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changeset 3:e1d4cab2daea draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 2e8d990fa8b6de085046195464071020b467ce5a"
author iuc
date Sun, 19 Jan 2020 04:34:14 -0500
parents a5145865e467
children b08ac10aed96
files est-abundance.xml test-data/test_db/database.kraken test-data/test_db/database100mers.kraken test-data/test_db/hash.k2d test-data/test_db/library/added/9C7DdW7GAD.fna test-data/test_db/library/added/9C7DdW7GAD.fna.masked test-data/test_db/library/added/cWk1IBlK73.fna test-data/test_db/library/added/cWk1IBlK73.fna.masked test-data/test_db/library/added/prelim_map.txt test-data/test_db/library/added/prelim_map_QXr8C5PiOX.txt test-data/test_db/library/added/prelim_map_l8ftMYsZv0.txt test-data/test_db/opts.k2d test-data/test_db/seqid2taxid.map test-data/test_db/taxo.k2d
diffstat 12 files changed, 3 insertions(+), 47 deletions(-) [+]
line wrap: on
line diff
--- a/est-abundance.xml	Thu Oct 17 15:50:37 2019 -0400
+++ b/est-abundance.xml	Sun Jan 19 04:34:14 2020 -0500
@@ -48,13 +48,13 @@
             <param name="input" value="NC_003198.1_simulated_kraken_report.txt" ftype="tabular"/>
             <param name="level" value="S" />
             <param name="bracken_database" value="test_entry"/>
-	    <output name="report" file="NC_003198.1_simulated_bracken_report.txt" ftype="tabular"/>
+            <output name="report" file="NC_003198.1_simulated_bracken_report.txt" ftype="tabular"/>
         </test>
-	<test>
+        <test>
             <param name="input" value="NC_011750.1_simulated_kraken_report.txt" ftype="tabular"/>
             <param name="level" value="S" />
             <param name="bracken_database" value="test_entry"/>
-	    <output name="report" file="NC_011750.1_simulated_bracken_report.txt" ftype="tabular"/>
+            <output name="report" file="NC_011750.1_simulated_bracken_report.txt" ftype="tabular"/>
         </test>
     </tests>
     <help>
--- a/test-data/test_db/database.kraken	Thu Oct 17 15:50:37 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-C	NC_003198.1	220341	910	220341:169 A:67 543:23 220341:9 A:42 220341:9 543:65 220341:134 543:2 220341:356
-C	NC_011750.1	585057	910	585057:11 A:41 585057:116 A:67 543:24 585057:7 A:42 585057:10 543:64 585057:134 543:2 585057:358
--- a/test-data/test_db/database100mers.kraken	Thu Oct 17 15:50:37 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-NC_003198.1	220341	220341	910	0:2 543:23 220341:786 
-NC_011750.1	585057	585057	910	0:2 543:24 585057:785 
Binary file test-data/test_db/hash.k2d has changed
--- a/test-data/test_db/library/added/9C7DdW7GAD.fna	Thu Oct 17 15:50:37 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,17 +0,0 @@
->NC_003198.1 Salmonella enterica subsp. enterica serovar Typhi str. CT18, complete genome
-AGAGATTACGTCTGGTTGCAAGAGATCATAACAGGGGAAATTGATTGAAAATAAATATAT
-CGCCAGCAGCACATGAACAAGTTTCGGAATGTGATCAATTTAAAAATTTATTGACTTAGG
-CGGGCAGATACTTTAACCAATATAGGAATACAAGACAGACAAATAAAAATGACAGAGTAC
-ACAACATCCATGAACCGCATCAGxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxAGGT
-AACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGAACAGTGCGG
-GCxxxxxxxxCGACCAGAGATCACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGT
-ACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATTCC
-AGGCAAGGGCAGGTAGCGACCGTACTTTCCGCCCCCGCGAAAATTACCAACCATCTGGTG
-GCGATGATTGAAAAAACTATCGGCGGCCAGGATGCTTTGCCGAATATCAGCGATGCCGAA
-CGTATTTTTTCTGACCTGCTCGCAGGACTTGCCAGCGCGCAGCCGGGATTCCCGCTTGCA
-CGGTTGAAAATGGTTGTCGAACAAGAATTCGCTCAGATCAAACATGTTTTGCATGGTATC
-AGCCTGCTGGGTCAGTGCCCGGATAGCATCAACGCCGCGCTGATTTGCCGTGGCGAAAAA
-ATGTCGATCGCGATTATGGCGGGACTCCTGGAGGCGCGTGGACATCGCGTCACGGTGATC
-GATCCGGTAGAAAAACTGCTGGCGGTGGGCCATTACCTTGAATCTACCGTCGATATCGCG
-GAATCGACTCGCCGTATCGCCGCCAGCCAGATCCCGGCCGATCACATGATCCTGATGGCG
-GGCTTTACTG
--- a/test-data/test_db/library/added/cWk1IBlK73.fna	Thu Oct 17 15:50:37 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,17 +0,0 @@
->NC_011750.1 Escherichia coli IAI39 chromosome, complete genome
-GCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTxxxxxxxGAGTGTCT
-GATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGT
-CACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACA
-CAACATCCATGAAACGCATTAGxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxAGGTA
-ACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGGC
-xxxxxxxxCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGTAC
-ATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAG
-GCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGC
-GATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACG
-TATTTTTGCCGAACTTCTGACGGGACTCGCCGCTGCCCAACCGGGATTCCCGCTGGCGCA
-ACTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATTAG
-TTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCTGATTTGCCGTGGCGAGAAAAT
-GTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACCGTTATCGA
-TCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCTGA
-GTCCACCCGCCGTATTGCGGCAAGTCGTATTCCGGCTGATCACATGGTGCTGATGGCAGG
-TTTCACCGCC
--- a/test-data/test_db/library/added/prelim_map.txt	Thu Oct 17 15:50:37 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-ACCNUM	NC_011750.1	NC_011750
-ACCNUM	NC_003198.1	NC_003198
--- a/test-data/test_db/library/added/prelim_map_QXr8C5PiOX.txt	Thu Oct 17 15:50:37 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-ACCNUM	NC_003198.1	NC_003198
--- a/test-data/test_db/library/added/prelim_map_l8ftMYsZv0.txt	Thu Oct 17 15:50:37 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-ACCNUM	NC_011750.1	NC_011750
Binary file test-data/test_db/opts.k2d has changed
--- a/test-data/test_db/seqid2taxid.map	Thu Oct 17 15:50:37 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-NC_003198.1	220341
-NC_011750.1	585057
Binary file test-data/test_db/taxo.k2d has changed