# HG changeset patch # User iuc # Date 1643372493 0 # Node ID d27a4ed006ee58c1c864c5c1a47253db7f5793d2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd" diff -r 000000000000 -r d27a4ed006ee jgi_summarize_bam_contig_depths.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/jgi_summarize_bam_contig_depths.xml Fri Jan 28 12:21:33 2022 +0000 @@ -0,0 +1,178 @@ + + for MetaBAT2 + + macros.xml + + + + + +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + + +

+ + + + + advanced["output_paired_contigs"] == "yes" + + + advanced["use_reference_cond"]["use_reference"] == "yes" + + + advanced["use_reference_cond"]["use_reference"] == "yes" + + + advanced["use_reference_cond"]["use_reference"] == "yes" + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +Calculates coverage depth for each sequence in one or more selected BAM files, producing a tabular file (for each input) +having mean and variance of base coverage depth that can be used as one of the inputs for the MetaBAT2 metagenome binning +tool. + +The algorithm used for calculating the coverage depth is adjusted by a few factors to improve the fidelity of the metrics +when correlating abundance coverage in the binning stage. By default the following adjustments are applied. + +**Edge bases are ignored** + +Edge bases are not counted as coverage, by the lesser of 1 AverageReadLength or (--maxEdgeBases=75). This is because most +mappers can not reliably place a read that would extend off the edge of a sequence, and coverage depth tends to drop towards +0 at the edge of a contig or scaffold. Use --includeEdgeBases to include the coverage in this region. + +**Reads with high mapping errors are skipped** + +Reads that map imperfectly are excluded when the %ID of the mapping drops below a threshold (--percentIdentity=97). +MetaBAT2 is designed to resolve strain variation and mapping reads with low %ID indicate that the read actually came from +a different strain/species. + +%ID is calculated from the CIGAR string and/or NM/MD fields and == 100 * MatchedBases / (MatchedBases + Substituions + +Insertions + Deletions). This ensures that clips, insertions, deletions and mismatches are excluded from the coverage count. +Only the read bases that exactly match the reference are counted as coverage. This generally has a small effect, except in +the case of long reads from PacBio and Nanopore. + +**More information** + +https://bitbucket.org/berkeleylab/metabat/src/master/ + +**Options** + + * **Select a reference genome** - optionally select the reference genome that was used to map the input bam file(s) and 3 additional outputs will be produced; gc coverage histogram, read statistics and perfect kmer counts. + + + + + diff -r 000000000000 -r d27a4ed006ee macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Jan 28 12:21:33 2022 +0000 @@ -0,0 +1,15 @@ + + 2.15 + 0 + 21.01 + + + metabat2 + + + + + 10.7717/peerj.7359 + + + diff -r 000000000000 -r d27a4ed006ee test-data/NC_002945v4.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NC_002945v4.fasta Fri Jan 28 12:21:33 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 d27a4ed006ee test-data/fasta_indexes.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fasta_indexes.loc Fri Jan 28 12:21:33 2022 +0000 @@ -0,0 +1,1 @@ +89 89 Mycobacterium_AF2122 ${__HERE__}/NC_002945v4.fasta diff -r 000000000000 -r d27a4ed006ee test-data/input0.fasta.gz Binary file test-data/input0.fasta.gz has changed diff -r 000000000000 -r d27a4ed006ee test-data/input1.bam Binary file test-data/input1.bam has changed diff -r 000000000000 -r d27a4ed006ee test-data/input2.bam Binary file test-data/input2.bam has changed diff -r 000000000000 -r d27a4ed006ee test-data/input_depth1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_depth1.tabular Fri Jan 28 12:21:33 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 d27a4ed006ee test-data/jgi_output1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/jgi_output1.tabular Fri Jan 28 12:21:33 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 d27a4ed006ee test-data/jgi_output2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/jgi_output2.tabular Fri Jan 28 12:21:33 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 d27a4ed006ee 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 12:21:33 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 d27a4ed006ee 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 12:21:33 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 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Deletions SoftClips HardClips PctId2 PctId3 PctId4 PctId5 PctId6 PctId7 PctId8 NM ReadGC MappedGC diff -r 000000000000 -r d27a4ed006ee test-data/process_log.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/process_log.txt Fri Jan 28 12:21:33 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 d27a4ed006ee 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 12:21:33 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 d27a4ed006ee 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 12:21:33 2022 +0000 @@ -0,0 +1,8 @@ + + + + value, dbkey, name, path + +

+ + diff -r 000000000000 -r d27a4ed006ee 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 12:21:33 2022 +0000 @@ -0,0 +1,7 @@ + + + value, dbkey, name, path + +

+ +