Mercurial > repos > iuc > metabat2
changeset 0:76bc4efa1aeb draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
| author | iuc |
|---|---|
| date | Fri, 28 Jan 2022 12:21:05 +0000 |
| parents | |
| children | 01f02c5ddff8 |
| files | macros.xml metabat2.xml test-data/NC_002945v4.fasta test-data/fasta_indexes.loc test-data/input0.fasta.gz test-data/input1.bam test-data/input2.bam test-data/input_depth1.tabular test-data/jgi_output1.tabular test-data/jgi_output2.tabular test-data/jgi_output_depth1.tabular test-data/jgi_output_gc1.tabular test-data/jgi_output_kmers1.tabular test-data/jgi_output_paired_contigs1.fasta test-data/jgi_output_read_stats1.tabular test-data/process_log.txt tool-data/fasta_indexes.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
| diffstat | 18 files changed, 663 insertions(+), 0 deletions(-) [+] |
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--- /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 @@ +<macros> + <token name="@TOOL_VERSION@">2.15</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">21.01</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">metabat2</requirement> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.7717/peerj.7359</citation> + </citations> + </xml> +</macros>
--- /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 @@ +<tool id="metabat2" name="MetaBAT2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>metagenome binning</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ +mkdir bins && +metabat2 +--inFile '$inFile' +--outFile 'bins/bin' +#if str($advanced.base_coverage_depth_cond.base_coverage_depth) == 'yes': + #if $advanced.base_coverage_depth_cond.abdFile: + --abdFile '$advanced.base_coverage_depth_cond.abdFile' + #else if $advanced.base_coverage_depth_cond.cvExt: + --cvExt '$advanced.base_coverage_depth_cond.cvExt' + #end if +#end if +--minContig $advanced.minContig +--maxP $advanced.maxP +--minS $advanced.minS +--maxEdges $advanced.maxEdges +--pTNF $advanced.pTNF +$advanced.noAdd +--minCV $advanced.minCV +--minCVSum $advanced.minCVSum +--minClsSize $advanced.minClsSize +--numThreads \${GALAXY_SLOTS:-4} +$advanced.onlyLabel +#if $advanced.saveCls: + $advanced.saveCls + --noBinOut +#end if +$advanced.unbinned +--seed $advanced.seed +> process_log.txt +#if str($advanced.output_process_log) == 'yes': + && mv process_log.txt '$process_log' +#end if + ]]></command> + <inputs> + <param argument="--inFile" type="data" format="fasta,fasta.gz" label="Fasta file containing contigs"/> + <section name="advanced" title="Advanced options"> + <conditional name="base_coverage_depth_cond"> + <param name="base_coverage_depth" type="select" label="Use a base coverage depth file?"> + <option value="no" selected="true">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"/> + <when value="yes"> + <param argument="--abdFile" type="data" format="tabular" optional="True" label="Tabular depth matrix file having mean and variance of base coverage depth" help="Generated by the Calculate contig depths for MetaBAT2 tool"/> + <param argument="--cvExt" type="data" format="tabular" optional="True" label="Base coverage depth file without variance" help="Generated by a tool - not the Calculate contig depths for MetaBAT2 tool"/> + </when> + </conditional> + <param argument="--minContig" type="integer" min="1500" value="1500" label="Minimum size of a contig for binning"/> + <param argument="--maxP" type="integer" min="1" max="100" value="95" label="Percentage of good contigs considered for binning decided by connection among contigs" help="The greater, the more sensitive"/> + <param argument="--minS" type="integer" min="1" max="99" value="60" label="Minimum score of an edge for binning" help="The greater, the more specific"/> + <param argument="--maxEdges" type="integer" value="200" label="Maximum number of edges per node" help="The greater, the more sensitive"/> + <param argument="--pTNF" type="integer" value="0" label="TNF probability cutoff for building TNF graph" help="Use it to skip the preparation step (0:auto)"/> + <param argument="--noAdd" type="boolean" truevalue="--noAdd" falsevalue="" checked="false" label="Turn off additional binning for lost or small contigs?"/> + <param argument="--minCV" type="float" value="1.0" label="Minimum mean coverage of a contig in each library for binning"/> + <param argument="--minCVSum" type="float" value="1.0" label="Minimum total effective mean coverage of a contig for binning" help="Sum of depth over minCV"/> + <param argument="--minClsSize" type="integer" value="200000" label="Minimum size of a bin as the output"/> + <param argument="--onlyLabel" type="boolean" truevalue="--onlyLabel" falsevalue="" checked="false" label="Output only sequence labels as a list in a column without sequences?"/> + <param argument="--saveCls" type="boolean" truevalue="--saveCls" falsevalue="" checked="false" label="Save cluster memberships as a matrix format?"/> + <param argument="--unbinned" type="boolean" truevalue="--unbinned" falsevalue="" checked="false" label="Output fasta file containing unbinned contigs?"/> + <param argument="--seed" type="integer" value="0" label="For exact reproducibility." help="Zero value will use random seed"/> + <param name="output_process_log" type="select" label="Output process log file?"> + <option value="no" selected="true">No</option> + <option value="yes">Yes</option> + </param> + </section> + </inputs> + <outputs> + <collection name="bin_files" type="list" label="${tool.name} on ${on_string}: (bins)"> + <discover_datasets pattern="(?P<designation>.*)\.fa" format="fasta" directory="bins"/> + </collection> + <data name="process_log" format="txt" label="${tool.name} on ${on_string} (process log)"> + <filter>advanced['output_process_log'] == 'yes'</filter> + </data> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="inFile" value="input0.fasta.gz" ftype="fasta.gz"/> + <param name="seed" value="345678"/> + <output_collection name="bin_files" type="list" count="2"> + <element name="bin.1" ftype="fasta"> + <assert_contents> + <has_size value="334554"/> + </assert_contents> + </element> + <element name="bin.2" ftype="fasta"> + <assert_contents> + <has_size value="577866"/> + </assert_contents> + </element> + </output_collection> + </test> + <test expect_num_outputs="2"> + <param name="inFile" value="input0.fasta.gz" ftype="fasta.gz"/> + <param name="base_coverage_depth" value="yes"/> + <param name="abdFile" value="input_depth1.tabular" ftype="tabular"/> + <param name="seed" value="345678"/> + <param name="output_process_log" value="yes"/> + <output_collection name="bin_files" type="list" count="0"/> + <output name="process_log" file="process_log.txt" ftype="txt"/> + </test> + </tests> + <help><![CDATA[ +**What it does** + +MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binning +software that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency. The +tool accepts a fast file containing contigs and produces a collection (i.e., bins) of fasta files. + +MetaBAT2 includes optionizations to MetaBAT. It requires virtually no parameter optimization. Default parameter +values are more reliable to use in most cases since MetaBAT2 adapts to the given data to find the best parameter. +Some parameter settings are still available for advanced users, helping to manage some exceptional cases by changing +the amount of data used for the analysis. + +**More information** + +https://bitbucket.org/berkeleylab/metabat/src/master/ + +**Options** + + * **Use base coverage depth file** - optionally select a base coverage depth file that was either generated by the Calculate contig depths for MetaBAT2 tool or another 3rd party tool. + + ]]></help> + <expand macro="citations"/> +</tool>
--- /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
--- /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
--- /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
--- /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
--- /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
--- /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
--- /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
--- /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 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--- /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
--- /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.
--- /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): +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +#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
--- /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 @@ +<tables> + <!-- Location of SAMTools indexes for FASTA files --> + <table name="fasta_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/fasta_indexes.loc" /> + </table> +</tables> +
--- /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 @@ +<tables> + <table name="fasta_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/fasta_indexes.loc" /> + </table> +</tables> +