	0.7796660703637448	100000	small_test_matrix_50kb_res.h5
+3	all	0.4811377245508982	150000	small_test_matrix_50kb_res.h5
+4	all	0.3259170174383644	200000	small_test_matrix_50kb_res.h5
+5	all	0.2530193236714976	250000	small_test_matrix_50kb_res.h5
+6	all	0.19278569263413156	300000	small_test_matrix_50kb_res.h5
+7	all	0.1475958612294583	350000	small_test_matrix_50kb_res.h5
+8	all	0.12736713500305435	400000	small_test_matrix_50kb_res.h5
+9	all	0.11737664725712535	450000	small_test_matrix_50kb_res.h5
+10	all	0.09348093480934809	500000	small_test_matrix_50kb_res.h5
+11	all	0.08145634063560629	550000	small_test_matrix_50kb_res.h5
+12	all	0.07492260061919505	600000	small_test_matrix_50kb_res.h5
+13	all	0.06803355079217148	650000	small_test_matrix_50kb_res.h5
+14	all	0.06016209476309227	700000	small_test_matrix_50kb_res.h5
+15	all	0.05411323115420707	750000	small_test_matrix_50kb_res.h5
+16	all	0.0514752040175769	800000	small_test_matrix_50kb_res.h5
+17	all	0.043464566929133856	850000	small_test_matrix_50kb_res.h5
+18	all	0.04835651074589128	900000	small_test_matrix_50kb_res.h5
+19	all	0.04281636536631779	950000	small_test_matrix_50kb_res.h5
+20	all	0.04010184595798854	1000000	small_test_matrix_50kb_res.h5
+21	all	0.034493771957840945	1050000	small_test_matrix_50kb_res.h5
+22	all	0.035256410256410256	1100000	small_test_matrix_50kb_res.h5
+23	all	0.030556449018977163	1150000	small_test_matrix_50kb_res.h5
+24	all	0.027437056165267915	1200000	small_test_matrix_50kb_res.h5
+25	all	0.030774214447683836	1250000	small_test_matrix_50kb_res.h5
+26	all	0.03153446033810143	1300000	small_test_matrix_50kb_res.h5
+27	all	0.026753670473083198	1350000	small_test_matrix_50kb_res.h5
+28	all	0.025867714472822528	1400000	small_test_matrix_50kb_res.h5
+29	all	0.028252299605781867	1450000	small_test_matrix_50kb_res.h5
+30	all	0.025379037574159526	1500000	small_test_matrix_50kb_res.h5
+31	all	0.026124338624338623	1550000	small_test_matrix_50kb_res.h5
+32	all	0.025547445255474453	1600000	small_test_matrix_50kb_res.h5
+33	all	0.0262982689747004	1650000	small_test_matrix_50kb_res.h5
+34	all	0.018036072144288578	1700000	small_test_matrix_50kb_res.h5
+35	all	0.028820375335120642	1750000	small_test_matrix_50kb_res.h5
+36	all	0.024546065904505716	1800000	small_test_matrix_50kb_res.h5
+37	all	0.025303643724696356	1850000	small_test_matrix_50kb_res.h5
+38	all	0.01963439404197698	1900000	small_test_matrix_50kb_res.h5
+39	all	0.020380434782608696	1950000	small_test_matrix_50kb_res.h5
+40	all	0.026244035446489435	2000000	small_test_matrix_50kb_res.h5
+41	all	0.024623803009575923	2050000	small_test_matrix_50kb_res.h5
+42	all	0.024365133836650652	2100000	small_test_matrix_50kb_res.h5
+43	all	0.01928374655647383	2150000	small_test_matrix_50kb_res.h5
+44	all	0.017622667588113337	2200000	small_test_matrix_50kb_res.h5
+45	all	0.015256588072122053	2250000	small_test_matrix_50kb_res.h5
+46	all	0.021224773834377174	2300000	small_test_matrix_50kb_res.h5
+47	all	0.01920391061452514	2350000	small_test_matrix_50kb_res.h5
+48	all	0.014365802382620883	2400000	small_test_matrix_50kb_res.h5
+49	all	0.014416315049226441	2450000	small_test_matrix_50kb_res.h5
+50	all	0.016231474947071278	2500000	small_test_matrix_50kb_res.h5
+51	all	0.013456090651558074	2550000	small_test_matrix_50kb_res.h5
+52	all	0.01492007104795737	2600000	small_test_matrix_50kb_res.h5
+53	all	0.020306376914855716	2650000	small_test_matrix_50kb_res.h5
+54	all	0.013576277241872096	2700000	small_test_matrix_50kb_res.h5
+55	all	0.0146900752418488	2750000	small_test_matrix_50kb_res.h5
+56	all	0.017966223499820338	2800000	small_test_matrix_50kb_res.h5
+57	all	0.017297297297297298	2850000	small_test_matrix_50kb_res.h5
+58	all	0.018070112034694615	2900000	small_test_matrix_50kb_res.h5
+59	all	0.013773106197897789	2950000	small_test_matrix_50kb_res.h5
+60	all	0.01599418393311523	3000000	small_test_matrix_50kb_res.h5