# HG changeset patch # User iuc # Date 1643372465 0 # Node ID 76bc4efa1aeb9e5dd0358126baad009c7e1a99b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd" diff -r 000000000000 -r 76bc4efa1aeb macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Jan 28 12:21:05 2022 +0000 @@ -0,0 +1,15 @@ + + 2.15 + 0 + 21.01 + + + metabat2 + + + + + 10.7717/peerj.7359 + + + diff -r 000000000000 -r 76bc4efa1aeb metabat2.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/metabat2.xml Fri Jan 28 12:21:05 2022 +0000 @@ -0,0 +1,131 @@ + + metagenome binning + + macros.xml + + + process_log.txt +#if str($advanced.output_process_log) == 'yes': + && mv process_log.txt '$process_log' +#end if + ]]> + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + advanced['output_process_log'] == 'yes' + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 000000000000 -r 76bc4efa1aeb test-data/NC_002945v4.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NC_002945v4.fasta Fri Jan 28 12:21:05 2022 +0000 @@ -0,0 +1,101 @@ +>NC_002945.4 Mycobacterium bovis AF2122/97 genome assembly, chromosome: Mycobacterium_bovis_AF2122/97 +TTGACCGATGACCCCGGTTCAGGCTTCACCACAGTGTGGAACGCGGTCGTCTCCGAACTTAACGGCGACC +CTAAGGTTGACGACGGACCCAGCAGTGATGCTAATCTCAGCGCTCCGCTGACCCCTCAGCAAAGGGCTTG +GCTCAATCTCGTCCAGCCATTGACCATCGTCGAGGGGTTTGCTCTGTTATCCGTGCCGAGCAGCTTTGTC +CAAAACGAAATCGAGCGCCATCTGCGGGCCCCGATTACCGACGCTCTCAGCCGCCGACTCGGACATCAGA +TCCAACTCGGGGTCCGCATCGCTCCGCCGGCGACCGACGAAGCCGACGACACTACCGTGCCGCCTTCCGA +AAATCCTGCTACCACATCGCCAGACACCACAACCGACAACGACGAGATTGATGACAGCGCTGCGGCACGG +GGCGATAACCAGCACAGTTGGCCAAGTTACTTCACCGAGCGCCCGCGCAATACCGATTCCGCTACCGCTG +GCGTAACCAGCCTTAACCGTCGCTACACCTTTGATACGTTCGTTATCGGCGCCTCCAACCGGTTCGCGCA +CGCCGCCGCCTTGGCGATCGCAGAAGCACCCGCCCGCGCTTACAACCCCCTGTTCATCTGGGGCGAGTCC +GGTCTCGGCAAGACACACCTGCTACACGCGGCAGGCAACTATGCCCAACGGTTGTTCCCGGGAATGCGGG +TCAAATATGTCTCCACCGAGGAATTCACCAACGACTTCATTAACTCGCTCCGCGATGACCGCAAGGTCGC +ATTCAAACGCAGCTACCGCGACGTAGACGTGCTGTTGGTCGACGACATCCAATTCATTGAAGGCAAAGAG +GGTATTCAAGAGGAGTTCTTCCACACCTTCAACACCTTGCACAATGCCAACAAGCAAATCGTCATCTCAT +CTGACCGCCCACCCAAGCAGCTCGCCACCCTCGAGGACCGGCTGAGAACCCGCTTTGAGTGGGGGCTGAT +CACTGACGTACAACCACCCGAGCTGGAGACCCGCATCGCCATCTTGCGCAAGAAAGCACAGATGGAACGG +CTCGCGATCCCCGACGATGTCCTCGAACTCATCGCCAGCAGTATCGAACGCAATATCCGTGAACTCGAGG +GCGCGCTGATCCGGGTCACCGCGTTCGCCTCATTGAACAAAACACCAATCGACAAAGCGCTGGCCGAGAT +TGTGCTTCGCGATCTGATCGCCGACGCCAACACCATGCAAATCAGCGCGGCGACGATCATGGCTGCCACC +GCCGAATACTTCGACACTACCGTCGAAGAGCTTCGCGGGCCCGGCAAGACCCGAGCACTGGCCCAGTCAC +GACAGATTGCGATGTACCTGTGTCGTGAGCTCACCGATCTTTCGTTGCCCAAAATCGGCCAAGCGTTCGG +CCGTGATCACACAACCGTCATGTACGCCCAACGCAAGATCCTGTCCGAGATGGCCGAGCGCCGTGAGGTC +TTTGATCACGTCAAAGAACTCACCACTCGCATCCGTCAGCGCTCCAAGCGCTAGCACGGCGTGTTCTTCC +GACAACGTTCTTAAAAAAACTTCTCTCTCCCAGGTCACACCAGTCACAGAGATTGGCTGTGAGTGTCGCT +GTGCACAAACCGCGCACAGACTCATACAGTCCCGGCGGTTCCGTTCACAACCCACGCCTCATCCCCACCG +ACCCAACACACACCCCACAGTCATCGCCACCGTCATCCACAACTCCGACCGACGTCGACCTGCACCAAGA +CCAGACTGTCCCCAAACTGCACACCCTCTAATACTGTTACCGAGATTTCTTCGTCGTTTGTTCTTGGAAA +GACAGCGCTGGGGATCGTTCGCTGGATACCACCCGCATAACTGGCTCGTCGCGGTGGGTCAGAGGTCAAT +GATGAACTTTCAAGTTGACGTGAGAAGCTCTACGGTTGTTGTTCGACTGCTGTTGCGGCCGTCGTGGCGG +GTCACGCGTCATGGGCGTTCGTCGTTGGCAGTCCCCACGCTAGCGGGGCGCTAGCCACGGGATCGAACTC +ATCGTGAGGTGAAAGGGCGCAATGGACGCGGCTACGACAAGAGTTGGCCTCACCGACTTGACGTTTCGTT +TGCTACGAGAGTCTTTCGCCGATGCGGTGTCGTGGGTGGCTAAAAATCTGCCAGCCAGGCCCGCGGTGCC +GGTGCTCTCCGGCGTGTTGTTGACCGGCTCGGACAACGGTCTGACGATTTCCGGATTCGACTACGAGGTT +TCCGCCGAGGCCCAGGTTGGCGCTGAAATTGTTTCTCCTGGAAGCGTTTTAGTTTCTGGCCGATTGTTGT +CCGATATTACCCGGGCGTTGCCTAACAAGCCCGTAGGCGTTCATGTCGAAGGTAACCGGGTCGCATTGAC +CTGCGGTAACGCCAGGTTTTCGCTACCGACGATGCCAGTCGAGGATTATCCGACGCTGCCGACGCTGCCG +GAAGAGACCGGATTGTTGCCTGCGGAATTATTCGCCGAGGCAATCAGTCAGGTCGCTATCGCCGCCGGCC +GGGACGACACGCTGCCTATGTTGACCGGCATCCGGGTCGAAATCCTCGGTGAGACGGTGGTTTTGGCCGC +TACCGACAGGTTTCGCCTGGCTGTTCGAGAACTGAAGTGGTCGGCGTCGTCGCCAGATATCGAAGCGGCT +GTGCTGGTCCCGGCCAAGACGCTGGCCGAGGCCGCCAAAGCGGGCATCGGCGGCTCTGACGTTCGTTTGT +CGTTGGGTACTGGGCCGGGGGTGGGCAAGGATGGCCTGCTCGGTATCAGTGGGAACGGCAAGCGCAGCAC +CACGCGACTTCTTGATGCCGAGTTCCCGAAGTTTCGGCAGTTGCTACCAACCGAACACACCGCGGTGGCC +ACCATGGACGTGGCCGAGTTGATCGAAGCGATCAAGCTGGTTGCGTTGGTAGCTGATCGGGGCGCGCAGG +TGCGCATGGAGTTCGCTGATGGCAGCGTGCGGCTTTCTGCGGGTGCCGATGATGTTGGACGAGCCGAGGA +AGATCTTGTTGTTGACTATGCCGGTGAACCATTGACGATTGCGTTTAACCCAACCTATCTAACGGACGGT +TTGAGTTCGTTGCGCTCGGAGCGAGTGTCTTTCGGGTTTACGACTGCGGGTAAGCCTGCCTTGCTACGTC +CGGTGTCCGGGGACGATCGCCCTGTGGCGGGTCTGAATGGCAACGGTCCGTTCCCGGCGGTGTCGACGGA +CTATGTCTATCTGTTGATGCCGGTTCGGTTGCCGGGCTGAGCACTTGGCGCCCGGGTAGGTGTACGTCCG +TCATTTGGGGCTGCGTGACTTCCGGTCCTGGGCATGTGTAGATCTGGAATTGCATCCAGGGCGGACGGTT +TTTGTTGGGCCTAACGGTTATGGTAAGACGAATCTTATTGAGGCACTGTGGTATTCGACGACGTTAGGTT +CGCACCGCGTTAGCGCCGATTTGCCGTTGATCCGGGTAGGTACCGATCGTGCGGTGATCTCCACGATCGT +GGTGAACGACGGTAGAGAATGTGCCGTCGACCTCGAGATCGCCACGGGGCGAGTCAACAAAGCGCGATTG +AATCGATCATCGGTCCGAAGTACACGTGATGTGGTCGGAGTGCTTCGAGCTGTGTTGTTTGCCCCTGAGG +ATCTGGGGTTGGTTCGTGGGGATCCCGCTGACCGGCGGCGCTATCTGGATGATCTGGCGATCGTGCGTAG +GCCTGCGATCGCTGCGGTACGAGCCGAATATGAGAGGGTGGTGCGCCAGCGGACGGCGTTATTGAAGTCC +GTACCTGGAGCACGGTATCGGGGTGACCGGGGTGTGTTTGACACTCTTGAGGTATGGGACAGTCGTTTGG +CGGAGCACGGGGCTGAACTGGTGGCCGCCCGCATCGATTTGGTCAACCAGTTGGCACCGGAAGTGAAGAA +GGCATACCAGCTGTTGGCGCCGGAATCGCGATCGGCGTCTATCGGTTATCGGGCCAGCATGGATGTAACC +GGTCCCAGCGAGCAGTCAGATACCGATCGGCAATTGTTAGCAGCTCGGCTGTTGGCGGCGCTGGCGGCCC +GTCGGGATGCCGAACTCGAGCGTGGGGTTTGTCTAGTTGGTCCGCACCGTGACGACCTAATACTGCGACT +AGGCGATCAACCCGCGAAAGGATTTGCTAGCCATGGGGAGGCGTGGTCGTTGGCGGTGGCACTGCGGTTG +GCGGCCTATCAACTGTTACGCGTTGATGGTGGTGAGCCGGTGTTGTTGCTCGACGACGTGTTCGCCGAAC +TGGATGTCATGCGCCGTCGAGCGTTGGCGACGGCGGCCGAGTCCGCCGAACAGGTGTTGGTGACTGCCGC +GGTGCTCGAGGATATTCCCGCCGGCTGGGACGCCAGGCGGGTGCACATCGATGTGCGTGCCGATGACACC +GGATCGATGTCGGTGGTTCTGCCATGACGGGTTCTGTTGACCGGCCCGACCAGAATCGCGGTGAGCGATT +AATGAAGTCACCAGGGTTGGATTTGGTCAGGCGCACCCTGGACGAAGCTCGTGCTGCTGCCCGCGCGCGC +GGACAAGACGCCGGTCGAGGGCGGGTCGCTTCCGTTGCGTCGGGTCGGGTGGCCGGACGGCGACGAAGCT +GGTCGGGTCCGGGGCCCGACATTCGTGATCCACAACCGCTGGGTAAGGCCGCTCGTGAGCTGGCAAAGAA +ACGCGGCTGGTCGGTGCGGGTCGCCGAGGGTATGGTGCTCGGCCAGTGGTCTGCGGTGGTCGGCCACCAG +ATCGCCGAACATGCACGCCCGACTGCGCTAAACGACGGGGTGTTGAGCGTGATTGCGGAGTCGACGGCGT +GGGCGACGCAGTTGAGGATCATGCAGGCCCAGCTTCTGGCCAAGATCGCCGCAGCGGTTGGCAACGATGT +GGTGCGATCGCTAAAGATCACCGGGCCGGCGGCACCATCGTGGCGCAAGGGGCCTCGCCATATTGCCGGT +AGGGGTCCGCGCGACACCTACGGATAACACGTCGATCGGCCCAGAACAAGGCGCTCCGGTCCCGGCCTGA +GAGCCTCGAGGACGAAGCGGATCCGTATGCCGGACGTCGGGACGCACCAGGAAGAAAGATGTCCGACGCA +CGGCGCGGTTAGATGGGTAAAAACGAGGCCAGAAGATCGGCCCTGGCGCCCGATCACGGTACAGTGGTGT +GCGACCCCCTGCGGCGACTCAACCGCATGCACGCAACCCCTGAGGAGAGTATTCGGATCGTGGCTGCCCA +GAAAAAGAAGGCCCAAGACGAATACGGCGCTGCGTCTATCACCATTCTCGAAGGGCTGGAGGCCGTCCGC +AAACGTCCCGGCATGTACATTGGCTCGACCGGTGAGCGCGGTTTACACCATCTCATTTGGGAGGTGGTCG +ACAACGCGGTCGACGAGGCGATGGCCGGTTATGCAACCACAGTGAACGTAGTGCTGCTTGAGGATGGCGG +TGTCGAGGTCGCCGACGACGGCCGCGGCATTCCGGTCGCCACCCACGCCTCCGGCATACCGACCGTCGAC +GTGGTGATGACACAACTACATGCCGGCGGCAAGTTCGACTCGGACGCGTATGCGATATCTGGTGGTCTGC +ACGGCGTCGGCGTGTCGGTGGTTAACGCGCTATCCACCCGGCTCGAAGTCGAGATCAAGCGCGACGGGTA +CGAGTGGTCTCAGGTTTATGAGAAGTCGGAACCCCTGGGCCTCAAGCAAGGGGCGCCGACCAAGAAGACG +GGGTCAACGGTACGGTTCTGGGCCGACCCCGCTGTTTTCGAAACCACGGAATACGACTTCGAAACCGTCG +CCCGCCGGCTGCAAGAGATGGCGTTCCTCAACAAGGGGCTGACCATCAACCTGACCGACGAGAGGGTGAC +CCAAGACGAGGTCGTCGACGAAGTGGTCAGCGACGTCGCCGAGGCGCCGAAGTCGGCAAGTGAACGCGCA +GCCGAATCCACTGCACCGCACAAAGTTAAGAGCCGCACCTTTCACTATCCGGGTGGCCTGGTGGACTTCG +TGAAACACATCAACCGCACCAAGAACGCGATTCATAGCAGCATCGTGGACTTTTCCGGCAAGGGCACCGG +GCACGAGGTGGAGATCGCGATGCAATGGAACGCCGGGTATTCGGAGTCGGTGCACACCTTCGCCAACACC +ATCAACACCCACGAGGGCGGCACCCACGAAGAGGGCTTCCGCAGCGCGCTGACGTCGGTGGTGAACAAGT +ACGCCAAGGACCGCAAGCTACTGAAGGACAAGGACCCCAACCTCACCGGTGACGATATCCGGGAAGGCCT +GGCCGCTGTGATCTCGGTGAAGGTCAGCGAACCGCAGTTCGAGGGCCAGACCAAGACCAAGTTGGGCAAC +ACCGAGGTCAAATCGTTTGTGCAGAAGGTCTGTAATGAACAGCTGACCCACTGGTTTGAAGCCAACCCCA +CCGACTCGAAAGTCGTTGTGAACAAGGCTGTGTCCTCGGCGCAAGCCCGTATCGCGGCACGTAAGGCACG +AGAGTTGGTGCGGCGTAAGAGCGCCACCGACATCGGTGGATTGCCCGGCAAGCTGGCCGATTGCCGTTCC +ACGGATCCGCGCAAGTCCGAACTGTATGTCGTAGAAGGTGACTCGGCCGGCGGTTCTGCAAAAAGCGGTC +GCGATTCGATGTTCCAGGCGATACTTCCGCTGCGCGGCAAGATCATCAATGTGGAGAAAGCGCGCATCGA +CCGGGTGCTAAAGAACACCGAAGTTCAGGCGATCATCACGGCGCTGGGCACCGGGATCCACGACGAGTTC +GATATCGGCAAGCTGCGCTACCACAAGATCGTGCTGATGGCCGACGCCGATGTTGACGGCCAACATATTT +CCACGCTGTTGTTGACGTTGTTGTTCCGGTTCATGCGGCCGCTCATCGAGAACGGGCATGTGTTTTTGGC +ACAACCGCCGCTGTACAAACTCAAGTGGCAGCGCAGTGACCCGGAATTCGCATACTCCGACCGCGAGCGC diff -r 000000000000 -r 76bc4efa1aeb test-data/fasta_indexes.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fasta_indexes.loc Fri Jan 28 12:21:05 2022 +0000 @@ -0,0 +1,1 @@ +89 89 Mycobacterium_AF2122 ${__HERE__}/NC_002945v4.fasta diff -r 000000000000 -r 76bc4efa1aeb test-data/input0.fasta.gz Binary file test-data/input0.fasta.gz has changed diff -r 000000000000 -r 76bc4efa1aeb test-data/input1.bam Binary file test-data/input1.bam has changed diff -r 000000000000 -r 76bc4efa1aeb test-data/input2.bam Binary file test-data/input2.bam has changed diff -r 000000000000 -r 76bc4efa1aeb test-data/input_depth1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_depth1.tabular Fri Jan 28 12:21:05 2022 +0000 @@ -0,0 +1,2 @@ +contigName contigLen totalAvgDepth dataset_2272.dat dataset_2272.dat-var +NC_002945.4 Mycobacterium bovis AF2122/97 genome assembly, chromosome: Mycobacterium_bovis_AF2122/97 7000 0 0 0 diff -r 000000000000 -r 76bc4efa1aeb test-data/jgi_output1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/jgi_output1.tabular Fri Jan 28 12:21:05 2022 +0000 @@ -0,0 +1,2 @@ +contigName contigLen totalAvgDepth +gi|251831106|ref|NC_012920.1| 16569 0.667885 0.667885 50.6321 diff -r 000000000000 -r 76bc4efa1aeb test-data/jgi_output2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/jgi_output2.tabular Fri Jan 28 12:21:05 2022 +0000 @@ -0,0 +1,2 @@ +contigName contigLen totalAvgDepth +gi|251831106|ref|NC_012920.1| 16569 1.33577 0.667885 50.6321 0.667885 50.6321 diff -r 000000000000 -r 76bc4efa1aeb test-data/jgi_output_depth1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/jgi_output_depth1.tabular Fri Jan 28 12:21:05 2022 +0000 @@ -0,0 +1,2 @@ +contigName contigLen totalAvgDepth +NC_002945.4 Mycobacterium bovis AF2122/97 genome assembly, chromosome: Mycobacterium_bovis_AF2122/97 7000 0 0 0 diff -r 000000000000 -r 76bc4efa1aeb test-data/jgi_output_gc1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/jgi_output_gc1.tabular Fri Jan 28 12:21:05 2022 +0000 @@ -0,0 +1,102 @@ +GC Ref Reads Coverage Mean Variance +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 1 0 0 0 0 +44 6 0 0 0 0 +45 8 0 0 0 0 +46 10 0 0 0 0 +47 10 0 0 0 0 +48 24 0 0 0 0 +49 45 0 0 0 0 +50 100 0 0 0 0 +51 122 0 0 0 0 +52 139 0 0 0 0 +53 187 0 0 0 0 +54 220 0 0 0 0 +55 254 0 0 0 0 +56 303 0 0 0 0 +57 366 0 0 0 0 +58 449 0 0 0 0 +59 576 0 0 0 0 +60 662 0 0 0 0 +61 581 0 0 0 0 +62 606 0 0 0 0 +63 521 0 0 0 0 +64 431 0 0 0 0 +65 377 0 0 0 0 +66 282 0 0 0 0 +67 229 0 0 0 0 +68 143 0 0 0 0 +69 97 0 0 0 0 +70 56 0 0 0 0 +71 27 0 0 0 0 +72 17 0 0 0 0 +73 6 0 0 0 0 +74 9 0 0 0 0 +75 15 0 0 0 0 +76 11 0 0 0 0 +77 4 0 0 0 0 +78 5 0 0 0 0 +79 1 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 0 0 0 0 0 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 0 0 +100 0 0 0 0 0 diff -r 000000000000 -r 76bc4efa1aeb test-data/jgi_output_kmers1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/jgi_output_kmers1.tabular Fri Jan 28 12:21:05 2022 +0000 @@ -0,0 +1,257 @@ +Kmer MappedReadCount UnmappedReadCount MappedKmers NumMappedReads Mean Variance Skewness Kurtosis +1 0 0 0 0 -nan 0 0 0 +2 0 0 0 0 -nan 0 0 0 +3 0 0 0 0 -nan 0 0 0 +4 0 0 0 0 -nan 0 0 0 +5 0 0 0 0 -nan 0 0 0 +6 0 0 0 0 -nan 0 0 0 +7 0 0 0 0 -nan 0 0 0 +8 0 0 0 0 -nan 0 0 0 +9 0 0 0 0 -nan 0 0 0 +10 0 0 0 0 -nan 0 0 0 +11 0 0 0 0 -nan 0 0 0 +12 0 0 0 0 -nan 0 0 0 +13 0 0 0 0 -nan 0 0 0 +14 0 0 0 0 -nan 0 0 0 +15 0 0 0 0 -nan 0 0 0 +16 0 0 0 0 -nan 0 0 0 +17 0 0 0 0 -nan 0 0 0 +18 0 0 0 0 -nan 0 0 0 +19 0 0 0 0 -nan 0 0 0 +20 0 0 0 0 -nan 0 0 0 +21 0 0 0 0 -nan 0 0 0 +22 0 0 0 0 -nan 0 0 0 +23 0 0 0 0 -nan 0 0 0 +24 0 0 0 0 -nan 0 0 0 +25 0 0 0 0 -nan 0 0 0 +26 0 0 0 0 -nan 0 0 0 +27 0 0 0 0 -nan 0 0 0 +28 0 0 0 0 -nan 0 0 0 +29 0 0 0 0 -nan 0 0 0 +30 0 0 0 0 -nan 0 0 0 +31 0 0 0 0 -nan 0 0 0 +32 0 0 0 0 -nan 0 0 0 +33 0 0 0 0 -nan 0 0 0 +34 0 0 0 0 -nan 0 0 0 +35 0 0 0 0 -nan 0 0 0 +36 0 0 0 0 -nan 0 0 0 +37 0 0 0 0 -nan 0 0 0 +38 0 0 0 0 -nan 0 0 0 +39 0 0 0 0 -nan 0 0 0 +40 0 0 0 0 -nan 0 0 0 +41 0 0 0 0 -nan 0 0 0 +42 0 0 0 0 -nan 0 0 0 +43 0 0 0 0 -nan 0 0 0 +44 0 0 0 0 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0 0 0 0 -nan 0 0 0 +256 0 0 0 0 -nan 0 0 0 diff -r 000000000000 -r 76bc4efa1aeb test-data/jgi_output_paired_contigs1.fasta diff -r 000000000000 -r 76bc4efa1aeb test-data/jgi_output_read_stats1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/jgi_output_read_stats1.tabular Fri Jan 28 12:21:05 2022 +0000 @@ -0,0 +1,1 @@ +ReadName ReadLen AlignedLen PctId MappedTID MappedPos ExactMatches Substitutions Insertions Deletions SoftClips HardClips PctId2 PctId3 PctId4 PctId5 PctId6 PctId7 PctId8 NM ReadGC MappedGC diff -r 000000000000 -r 76bc4efa1aeb test-data/process_log.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/process_log.txt Fri Jan 28 12:21:05 2022 +0000 @@ -0,0 +1,3 @@ +MetaBAT 2 (2.15 (Bioconda)) using minContig 1500, minCV 1.0, minCVSum 1.0, maxP 95%, minS 60, maxEdges 200 and minClsSize 200000. with random seed=345678 +No edges were formed by TNF. +0 bins (0 bases in total) formed. diff -r 000000000000 -r 76bc4efa1aeb tool-data/fasta_indexes.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/fasta_indexes.loc.sample Fri Jan 28 12:21:05 2022 +0000 @@ -0,0 +1,29 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Samtools indexed sequences data files. You will need +#to create these data files and then create a fasta_indexes.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The fasta_indexes.loc +#file has this format (white space characters are TAB characters): +# +# +# +#So, for example, if you had hg19 Canonical indexed stored in +# +# /depot/data2/galaxy/hg19/sam/, +# +#then the fasta_indexes.loc entry would look like this: +# +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +# +#and your /depot/data2/galaxy/hg19/sam/ directory +#would contain hg19canon.fa and hg19canon.fa.fai files. +# +#Your fasta_indexes.loc file should include an entry per line for +#each index set you have stored. The file in the path does actually +#exist, but it should never be directly used. Instead, the name serves +#as a prefix for the index file. For example: +# +#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa +#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa diff -r 000000000000 -r 76bc4efa1aeb tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Fri Jan 28 12:21:05 2022 +0000 @@ -0,0 +1,8 @@ + + + + value, dbkey, name, path + +
+ + diff -r 000000000000 -r 76bc4efa1aeb tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Fri Jan 28 12:21:05 2022 +0000 @@ -0,0 +1,7 @@ + + + value, dbkey, name, path + +
+ +