# HG changeset patch
# User iuc
# Date 1645189963 0
# Node ID f350d182f7867d0a4d77175db04905c3040a3c35
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
diff -r 000000000000 -r f350d182f786 binning_refiner.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/binning_refiner.xml Fri Feb 18 13:12:43 2022 +0000
@@ -0,0 +1,125 @@
+
+ refines metagenome bins
+
+ macros.xml
+
+
+ 'input_bin_dir/bins/${file_name}' &&
+ #else:
+ ln -s '${f}' 'input_bin_dir/bins/${file_name}' &&
+ #end if
+#end for
+
+Binning_refiner
+-i input_bin_dir
+-p 'refined'
+&& mv 'refined_Binning_refiner_outputs/refined_contigs.txt' '$output_refined_contigs'
+&& mv 'refined_Binning_refiner_outputs/refined_sources_and_length.txt' '$output_sources_and_length'
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff -r 000000000000 -r f350d182f786 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Fri Feb 18 13:12:43 2022 +0000
@@ -0,0 +1,15 @@
+
+ 1.4.3
+ 0
+ 21.09
+
+
+ binning_refiner
+
+
+
+
+ 10.1093/bioinformatics/btx086
+
+
+
diff -r 000000000000 -r f350d182f786 test-data/Concoct_1.fa.gz
Binary file test-data/Concoct_1.fa.gz has changed
diff -r 000000000000 -r f350d182f786 test-data/Concoct_3.fa.gz
Binary file test-data/Concoct_3.fa.gz has changed
diff -r 000000000000 -r f350d182f786 test-data/Concoct_8.fa.gz
Binary file test-data/Concoct_8.fa.gz has changed
diff -r 000000000000 -r f350d182f786 test-data/MetaBAT_17.fa.gz
Binary file test-data/MetaBAT_17.fa.gz has changed
diff -r 000000000000 -r f350d182f786 test-data/MetaBAT_18.fa.gz
Binary file test-data/MetaBAT_18.fa.gz has changed
diff -r 000000000000 -r f350d182f786 test-data/MetaBAT_19.fa.gz
Binary file test-data/MetaBAT_19.fa.gz has changed
diff -r 000000000000 -r f350d182f786 test-data/MetaBAT_20.fa.gz
Binary file test-data/MetaBAT_20.fa.gz has changed
diff -r 000000000000 -r f350d182f786 test-data/MetaBAT_21.fa.gz
Binary file test-data/MetaBAT_21.fa.gz has changed
diff -r 000000000000 -r f350d182f786 test-data/MetaBAT_22.fa.gz
Binary file test-data/MetaBAT_22.fa.gz has changed
diff -r 000000000000 -r f350d182f786 test-data/MetaBAT_23.fa.gz
Binary file test-data/MetaBAT_23.fa.gz has changed
diff -r 000000000000 -r f350d182f786 test-data/output_refined_contigs.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_refined_contigs.tabular Fri Feb 18 13:12:43 2022 +0000
@@ -0,0 +1,8 @@
+Refined_bin Contigs
+refined_1 scaffold_1016,scaffold_1020,scaffold_1044,scaffold_1066,scaffold_1069,scaffold_1073,scaffold_1086,scaffold_1096,scaffold_1116,scaffold_1122,scaffold_1129,scaffold_1137,scaffold_1167,scaffold_1170,scaffold_1201,scaffold_1253,scaffold_1275,scaffold_1287,scaffold_1296,scaffold_1306,scaffold_1331,scaffold_1333,scaffold_1350,scaffold_1351,scaffold_1353,scaffold_1385,scaffold_1395,scaffold_1425,scaffold_1442,scaffold_1452,scaffold_1455,scaffold_1470,scaffold_1474,scaffold_1499,scaffold_1514,scaffold_1538,scaffold_1541,scaffold_1555,scaffold_1556,scaffold_1559,scaffold_1570,scaffold_1572,scaffold_1599,scaffold_1612,scaffold_1625,scaffold_1628,scaffold_1634,scaffold_1646,scaffold_1771,scaffold_1779,scaffold_1781,scaffold_1808,scaffold_1827,scaffold_1847,scaffold_1879,scaffold_1891,scaffold_1906,scaffold_1909,scaffold_1921,scaffold_1934,scaffold_1936,scaffold_1952,scaffold_1960,scaffold_1985,scaffold_1995,scaffold_2033,scaffold_2039,scaffold_2064,scaffold_2080,scaffold_2102,scaffold_2124,scaffold_2128,scaffold_2172,scaffold_2196,scaffold_563,scaffold_583,scaffold_602,scaffold_655,scaffold_734,scaffold_752,scaffold_838,scaffold_895,scaffold_928,scaffold_929,scaffold_933,scaffold_945,scaffold_965,scaffold_967,scaffold_973
+refined_2 scaffold_1064,scaffold_1162,scaffold_1200,scaffold_1236,scaffold_1248,scaffold_1301,scaffold_138,scaffold_150,scaffold_1825,scaffold_2013,scaffold_2040,scaffold_205,scaffold_2134,scaffold_214,scaffold_2164,scaffold_247,scaffold_377,scaffold_380,scaffold_419,scaffold_486,scaffold_488,scaffold_558
+refined_3 scaffold_15,scaffold_20,scaffold_222,scaffold_262,scaffold_660,scaffold_684,scaffold_77,scaffold_861
+refined_4 scaffold_1014,scaffold_1061,scaffold_1081,scaffold_1177,scaffold_1193,scaffold_1257,scaffold_1349,scaffold_1377,scaffold_1428,scaffold_1503,scaffold_1520,scaffold_1558,scaffold_1576,scaffold_1598,scaffold_1635,scaffold_1698,scaffold_1704,scaffold_1759,scaffold_1763,scaffold_1784,scaffold_1867,scaffold_1945,scaffold_2046,scaffold_2139,scaffold_2210,scaffold_437,scaffold_537,scaffold_568,scaffold_667,scaffold_680,scaffold_699,scaffold_700,scaffold_768,scaffold_804,scaffold_832,scaffold_834,scaffold_923,scaffold_939,scaffold_986
+refined_5 scaffold_1048,scaffold_1049,scaffold_1150,scaffold_126,scaffold_14,scaffold_232,scaffold_571,scaffold_66
+refined_6 scaffold_1667,scaffold_186,scaffold_259,scaffold_301,scaffold_32,scaffold_461,scaffold_466,scaffold_659,scaffold_708
+refined_7 scaffold_1140,scaffold_1172,scaffold_1303,scaffold_1510,scaffold_1614,scaffold_1649,scaffold_1814,scaffold_1852,scaffold_2104,scaffold_2153,scaffold_260,scaffold_273,scaffold_361,scaffold_369,scaffold_429,scaffold_589,scaffold_906,scaffold_987,scaffold_988
diff -r 000000000000 -r f350d182f786 test-data/output_sources_and_length.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_sources_and_length.tabular Fri Feb 18 13:12:43 2022 +0000
@@ -0,0 +1,8 @@
+Refined_bin Size(Kbp) Source
+refined_1 1267.23 Concoct_3_fa_gz.fasta.gz
+refined_2 904.03 MetaBAT_17_fa_gz.fasta.gz
+refined_3 848.68 MetaBAT_18_fa_gz.fasta.gz
+refined_4 728.02 MetaBAT_20_fa_gz.fasta.gz
+refined_5 693.6 MetaBAT_21_fa_gz.fasta.gz
+refined_6 612.08 MetaBAT_22_fa_gz.fasta.gz
+refined_7 538.59 MetaBAT_23_fa_gz.fasta.gz