Mercurial > repos > lldelisle > cooler_balance
changeset 0:8f71aaf6e59d draft
planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
| author | lldelisle |
|---|---|
| date | Mon, 24 Oct 2022 15:20:46 +0000 |
| parents | |
| children | 9655af207032 |
| files | cooler_balance.xml macros.xml test-data/chr19.1M.bins test-data/chr19.size test-data/chrM.40kb.bins test-data/chrM.fa test-data/chrM.fa.fai test-data/fasta_indexes.loc test-data/input.cool test-data/input.validPairs.tabix test-data/input.validPairs.tabix.tbi test-data/input.validPairs.txt test-data/output.cool tool-data/fasta_indexes.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test workflow_cooler.pdf |
| diffstat | 17 files changed, 20559 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cooler_balance.xml Mon Oct 24 15:20:46 2022 +0000 @@ -0,0 +1,74 @@ +<tool id="cooler_balance" name="cooler_balance" version="@VERSION@+galaxy0" profile="18.01"> + <description>Copy and balance a cool file.</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <command detect_errors="exit_code"><![CDATA[ + cp '$input' '$output' && + cooler balance -p \${GALAXY_SLOTS:-1} --mad-max $madmax --min-nnz $minnnz --min-count $mincount --ignore-diags $ignorediags --ignore-dist $ignoredist --tol $tol --max-iters $maxiters $cistrans -f --convergence-policy $convergencepolicy + #if $blacklist: + --blacklist '$blacklist' + #end if + '$output' + ]]> + </command> + <inputs> + <param name="input" multiple="false" type="data" format="cool" label="Select the input cool file to balance."/> + <param argument="--mad-max" name="madmax" type="integer" value="5" label="Ignore bins from the contact matrix using the 'MAD-max' filter: bins whose log marginal sum is less than ``mad-max`` median absolute deviations below the median log marginal sum of all the bins in the same chromosome."/> + <param argument="--min-nnz" name="minnnz" type="integer" value="10" label="Ignore bins from the contact matrix whose marginal number of nonzeros is less than this number."/> + <param argument="--min-count" name="mincount" type="integer" value="0" label="Ignore bins from the contact matrix whose marginal count is less than this number."/> + <param argument="--ignore-diags" name="ignorediags" type="integer" value="2" label="Number of diagonals of the contact matrix to ignore, including the main diagonal. Examples: 0 ignores nothing, 1 ignores the main diagonal, 2 ignores diagonals (-1, 0, 1), etc."/> + <param argument="--ignore-dist" name="ignoredist" type="integer" value="0" label="Distance in bp to ignore." help="Max between distance and diags will be used."/> + <param argument="--tol" type="float" value="1e-5" label="Threshold value of variance of the marginals for the algorithm to converge."/> + <param argument="--max-iters" name="maxiters" type="integer" value="200" label="Maximum number of iterations to perform if convergence is not achieved.."/> + <param name="cistrans" type="select" label="Interactions to consider to calculate weights."> + <option value="">Genome wide </option> + <option value="--cis-only">Cis only </option> + <option value="--trans-only">Trans only </option> + </param> + <param argument="--blacklist" type="data" format="bed" optional="true" label="Path to a 3-column BED file containing genomic regions to mask out during the balancing procedure, e.g. sequence gaps or regions of poor mappability."/> + <param argument="--name" type="text" value="weight" label="Name of column to write to." /> + <param name="convergencepolicy" type="select" label="Convergence policy: What to do with weights when balancing doesn't converge in max_iters." + help="'store_final': Store the final result, regardless of whether the iterations converge to the specified tolerance; 'store_nan': Store a vector of NaN values to indicate that the matrix failed to converge; 'discard': Store nothing and exit gracefully; 'error': Abort with non-zero exit status."> + <option value="store_final">store_final</option> + <option value="store_nan">store_nan</option> + <option value="discard">discard</option> + <option value="error">error</option> + </param> + </inputs> + + <outputs> + <data format="cool" name="output" label="balanced of $input.name"/> + </outputs> + + <tests> + <test> + <param name="input" value="input.cool" ftype="cool"/> + <param name="madmax" value="5"/> + <param name="mincount" value="0"/> + <param name="ignorediags" value="2"/> + <param name="tol" value="1e-5"/> + <param name="maxiters" value="1000"/> + <param name="cistrans" value="--cis-only"/> + <output name="output" file="output.cool" compare="sim_size"/> + </test> + </tests> + + <help> + **cooler balance** + tool developped by mirnylab + see https://github.com/mirnylab/cooler + and https://cooler.readthedocs.io/en/latest/cli.html#cooler-balance + + command-line:: + + cp $input $output + cooler balance -p \${GALAXY_SLOTS:-1} --mad-max madmax --min-nnz minnnz --min-count mincount --ignore-diags ignorediags --ignore-dist ignoredist --tol tol --max-iters maxiters cistrans -f + --blacklist 'blacklist' + + + </help> + <expand macro="citation_cooler" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Oct 24 15:20:46 2022 +0000 @@ -0,0 +1,44 @@ +<macros> + <token name="@VERSION@">0.8.11</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.16">htslib</requirement> + <requirement type="package" version="3.7.0">h5py</requirement> + <requirement type="package" version="@VERSION@">cooler</requirement> + </requirements> + </xml> + <xml name="stdio"> + <stdio> + <!-- Anything other than zero is an error --> + <exit_code range="1:" /> + <exit_code range=":-1" /> + <!-- In case the return code has not been set propery check stderr too --> + <regex match="Error:" /> + <regex match="Exception:" /> + </stdio> + <version_command>cooler --version</version_command> + </xml> + <xml name="size_macro"> + <conditional name="size_source"> + <param name="size_source_selector" type="select" label="Choose the source for the chromosome sizes"> + <option value="cached">Locally cached</option> + <option value="history">History</option> + </param> + <when value="cached"> + <param name="fasta_cached" type="select" label="Fasta availables"> + <options from_data_table="fasta_indexes"> + <validator type="no_options" message="No cached fasta is available"/> + </options> + </param> + </when> + <when value="history"> + <param name="chromosomeSize" multiple="false" type="data" format="tabular" label="Select a file with the size of chromosome (One column with the chromosome names in the desired order, one column with the sizes)."/> + </when> + </conditional> + </xml> + <xml name="citation_cooler"> + <citations> + <citation type="doi">10.1093/bioinformatics/btz540</citation> + </citations> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chr19.1M.bins Mon Oct 24 15:20:46 2022 +0000 @@ -0,0 +1,62 @@ +chr19 0 1000000 +chr19 1000000 2000000 +chr19 2000000 3000000 +chr19 3000000 4000000 +chr19 4000000 5000000 +chr19 5000000 6000000 +chr19 6000000 7000000 +chr19 7000000 8000000 +chr19 8000000 9000000 +chr19 9000000 10000000 +chr19 10000000 11000000 +chr19 11000000 12000000 +chr19 12000000 13000000 +chr19 13000000 14000000 +chr19 14000000 15000000 +chr19 15000000 16000000 +chr19 16000000 17000000 +chr19 17000000 18000000 +chr19 18000000 19000000 +chr19 19000000 20000000 +chr19 20000000 21000000 +chr19 21000000 22000000 +chr19 22000000 23000000 +chr19 23000000 24000000 +chr19 24000000 25000000 +chr19 25000000 26000000 +chr19 26000000 27000000 +chr19 27000000 28000000 +chr19 28000000 29000000 +chr19 29000000 30000000 +chr19 30000000 31000000 +chr19 31000000 32000000 +chr19 32000000 33000000 +chr19 33000000 34000000 +chr19 34000000 35000000 +chr19 35000000 36000000 +chr19 36000000 37000000 +chr19 37000000 38000000 +chr19 38000000 39000000 +chr19 39000000 40000000 +chr19 40000000 41000000 +chr19 41000000 42000000 +chr19 42000000 43000000 +chr19 43000000 44000000 +chr19 44000000 45000000 +chr19 45000000 46000000 +chr19 46000000 47000000 +chr19 47000000 48000000 +chr19 48000000 49000000 +chr19 49000000 50000000 +chr19 50000000 51000000 +chr19 51000000 52000000 +chr19 52000000 53000000 +chr19 53000000 54000000 +chr19 54000000 55000000 +chr19 55000000 56000000 +chr19 56000000 57000000 +chr19 57000000 58000000 +chr19 58000000 59000000 +chr19 59000000 60000000 +chr19 60000000 61000000 +chr19 61000000 61431566
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chr19.size Mon Oct 24 15:20:46 2022 +0000 @@ -0,0 +1,1 @@ +chr19 61431566
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chrM.40kb.bins Mon Oct 24 15:20:46 2022 +0000 @@ -0,0 +1,1 @@ +chrM 0 16569
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chrM.fa Mon Oct 24 15:20:46 2022 +0000 @@ -0,0 +1,333 @@ +>chrM +GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCAT +TTGGTATTTTCGTCTGGGGGGTATGCACGCGATAGCATTGCGAGACGCTG +GAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATC +CTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTA +AAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATAACAATTGAAT +GTCTGCACAGCCACTTTCCACACAGACATCATAACAAAAAATTTCCACCA +AACCCCCCCTCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCA +AACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTT +TATCTTTTGGCGGTATGCACTTTTAACAGTCACCCCCCAACTAACACATT +ATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATACAACCCCCGC +CCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAACCA +ACCAAACCCCAAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCAAA +GCAATACACTGAAAATGTTTAGACGGGCTCACATCACCCCATAAACAAAT +AGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAA +GCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGA +ACAAGCATCAAGCACGCAGCAATGCAGCTCAAAACGCTTAGCCTAGCCAC +ACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAAACGAAAGTTT +AACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGC +GGTCACACGATTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTA +GATCACCCCCTCCCCAATAAAGCTAAAACTCACCTGAGTTGTAAAAAACT +CCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAACAC +ACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCC +TAAACCTCAACAGTTAAATCAACAAAACTGCTCGCCAGAACACTACGAGC +CACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATCCCTCTAGAGG +AGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTC +AGCCTATATACCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAA +GCGCAAGTACCCACGTAAAGACGTTAGGTCAAGGTGTAGCCCATGAGGTG +GCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTAT +GAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTAAGAGTAGAGTGC +TTAGTTGAACAGGGCCCTGAAGCGCGTACACACCGCCCGTCACCCTCCTC +AAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCATTTATATAGA +GGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAA +CCAGAGTGTAGCTTAACACAAAGCACCCAACTTACACTTAGGAGATTTCA +ACTTAACTTGACCGCTCTGAGCTAAACCTAGCCCCAAACCCACTCCACCT +TACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCG 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+AATTACCCCCATACTCCTTACACTATTCCTCATCACCCAACTAAAAATAT +TAAACACAAACTACCACCTACCTCCCTCACCAAAGCCCATAAAAATAAAA +AATTATAACAAACCCTGAGAACCAAAATGAACGAAAATCTGTTCGCTTCA +TTCATTGCCCCCACAATCCTAGGCCTACCCGCCGCAGTACTGATCATTCT +ATTTCCCCCTCTATTGATCCCCACCTCCAAATATCTCATCAACAACCGAC +TAATCACCACCCAACAATGACTAATCAAACTAACCTCAAAACAAATGATA +ACCATACACAACACTAAAGGACGAACCTGATCTCTTATACTAGTATCCTT +AATCATTTTTATTGCCACAACTAACCTCCTCGGACTCCTGCCTCACTCAT +TTACACCAACCACCCAACTATCTATAAACCTAGCCATGGCCATCCCCTTA +TGAGCGGGCACAGTGATTATAGGCTTTCGCTCTAAGATTAAAAATGCCCT +AGCCCACTTCTTACCACAAGGCACACCTACACCCCTTATCCCCATACTAG +TTATTATCGAAACCATCAGCCTACTCATTCAACCAATAGCCCTGGCCGTA +CGCCTAACCGCTAACATTACTGCAGGCCACCTACTCATGCACCTAATTGG +AAGCGCCACCCTAGCAATATCAACCATTAACCTTCCCTCTACACTTATCA +TCTTCACAATTCTAATTCTACTGACTATCCTAGAAATCGCTGTCGCCTTA +ATCCAAGCCTACGTTTTCACACTTCTAGTAAGCCTCTACCTGCACGACAA +CACATAATGACCCACCAATCACATGCCTATCATATAGTAAAACCCAGCCC +ATGACCCCTAACAGGGGCCCTCTCAGCCCTCCTAATGACCTCCGGCCTAG +CCATGTGATTTCACTTCCACTCCATAACGCTCCTCATACTAGGCCTACTA +ACCAACACACTAACCATATACCAATGATGGCGCGATGTAACACGAGAAAG +CACATACCAAGGCCACCACACACCACCTGTCCAAAAAGGCCTTCGATACG +GGATAATCCTATTTATTACCTCAGAAGTTTTTTTCTTCGCAGGATTTTTC +TGAGCCTTTTACCACTCCAGCCTAGCCCCTACCCCCCAATTAGGAGGGCA +CTGGCCCCCAACAGGCATCACCCCGCTAAATCCCCTAGAAGTCCCACTCC +TAAACACATCCGTATTACTCGCATCAGGAGTATCAATCACCTGAGCTCAC +CATAGTCTAATAGAAAACAACCGAAACCAAATAATTCAAGCACTGCTTAT +TACAATTTTACTGGGTCTCTATTTTACCCTCCTACAAGCCTCAGAGTACT +TCGAGTCTCCCTTCACCATTTCCGACGGCATCTACGGCTCAACATTTTTT +GTAGCCACAGGCTTCCACGGACTTCACGTCATTATTGGCTCAACTTTCCT +CACTATCTGCTTCATCCGCCAACTAATATTTCACTTTACATCCAAACATC +ACTTTGGCTTCGAAGCCGCCGCCTGATACTGGCATTTTGTAGATGTGGTT +TGACTATTTCTGTATGTCTCCATCTATTGATGAGGGTCTTACTCTTTTAG +TATAAATAGTACCGTTAACTTCCAATTAACTAGTTTTGACAACATTCAAA +AAAGAGTAATAAACTTCGCCTTAATTTTAATAATCAACACCCTCCTAGCC +TTACTACTAATAATTATTACATTTTGACTACCACAACTCAACGGCTACAT +AGAAAAATCCACCCCTTACGAGTGCGGCTTCGACCCTATATCCCCCGCCC +GCGTCCCTTTCTCCATAAAATTCTTCTTAGTAGCTATTACCTTCTTATTA +TTTGATCTAGAAATTGCCCTCCTTTTACCCCTACCATGAGCCCTACAAAC +AACTAACCTGCCACTAATAGTTATGTCATCCCTCTTATTAATCATCATCC +TAGCCCTAAGTCTGGCCTATGAGTGACTACAAAAAGGATTAGACTGAACC +GAATTGGTATATAGTTTAAACAAAACGAATGATTTCGACTCATTAAATTA +TGATAATCATATTTACCAAATGCCCCTCATTTACATAAATATTATACTAG +CATTTACCATCTCACTTCTAGGAATACTAGTATATCGCTCACACCTCATA +TCCTCCCTACTATGCCTAGAAGGAATAATACTATCGCTGTTCATTATAGC +TACTCTCATAACCCTCAACACCCACTCCCTCTTAGCCAATATTGTGCCTA +TTGCCATACTAGTCTTTGCCGCCTGCGAAGCAGCGGTGGGCCTAGCCCTA +CTAGTCTCAATCTCCAACACATATGGCCTAGACTACGTACATAACCTAAA +CCTACTCCAATGCTAAAACTAATCGTCCCAACAATTATATTACTACCACT +GACATGACTTTCCAAAAAACACATAATTTGAATCAACACAACCACCCACA +GCCTAATTATTAGCATCATCCCTCTACTATTTTTTAACCAAATCAACAAC +AACCTATTTAGCTGTTCCCCAACCTTTTCCTCCGACCCCCTAACAACCCC +CCTCCTAATACTAACTACCTGACTCCTACCCCTCACAATCATGGCAAGCC +AACGCCACTTATCCAGTGAACCACTATCACGAAAAAAACTCTACCTCTCT +ATACTAATCTCCCTACAAATCTCCTTAATTATAACATTCACAGCCACAGA +ACTAATCATATTTTATATCTTCTTCGAAACCACACTTATCCCCACCTTGG +CTATCATCACCCGATGAGGCAACCAGCCAGAACGCCTGAACGCAGGCACA +TACTTCCTATTCTACACCCTAGTAGGCTCCCTTCCCCTACTCATCGCACT +AATTTACACTCACAACACCCTAGGCTCACTAAACATTCTACTACTCACTC +TCACTGCCCAAGAACTATCAAACTCCTGAGCCAACAACTTAATATGACTA +GCTTACACAATAGCTTTTATAGTAAAGATACCTCTTTACGGACTCCACTT +ATGACTCCCTAAAGCCCATGTCGAAGCCCCCATCGCTGGGTCAATAGTAC +TTGCCGCAGTACTCTTAAAACTAGGCGGCTATGGTATAATACGCCTCACA +CTCATTCTCAACCCCCTGACAAAACACATAGCCTACCCCTTCCTTGTACT +ATCCCTATGAGGCATAATTATAACAAGCTCCATCTGCCTACGACAAACAG +ACCTAAAATCGCTCATTGCATACTCTTCAATCAGCCACATAGCCCTCGTA +GTAACAGCCATTCTCATCCAAACCCCCTGAAGCTTCACCGGCGCAGTCAT +TCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAA +ACTCAAACTACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGA +CTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCCT +CGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCTG +TGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGA +CTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACAAC +ACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCA +CACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTA +TCCCTCAACCCCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTTT +AACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTTACGACCCCTTA +TTTACCGAGAAAGCTCACAAGAACTGCTAACTCATGCCCCCATGTCTAAC +AACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAG +GCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACAC +TACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACCA +CCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCC +ATTGTCGCATCCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCAT +GTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACTGAGCCACAACCC +AAACAACCCAGCTCTCCCTAAGCTTCAAACTAGACTACTTCTCCATAATA +TTCATCCCTGTAGCATTGTTCGTTACATGGTCCATCATAGAATTCTCACT +GTGATATATAAACTCAGACCCAAACATTAATCAGTTCTTCAAATATCTAC +TCATCTTCCTAATTACCATACTAATCTTAGTTACCGCTAACAACCTATTC +CAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCAT +CAGTTGATGATACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCAA +TCCTATACAACCGTATCGGCGATATCGGTTTCATCCTCGCCTTAGCATGA +TTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAA +CGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAG +GCAAATCAGCCCAATTAGGTCTCCACCCCTGACTCCCCTCAGCCATAGAA +GGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTATAGTTGTAGC +AGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCAC +TAATCCAAACTCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCA +GCAGTCTGCGCCCTTACACAAAATGACATCAAAAAAATCGTAGCCTTCTC +CACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAAC +CACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCATA +CTATTTATGTGCTCCGGGTCCATCATCCACAACCTTAACAATGAACAAGA +TATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTCACTTCAACCT +CCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGGT +TTCTACTCCAAAGACCACATCATCGAAACCGCAAACATATCATACACAAA +CGCCTGAGCCCTATCTATTACTCTCATCGCTACCTCCCTGACAAGCGCCT +ATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCCC +ACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTAA +ACGCCTGGCAGCCGGAAGCCTATTCGCAGGATTTCTCATTACTAACAACA +TTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTACCTAAAACTC +ACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAA +CTACCTAACCAACAAACTTAAAATAAAATCCCCACTATGCACATTTTATT +TCTCCAACATACTCGGATTCTACCCTAGCATCACACACCGCACAATCCCC +TATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACCT +AACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATCT +CCACCTCCATCATCACCTCAACCCAAAAAGGCATAATTAAACTTTACTTC +CTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAATCACATAACC +TATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGTT +CAACCAGTAACTACTACTAATCAACGCCCATAATCATACAAAGCCCCCGC +ACCAATAGGATCCTCCCGAATCAACCCTGACCCCTCTCCTTCATAAATTA +TTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATAC +TCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAAC +ACTCACCAAGACCTCAACCCCTGACCCCCATGCCTCAGGATACTCCTCAA +TAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCCCCCTAAATAA +ATTAAAAAAACTATTAAACCCATATAACCTCCCCCAAAATTCAGAATAAT +AACACACCCGACCACACCGCTAACAATCAATACTAAACCCCCATAAATAG +GAGAAGGCTTAGAAGAAAACCCCACAAACCCCATTACTAAACCCACACTC +AACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGAC +CAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGA +CCCCAATACGCAAAACTAACCCCCTAATAAAATTAATTAACCACTCATTC +ATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAAACTTCGGCTC +ACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGGACTATTCCTAG +CCATGCACTACTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCAC +ATCACTCGAGACGTAAATTATGGCTGAATCATCCGCTACCTTCACGCCAA +TGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCC +TATATTACGGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATC +CTCCTGCTTGCAACTATAGCAACAGCCTTCATAGGCTATGTCCTCCCGTG +AGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAACTTACTATCCG +CCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTAC +TCAGTAGACAGTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCTT +GCCCTTCATTATTGCAGCCCTAGCAACACTCCACCTCCTATTCTTGCACG +AAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATC +ACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCTT +CCTTCTCTCCTTAATGACATTAACACTATTCTCACCAGACCTCCTAGGCG +ACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCCTCCCCACATC +AAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCCC +TAACAAACTAGGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAG +CAATAATCCCCATCCTCCATATATCCAAACAACAAAGCATAATATTTCGC +CCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTCT +AACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGAC +AAGTAGCATCCGTACTATACTTCACAACAATCCTAATCCTAATACCAACT +ATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTCCTTGTAGTAT +AAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCAAGG +ACAAATCAGAGAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAG +ATTCTAATTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGT +ACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACA +TTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCAC +CTGTAGTACATAAAAACCCAATCCACATCAAAACCCCCTCCCCATGCTTA +CAAGcaagtacagcaatcaaccctcaactatcacacatcaactgcaactC +CAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAA +CAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAA +ATCCCTTCTCGTCCCCATGGATGACCCCCCTCAGATAGGGGTCCCTTGAC +CACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCTCG +CTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACAT +CTGGTTCCTACTTCAGGGTCATAAAGCCTAAATAGCCCACACGTTCCCCT +TAAATAAGACATCACGATG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chrM.fa.fai Mon Oct 24 15:20:46 2022 +0000 @@ -0,0 +1,1 @@ +chrM 16569 6 50 51
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fasta_indexes.loc Mon Oct 24 15:20:46 2022 +0000 @@ -0,0 +1,1 @@ +chrM hg19 human mitochondrial genome ${__HERE__}/chrM.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.validPairs.txt Mon Oct 24 15:20:46 2022 +0000 @@ -0,0 +1,20000 @@ +83 0 chr19 23041923 6434 0 chr19 22468767 6238 42 42 +177 0 chr19 7494919 1129 1 chr19 7590087 1161 42 40 +197 0 chr19 46286176 13818 0 chr19 46765336 13943 42 42 +288 0 chr19 36244729 10819 0 chr19 36745142 10979 42 42 +458 0 chr19 32210012 9428 1 chr19 36832116 11004 42 34 +601 0 chr19 3909853 271 1 chr19 3922275 277 42 42 +602 0 chr19 25351870 7147 1 chr19 25376235 7154 42 42 +711 0 chr19 28229621 8128 0 chr19 27983277 8051 42 42 +775 0 chr19 40964930 12289 1 chr19 41036736 12313 42 42 +782 1 chr19 41390888 12410 1 chr19 34916158 10345 42 42 +830 0 chr19 5802570 767 1 chr19 5605692 722 42 42 +871 0 chr19 21406650 5899 1 chr19 21534141 5936 42 42 +949 0 chr19 19843854 5329 1 chr19 19839772 5326 42 42 +1043 1 chr19 27439787 7847 1 chr19 27577107 7901 42 42 +1131 1 chr19 5100343 603 1 chr19 4752092 472 42 42 +1257 1 chr19 38049729 11386 0 chr19 37952044 11358 42 42 +1420 0 chr19 10387209 2112 1 chr19 10400249 2115 42 42 +1481 0 chr19 45074815 13468 1 chr19 44795267 13402 42 42 +1690 0 chr19 34494677 10211 1 chr19 32162326 9414 42 42 +1717 0 chr19 47913242 14247 0 chr19 48200469 14329 42 40 +1768 1 chr19 26477924 7505 1 chr19 26542344 7527 42 42 +2197 1 chr19 10909784 2240 0 chr19 10805735 2212 42 42 +2231 0 chr19 8665734 1549 1 chr19 3467945 134 42 42 +2357 0 chr19 5996648 817 0 chr19 6295093 887 42 42 +2728 0 chr19 32364510 9484 0 chr19 11938051 2597 23 42 +2795 1 chr19 22093986 6123 1 chr19 22039985 6107 42 42 +3101 0 chr19 49834691 14870 0 chr19 49349403 14704 42 42 +3138 0 chr19 18945080 4997 0 chr19 18996422 5019 42 42 +3210 1 chr19 44146243 13204 1 chr19 43554061 13049 40 42 +3532 0 chr19 18795442 4938 0 chr19 17264367 4431 42 42 +3846 1 chr19 26373848 7460 1 chr19 29141130 8443 42 42 +3950 1 chr19 46286176 13818 1 chr19 10553114 2141 42 42 +4102 1 chr19 14529186 3465 0 chr19 14709502 3534 42 42 +4207 0 chr19 29304304 8496 1 chr19 29247860 8474 42 42 +4264 1 chr19 10450271 2123 1 chr19 10383171 2111 42 42 +4631 1 chr19 24330813 6851 0 chr19 19049871 5045 42 42 +4867 1 chr19 31911918 9319 1 chr19 20856791 5699 42 42 +5101 1 chr19 16516055 4169 0 chr19 16430755 4146 42 42 +5231 1 chr19 42094834 12604 1 chr19 42087964 12598 42 42 +5258 0 chr19 28281552 8146 0 chr19 31338426 9149 42 42 +5315 0 chr19 17142848 4392 0 chr19 17210309 4411 42 42 +5342 1 chr19 38776630 11611 1 chr19 34816725 10315 42 42 +5499 1 chr19 46086483 13757 1 chr19 46943336 13991 40 42 +5585 1 chr19 44387343 13282 0 chr19 45078127 13471 42 42 +5596 1 chr19 8886188 1605 0 chr19 9010852 1633 42 42 +5836 1 chr19 47628422 14164 1 chr19 47135679 14036 42 42 +6108 0 chr19 38039057 11384 0 chr19 37706566 11273 8 42 +6195 1 chr19 42623198 12761 1 chr19 43393936 13002 42 40 +6480 0 chr19 34991110 10373 0 chr19 3756175 211 42 42 +6552 0 chr19 38676177 11579 1 chr19 38716449 11596 42 35 +6571 0 chr19 29275366 8482 1 chr19 23110150 6456 40 42 +6756 1 chr19 41000059 12306 0 chr19 7299136 1075 42 42 +6771 0 chr19 21451274 5912 1 chr19 49380031 14716 42 42 +6932 0 chr19 11399388 2407 1 chr19 11783418 2542 42 42 +6946 0 chr19 22597466 6290 0 chr19 22499051 6255 42 40 +7152 1 chr19 45904492 13702 0 chr19 18900938 4980 42 42 +7201 1 chr19 21160025 5818 1 chr19 11873008 2575 40 42 +7211 1 chr19 16140612 4030 1 chr19 23911601 6740 42 42 +7327 1 chr19 28184231 8112 1 chr19 28539598 8236 42 42 +7598 0 chr19 6677330 973 0 chr19 6667956 970 42 42 +7758 1 chr19 33262507 9803 1 chr19 33034504 9724 42 39 +7835 0 chr19 44587914 13344 0 chr19 43786819 13106 42 42 +8055 0 chr19 32076137 9380 1 chr19 32121774 9401 42 42 +8131 0 chr19 15906103 3948 1 chr19 15909954 3950 42 0 +8534 0 chr19 42251250 12645 0 chr19 41290915 12378 42 42 +8764 1 chr19 16378883 4135 0 chr19 16326023 4112 42 42 +9221 1 chr19 34478986 10201 0 chr19 36759311 10983 23 42 +9376 1 chr19 37424513 11194 0 chr19 15614447 3853 42 42 +9538 0 chr19 46833110 13956 1 chr19 47267243 14072 8 40 +9645 1 chr19 45494147 13595 1 chr19 45487608 13592 42 42 +9662 1 chr19 28527330 8233 0 chr19 27562159 7895 42 39 +9896 0 chr19 20843774 5692 0 chr19 20778038 5664 3 42 +10009 0 chr19 33000121 9703 0 chr19 33023502 9717 42 40 +10114 1 chr19 30881444 9016 1 chr19 20227569 5448 42 42 +10152 1 chr19 30489968 8886 0 chr19 32638640 9571 42 40 +10375 1 chr19 17893587 4628 1 chr19 17679986 4551 42 40 +10380 1 chr19 4244428 356 0 chr19 4277085 360 42 42 +10415 0 chr19 23446785 6570 0 chr19 32719596 9599 42 42 +10428 0 chr19 47205312 14058 0 chr19 45815193 13675 42 42 +10543 0 chr19 17033110 4347 0 chr19 16777964 4256 24 42 +10679 1 chr19 25854736 7293 1 chr19 26589536 7541 42 42 +11054 1 chr19 22077955 6116 0 chr19 22139690 6136 42 42 +11183 1 chr19 42943023 12856 1 chr19 42950901 12859 42 42 +11315 0 chr19 7022465 1013 0 chr19 16995393 4334 42 42 +11331 1 chr19 28072888 8083 0 chr19 28079965 8088 42 42 +11382 0 chr19 33314192 9822 0 chr19 33326622 9829 42 42 +11473 0 chr19 24427292 6881 0 chr19 23078774 6446 42 42 +11520 1 chr19 37218900 11132 1 chr19 36237813 10817 42 42 +11526 0 chr19 27181058 7749 1 chr19 27111314 7726 42 42 +11589 1 chr19 26877780 7643 1 chr19 26939509 7658 42 42 +11781 1 chr19 28826207 8330 0 chr19 26898940 7648 42 42 +11871 1 chr19 37266517 11144 0 chr19 37074904 11089 42 42 +11946 0 chr19 44084898 13185 1 chr19 44119792 13195 42 42 +12146 1 chr19 22484847 6250 1 chr19 29854632 8681 42 42 +12295 0 chr19 18001120 4665 1 chr19 17485191 4478 42 23 +12352 1 chr19 33450357 9868 0 chr19 36404269 10864 35 42 +12375 1 chr19 32973130 9693 0 chr19 33057983 9737 42 42 +12405 1 chr19 4924950 559 0 chr19 6660169 969 42 42 +12435 0 chr19 33942585 10025 1 chr19 18662512 4897 42 42 +12531 0 chr19 29832506 8669 1 chr19 32761311 9622 42 42 +12651 1 chr19 20439814 5528 0 chr19 21476594 5920 42 42 +12729 1 chr19 48550935 14447 0 chr19 42496636 12715 42 23 +12983 1 chr19 40958497 12288 0 chr19 40969570 12290 42 36 +13011 1 chr19 43718884 13083 0 chr19 43786819 13106 42 42 +13266 0 chr19 27995902 8056 0 chr19 28745640 8309 42 42 +13442 0 chr19 35753059 10652 1 chr19 35886571 10703 42 42 +13575 1 chr19 45504551 13600 0 chr19 45498035 13598 42 42 +13655 1 chr19 30784701 8972 0 chr19 31533533 9202 42 34 +13763 0 chr19 44784574 13399 1 chr19 42150154 12622 40 42 +13802 0 chr19 23250684 6500 1 chr19 42066941 12588 42 42 +13900 0 chr19 4917018 557 0 chr19 4358376 379 42 42 +14333 1 chr19 9163915 1676 1 chr19 11612126 2484 42 42 +14375 1 chr19 24351637 6857 0 chr19 40466572 12136 42 42 +14544 0 chr19 36146121 10792 0 chr19 33668905 9937 42 39 +14596 1 chr19 37302141 11156 1 chr19 34777956 10297 42 24 +14727 1 chr19 46165986 13772 0 chr19 46159391 13770 40 42 +14799 0 chr19 20984182 5748 1 chr19 18745562 4919 39 42 +14833 0 chr19 31211558 9105 1 chr19 32677910 9585 42 42 +15084 0 chr19 8831505 1591 1 chr19 8917776 1613 23 42 +15242 0 chr19 29836939 8673 0 chr19 43812834 13113 42 42 +15280 0 chr19 28797811 8324 1 chr19 28420681 8204 42 42 +15705 0 chr19 12517282 2778 0 chr19 11809627 2549 23 42 +15717 1 chr19 25201136 7106 1 chr19 12502309 2776 42 42 +15886 1 chr19 49263587 14680 0 chr19 49277415 14688 42 42 +15918 0 chr19 17575582 4508 1 chr19 18115657 4694 42 42 +16042 0 chr19 25368746 7151 1 chr19 25399455 7161 42 42 +16510 1 chr19 39875617 11957 1 chr19 8221528 1397 32 42 +16798 0 chr19 24397063 6872 1 chr19 38784704 11614 24 42 +16936 1 chr19 23896603 6735 1 chr19 4090245 324 42 42 +17042 0 chr19 17614412 4522 1 chr19 17688975 4553 42 42 +17327 1 chr19 23044690 6435 1 chr19 26752725 7598 42 40 +17447 1 chr19 21046232 5775 0 chr19 20890187 5715 42 42 +17538 1 chr19 46960692 13997 0 chr19 3965545 286 42 37 +17663 0 chr19 36351429 10846 1 chr19 42922758 12848 23 42 +17779 1 chr19 18953455 5003 0 chr19 8905856 1611 42 42 +17844 0 chr19 4292547 362 0 chr19 3753501 209 42 42 +17904 1 chr19 7022465 1013 0 chr19 5600826 721 42 42 +17964 1 chr19 4844965 537 0 chr19 4853337 541 39 42 +18136 1 chr19 44123112 13197 1 chr19 44106931 13190 42 42 +18258 0 chr19 33054521 9736 1 chr19 30844725 8990 42 42 +18276 0 chr19 14944114 3622 0 chr19 14705683 3530 42 42 +18283 0 chr19 25399455 7161 1 chr19 46482009 13866 40 42 +18400 1 chr19 29228098 8466 1 chr19 26369189 7459 38 8 +18744 0 chr19 23801931 6705 1 chr19 22533973 6270 42 42 +18749 1 chr19 17968372 4655 0 chr19 18205143 4726 42 42 +18843 0 chr19 16956153 4322 0 chr19 16337551 4115 40 42 +19052 1 chr19 49418268 14730 0 chr19 49034584 14597 42 40 +19125 0 chr19 46635704 13903 1 chr19 46521469 13875 42 42 +19630 1 chr19 12324739 2729 1 chr19 41129017 12340 37 42 +19776 0 chr19 43444521 13018 0 chr19 43440108 13017 42 42 +19846 0 chr19 15035351 3649 1 chr19 15572171 3829 0 42 +19927 1 chr19 12321514 2728 1 chr19 12332751 2732 42 40 +20575 1 chr19 34797360 10309 1 chr19 34791982 10307 42 42 +20606 0 chr19 47176845 14049 0 chr19 47222487 14063 42 42 +20702 1 chr19 4888314 549 0 chr19 5084027 599 42 42 +21082 1 chr19 28877469 8349 1 chr19 21994648 6087 42 42 +21088 0 chr19 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/fasta_indexes.loc.sample Mon Oct 24 15:20:46 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 Mon Oct 24 15:20:46 2022 +0000 @@ -0,0 +1,7 @@ +<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 Mon Oct 24 15:20:46 2022 +0000 @@ -0,0 +1,6 @@ +<tables> + <table name="fasta_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/fasta_indexes.loc" /> + </table> +</tables>