# HG changeset patch
# User youyuh48
# Date 1535632785 14400
# Node ID d4372c7fa79d99b24a8850bc5a7d27883586301c
planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/centrifuge
diff -r 000000000000 -r d4372c7fa79d centrifuge_kreport.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/centrifuge_kreport.xml Thu Aug 30 08:39:45 2018 -0400
@@ -0,0 +1,48 @@
+
+ Centrifuge-kreport creates Kraken-style reports from centrifuge out files
+
+ centrifuge
+
+ output.txt
+ ]]>
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+ OPTIONS
+
+centrifuge-kreport creates Kraken-style reports from centrifuge out files.
+
+Options:
+ -x INDEX (REQUIRED) Centrifuge index
+
+ --only-unique Only count reads that were uniquely assigned to one taxon
+ --show-zeros Show clades that have zero reads, too
+ --is-count-table The format of the file is 'TAXIDCOUNT' instead of the standard
+ Centrifuge output format
+
+ --min-score SCORE Require a minimum score for reads to be counted
+ --min-length LENGTH Require a minimum alignment length to the read
+ ]]>
+
+ 10.1101/gr.210641.116
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+
diff -r 000000000000 -r d4372c7fa79d test-data/centrifuge_indices.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/centrifuge_indices.loc Thu Aug 30 08:39:45 2018 -0400
@@ -0,0 +1,15 @@
+# centrifuge_indices.loc.sample
+# This is a *.loc.sample file distributed with Galaxy that enables tools
+# to use a directory of indexed data files. This one is for GOTTCHA.
+# See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
+# First create these data files and save them in your own data directory structure.
+# Then, create a bowtie_indices.loc file to use those indexes with tools.
+# Copy this file, save it with the same name (minus the .sample),
+# follow the format examples, and store the result in this directory.
+# The file should include an one line entry for each index set.
+# The path points to the "basename" for the set, not a specific file.
+# It has three text columns seperated by TABS.
+#
+#
+#
+test test ${__HERE__}/centrifuge_test
diff -r 000000000000 -r d4372c7fa79d test-data/centrifuge_test.1.cf
Binary file test-data/centrifuge_test.1.cf has changed
diff -r 000000000000 -r d4372c7fa79d test-data/centrifuge_test.2.cf
Binary file test-data/centrifuge_test.2.cf has changed
diff -r 000000000000 -r d4372c7fa79d test-data/centrifuge_test.3.cf
Binary file test-data/centrifuge_test.3.cf has changed
diff -r 000000000000 -r d4372c7fa79d test-data/defaults.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/defaults.tsv Thu Aug 30 08:39:45 2018 -0400
@@ -0,0 +1,17 @@
+readID seqID taxID score 2ndBestScore hitLength queryLength numMatches
+C_1 gi|7 9913 4225 4225 80 80 2
+C_1 gi|4 9646 4225 4225 80 80 2
+C_2 gi|4 9646 4225 4225 80 80 2
+C_2 gi|7 9913 4225 4225 80 80 2
+C_3 gi|7 9913 4225 4225 80 80 2
+C_3 gi|4 9646 4225 4225 80 80 2
+C_4 gi|4 9646 4225 4225 80 80 2
+C_4 gi|7 9913 4225 4225 80 80 2
+1_1 gi|4 9646 4225 0 80 80 1
+1_2 gi|4 9646 4225 0 80 80 1
+2_1 gi|7 9913 4225 0 80 80 1
+2_2 gi|7 9913 4225 0 80 80 1
+2_3 gi|7 9913 4225 0 80 80 1
+2_4 gi|7 9913 4225 0 80 80 1
+2_5 gi|7 9913 4225 0 80 80 1
+2_6 gi|7 9913 4225 0 80 80 1
diff -r 000000000000 -r d4372c7fa79d test-data/defaults.tsv.kreport
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/defaults.tsv.kreport Thu Aug 30 08:39:45 2018 -0400
@@ -0,0 +1,36 @@
+ 0.00 0 0 U 0 unclassified
+ 75.00 12 0 - 1 root
+ 75.00 12 0 - 131567 cellular organisms
+ 75.00 12 0 D 2759 Eukaryota
+ 75.00 12 0 - 33154 Opisthokonta
+ 75.00 12 0 K 33208 Metazoa
+ 75.00 12 0 - 6072 Eumetazoa
+ 75.00 12 0 - 33213 Bilateria
+ 75.00 12 0 - 33511 Deuterostomia
+ 75.00 12 0 P 7711 Chordata
+ 75.00 12 0 - 89593 Craniata
+ 75.00 12 0 - 7742 Vertebrata
+ 75.00 12 0 - 7776 Gnathostomata
+ 75.00 12 0 - 117570 Teleostomi
+ 75.00 12 0 - 117571 Euteleostomi
+ 75.00 12 0 - 8287 Sarcopterygii
+ 75.00 12 0 - 1338369 Dipnotetrapodomorpha
+ 75.00 12 0 - 32523 Tetrapoda
+ 75.00 12 0 - 32524 Amniota
+ 75.00 12 0 C 40674 Mammalia
+ 75.00 12 0 - 32525 Theria
+ 75.00 12 0 - 9347 Eutheria
+ 75.00 12 0 - 1437010 Boreoeutheria
+ 75.00 12 0 - 314145 Laurasiatheria
+ 50.00 8 0 - 91561 Cetartiodactyla
+ 50.00 8 0 - 9845 Ruminantia
+ 50.00 8 0 - 35500 Pecora
+ 50.00 8 0 F 9895 Bovidae
+ 50.00 8 0 - 27592 Bovinae
+ 50.00 8 0 G 9903 Bos
+ 50.00 8 8 S 9913 Bos taurus
+ 25.00 4 0 O 33554 Carnivora
+ 25.00 4 0 - 379584 Caniformia
+ 25.00 4 0 F 9632 Ursidae
+ 25.00 4 0 G 9645 Ailuropoda
+ 25.00 4 4 S 9646 Ailuropoda melanoleuca
diff -r 000000000000 -r d4372c7fa79d tool-data/centrifuge_indices.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/centrifuge_indices.loc.sample Thu Aug 30 08:39:45 2018 -0400
@@ -0,0 +1,15 @@
+# centrifuge_indices.loc.sample
+# This is a *.loc.sample file distributed with Galaxy that enables tools
+# to use a directory of indexed data files. This one is for GOTTCHA.
+# See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
+# First create these data files and save them in your own data directory structure.
+# Then, create a bowtie_indices.loc file to use those indexes with tools.
+# Copy this file, save it with the same name (minus the .sample),
+# follow the format examples, and store the result in this directory.
+# The file should include an one line entry for each index set.
+# The path points to the "basename" for the set, not a specific file.
+# It has three text columns seperated by TABS.
+#
+#
+#
+#p_compressed p_compressed_2018_4_15 /galaxy-central/tool-data/centrifuge/p_compressed
diff -r 000000000000 -r d4372c7fa79d tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Thu Aug 30 08:39:45 2018 -0400
@@ -0,0 +1,7 @@
+
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diff -r 000000000000 -r d4372c7fa79d tool_data_table_conf.xml.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test Thu Aug 30 08:39:45 2018 -0400
@@ -0,0 +1,6 @@
+
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