Mercurial > repos > iuc > metabat2_jgi_summarize_bam_contig_depths
changeset 0:d27a4ed006ee draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
| author | iuc |
|---|---|
| date | Fri, 28 Jan 2022 12:21:33 +0000 |
| parents | |
| children | 1592150e38d2 |
| files | jgi_summarize_bam_contig_depths.xml macros.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, 710 insertions(+), 0 deletions(-) [+] |
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--- /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 @@ +<tool id="metabat2_jgi_summarize_bam_contig_depths" name="Calculate contig depths" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>for MetaBAT2</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ +jgi_summarize_bam_contig_depths +--outputDepth '$outputDepth' +--percentIdentity $advanced.percentIdentity +#if str($advanced.output_paired_contigs) == 'yes': + --pairedContigs '$outputPairedContigs' +#end if +$advanced.noIntraDepthVariance +$advanced.showDepth +--minMapQual $advanced.minMapQual +--weightMapQual $advanced.weightMapQual +$advanced.includeEdgeBases +--maxEdgeBases $advanced.maxEdgeBases +#if str($advanced.use_reference_cond.use_reference) == 'yes': + #if str($advanced.use_reference_cond.reference_cond.reference_source) == 'cached' + --referenceFasta '$advanced.use_reference_cond.reference_cond.referenceFasta.fields.path' + #else: + --referenceFasta '$advanced.use_reference_cond.reference_cond.referenceFasta' + #end if + --outputGC '$outputGC' + --gcWindow $advanced.use_reference_cond.gcWindow + --outputReadStats '$outputReadStats' + --outputKmers '$outputKmers' +#end if +--shredLength $shredding.shredLength +--shredDepth $shredding.shredDepth +--minContigLength $shredding.minContigLength +--minContigDepth $shredding.minContigDepth +#for bam_input in $bam_inputs: + '$bam_input' +#end for + ]]></command> + <inputs> + <param name="bam_inputs" type="data" format="bam" multiple="true" label="Sorted bam files"/> + <section name="advanced" title="Advanced options"> + <param argument="--percentIdentity" type="integer" value="97" label="Minimum end-to-end percent identity of qualifying reads"/> + <param name="output_paired_contigs" type="select" display="radio" label="Output the sparse matrix of contigs which paired reads span?"> + <option value="no" selected="true">No</option> + <option value="yes">Yes</option> + </param> + <param argument="--noIntraDepthVariance" type="boolean" truevalue="--noIntraDepthVariance" falsevalue="" checked="false" label="Remove variance from mean depth along the contig?"/> + <param argument="--showDepth" type="boolean" truevalue="--showDepth" falsevalue="" checked="false" label="Output a depth file per bam for each contig base?"/> + <param argument="--minMapQual" type="integer" value="0" label="Minimum mapping quality necessary to count a read as mapped"/> + <param argument="--weightMapQual" type="float" value="0.0" label="Weight per-base depth based on the MQ of the read" help="Zero value disables"/> + <param argument="--includeEdgeBases" type="boolean" truevalue="--includeEdgeBases" falsevalue="" checked="false" label="Include 1-readlength edges when calculating depth and variance?"/> + <param argument="--maxEdgeBases" type="integer" value="75" label="Maximum length when calculating depth and variance" help="Ignored when including 1-readlength edges when calculating depth and variance"/> + <conditional name="use_reference_cond"> + <param name="use_reference" type="select" label="Select a reference genome?"> + <option value="no" selected="true">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"/> + <when value="yes"> + <conditional name="reference_cond"> + <param name="reference_source" type="select" label="Choose the source for the reference genome"> + <option value="cached" selected="true">locally cached</option> + <option value="history">from history</option> + </param> + <when value="cached"> + <param argument="--referenceFasta" type="select" label="Using reference genome"> + <options from_data_table="fasta_indexes"> + <filter type="data_meta" column="1" key="dbkey" ref="bam_inputs"/> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected BAM file(s)"/> + </options> + </param> + </when> + <when value="history"> + <param argument="--referenceFasta" type="data" format="fasta,fasta.gz" label="Using reference genome" help="Must be the reference used to map the input bam files"/> + </when> + </conditional> + <param argument="--gcWindow" type="integer" value ="100" label="Sliding window size for GC calculations"/> + </when> + </conditional> + </section> + <section name="shredding" title="Options to control shredding contigs that are under-represented by the reads"> + <param argument="--shredLength" type="integer" value="16000" label="Maximum length of the shreds"/> + <param argument="--shredDepth" type="integer" value="5" label="Depth to generate overlapping shreds"/> + <param argument="--minContigLength" type="integer" value="1" label="Mimimum length of contig to include for mapping and shredding"/> + <param argument="--minContigDepth" type="float" value="0.0" label="Minimum depth along the contig at which to break the contig"/> + </section> + </inputs> + <outputs> + <data name="outputDepth" format="tabular" label="${tool.name} on ${on_string} (depth matrix)"/> + <data name="outputPairedContigs" format="fasta" label="${tool.name} on ${on_string} (paired contigs)"> + <filter>advanced["output_paired_contigs"] == "yes"</filter> + </data> + <data name="outputGC" format="tabular" label="${tool.name} on ${on_string} (gc coverage histogram)"> + <filter>advanced["use_reference_cond"]["use_reference"] == "yes"</filter> + </data> + <data name="outputReadStats" format="tabular" label="${tool.name} on ${on_string} (read statistics)"> + <filter>advanced["use_reference_cond"]["use_reference"] == "yes"</filter> + </data> + <data name="outputKmers" format="tabular" label="${tool.name} on ${on_string} (perfect kmer counts)"> + <filter>advanced["use_reference_cond"]["use_reference"] == "yes"</filter> + </data> + </outputs> + <tests> + <!-- Single input, default settings --> + <test expect_num_outputs="1"> + <param name="bam_inputs" value="input1.bam" ftype="bam"/> + <output name="outputDepth" file="jgi_output1.tabular" ftype="tabular" compare="contains"/> + </test> + <!-- Multiple inputs, default settings --> + <test expect_num_outputs="1"> + <param name="bam_inputs" value="input1.bam,input1.bam" ftype="bam"/> + <output name="outputDepth" file="jgi_output2.tabular" ftype="tabular" compare="contains"/> + </test> + <!-- Single input, output paired contigs, reference from history --> + <test expect_num_outputs="5"> + <param name="bam_inputs" value="input2.bam" ftype="bam" dbkey="89"/> + <param name="output_paired_contigs" value="yes"/> + <param name="use_reference" value="yes"/> + <param name="reference_source" value="history"/> + <param name="referenceFasta" value="NC_002945v4.fasta" ftype="fasta"/> + <output name="outputDepth" file="jgi_output_depth1.tabular" ftype="tabular" compare="contains"/> + <output name="outputPairedContigs" file="jgi_output_paired_contigs1.fasta" ftype="fasta"/> + <output name="outputGC" file="jgi_output_gc1.tabular" ftype="tabular"/> + <output name="outputReadStats" file="jgi_output_read_stats1.tabular" ftype="tabular"/> + <output name="outputKmers" file="jgi_output_kmers1.tabular" ftype="tabular"/> + </test> + <!-- Single input, output paired contigs, cached reference --> + <test expect_num_outputs="5"> + <param name="bam_inputs" value="input2.bam" ftype="bam" dbkey="89"/> + <param name="output_paired_contigs" value="yes"/> + <param name="use_reference" value="yes"/> + <param name="reference_source" value="cached"/> + <output name="outputDepth" file="jgi_output_depth1.tabular" ftype="tabular" compare="contains"/> + <output name="outputPairedContigs" file="jgi_output_paired_contigs1.fasta" ftype="fasta"/> + <output name="outputGC" file="jgi_output_gc1.tabular" ftype="tabular"/> + <output name="outputReadStats" file="jgi_output_read_stats1.tabular" ftype="tabular"/> + <output name="outputKmers" file="jgi_output_kmers1.tabular" ftype="tabular"/> + </test> + </tests> + <help> +**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. + + </help> + <expand macro="citations"/> +</tool> +
--- /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 @@ +<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/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
--- /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
--- /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
--- /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
--- /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
--- /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
--- /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 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 12:21:33 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 12:21:33 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 12:21:33 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.
--- /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): +# +# <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 12:21:33 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 12:21:33 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> +