# HG changeset patch
# User iuc
# Date 1514906092 18000
# Node ID 30d42784676423144bc106affb6eebcaaed9c047
# Parent  3bc1425f90002a408464a0ab4e55a10376296395
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 8def073a083b0619e366436a067a614555190058

diff -r 3bc1425f9000 -r 30d427846764 hicBuildMatrix.xml
--- a/hicBuildMatrix.xml	Sat Dec 30 09:26:27 2017 -0500
+++ b/hicBuildMatrix.xml	Tue Jan 02 10:14:52 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_hicbuildmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+<tool id="hicexplorer_hicbuildmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.1">
     <description>creates a contact matrix</description>
     <macros>
         <token name="@BINARY@">hicBuildMatrix</token>
@@ -61,6 +61,7 @@
         mv ./QCfolder/* $qc.files_path/
         &&
         mv $qc.files_path/hicQC.html $qc
+        && mv $qc.files_path/*.log raw_qc
         && samtools sort ./unsorted.bam -o sorted.bam
        
 ]]>
@@ -128,6 +129,7 @@
             <filter>outputFormat == 'cool'</filter>
         </data>
         <data name="qc" format="html" label="${tool.name} QC"/>
+        <data name="raw_qc" from_work_dir='raw_qc' label="${tool.name} raw QC" />
     </outputs>
     <tests>
         <test>
@@ -145,6 +147,7 @@
 
             <output name="outBam" file="small_test_matrix_result_sorted.bam" ftype="bam"/>
             <output name="outFileName_h5" file="small_test_matrix_2.h5" ftype="h5" compare="sim_size"/>
+            <output name="raw_qc" file='raw_qc_report' compare='diff' lines_diff='2'/>
         </test>
     </tests>
     <help><![CDATA[
diff -r 3bc1425f9000 -r 30d427846764 macros.xml
--- a/macros.xml	Sat Dec 30 09:26:27 2017 -0500
+++ b/macros.xml	Tue Jan 02 10:14:52 2018 -0500
@@ -11,7 +11,7 @@
 
     <xml name="citations">
         <citations>
-            <citation type="doi">10.5281/zenodo.1123667</citation>
+            <citation type="doi">10.5281/zenodo.1133705</citation>
             <yield />
         </citations>
     </xml>
diff -r 3bc1425f9000 -r 30d427846764 test-data/raw_qc_report
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/raw_qc_report	Tue Jan 02 10:14:52 2018 -0500
@@ -0,0 +1,29 @@
+
+File	text_matrix.h5		
+Pairs considered	983		
+Min rest. site distance	300		
+Max library insert size	1000		
+
+#	count	(percentage w.r.t. total sequenced reads)
+Pairs mappable, unique and high quality	300	(30.52)
+Pairs used	215	(21.87)
+One mate unmapped	506	(51.48)
+One mate not unique	13	(1.32)
+One mate low quality	164	(16.68)
+
+#	count	(percentage w.r.t. mappable, unique and high quality pairs)
+dangling end	0	(0.00)
+self ligation (removed)	0	(0.00)
+One mate not close to rest site	0	(0.00)
+same fragment	85	(28.33)
+self circle	0	(0.00)
+duplicated pairs	0	(0.00)
+
+#	count	(percentage w.r.t. total valid pairs used)
+inter chromosomal	24	(11.16)
+short range < 20kb	61	(28.37)
+long range	130	(60.47)
+inward pairs	42	(19.53)
+outward pairs	66	(30.70)
+left pairs	48	(22.33)
+right pairs	35	(16.28)