| Next changeset 1:3ff6eeca667e (2022-12-01) |
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Commit message:
planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296 |
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added:
cooler_cload_tabix.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 |
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| diff -r 000000000000 -r 8745321ccc3e cooler_cload_tabix.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cooler_cload_tabix.xml Mon Oct 24 15:19:04 2022 +0000 |
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| @@ -0,0 +1,71 @@ +<tool id="cooler_cload_tabix" name="cooler_cload_tabix" version="@VERSION@+galaxy0" profile="18.01"> + <description> Create a cool file from a tabix-indexed contact file and a list of genomic bins.</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <command detect_errors="exit_code"><![CDATA[ + ##set up input files + ln -s '$input_pairs' pairs.tabix && + #if str( $input_pairs.metadata.tabix_index ) != "None": + ln -s '$input_pairs.metadata.tabix_index' pairs.tabix.tbi && + #else: + tabix -s $pairs_advanced.c1 -b $pairs_advanced.p1 -e $pairs_advanced.p1 pairs.tabix && + #end if + cooler cload tabix --assembly '$assembly' -c2 $c2 -p2 $p2 '$input_bed' pairs.tabix '$output' + ]]> + </command> + <inputs> + <param name="input_pairs" multiple="false" type="data" format="bgzip,tabix" label="Select the output of csort_tabix."/> + <section name="pairs_advanced" title="If your input is not already indexed" expanded="False"> + <param name="c1" type="integer" value="1" label="field number in the input file (starting from 1) of the chromosome of mate 1."> + <validator type="in_range" min="1" /> + </param> + <param name="p1" type="integer" value="2" label="field number in the input file (starting from 1) of the position of mate 1."> + <validator type="in_range" min="1" /> + </param> + </section> + <param name="c2" type="integer" value="3" label="field number in the input file (starting from 1) of the chromosome of mate 2 (same as in csort)."> + <validator type="in_range" min="1" /> + </param> + <param name="p2" type="integer" value="4" label="field number in the input file (starting from 1) of the position of mate 2 (same as in csort)."> + <validator type="in_range" min="1" /> + </param> + <param name="assembly" type="text" label="name of genome assembly"/> + <param name="input_bed" multiple="false" type="data" format="bed" label="Select the output of makebins."/> + </inputs> + + <outputs> + <data format="cool" name="output" label="cool file from $input_pairs.name and $input_bed.name"/> + </outputs> + + <tests> + <!-- For the moment I cannot test this tool --> + <!-- <test> + <param name="input_pairs" value="input.validPairs.tabix" ftype="bgzip"/> + <param name="input_bed" value="chr19.1M.bins"/> + <param name="assembly" value="chr19"/> + <section name="pairs_advanced"> + <param name="c1" value="3"/> + <param name="p1" value="4"/> + </section> + <param name="c2" value="7"/> + <param name="p2" value="8"/> + <output name="output" file="input.cool" compare="sim_size"/> + </test> --> + </tests> + + <help> + **cooler cload** + tool developped by mirnylab + see https://github.com/open2c/cooler + and https://cooler.readthedocs.io/en/latest/cli.html#cooler-cload-tabix + + command-line:: + + cooler cload tabix --assembly assembly -c2 c2 -p2 p2 input_bed input_pairs output + + </help> + <expand macro="citation_cooler" /> +</tool> |
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| diff -r 000000000000 -r 8745321ccc3e macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Oct 24 15:19:04 2022 +0000 |
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| @@ -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> |
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| diff -r 000000000000 -r 8745321ccc3e test-data/chr19.1M.bins --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chr19.1M.bins Mon Oct 24 15:19:04 2022 +0000 |
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| @@ -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 |
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| diff -r 000000000000 -r 8745321ccc3e test-data/chr19.size --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chr19.size Mon Oct 24 15:19:04 2022 +0000 |
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| @@ -0,0 +1,1 @@ +chr19 61431566 |
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| diff -r 000000000000 -r 8745321ccc3e test-data/chrM.40kb.bins --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chrM.40kb.bins Mon Oct 24 15:19:04 2022 +0000 |
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| @@ -0,0 +1,1 @@ +chrM 0 16569 |
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| diff -r 000000000000 -r 8745321ccc3e test-data/chrM.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chrM.fa Mon Oct 24 15:19:04 2022 +0000 |
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| b'@@ -0,0 +1,333 @@\n+>chrM\n+GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCAT\n+TTGGTATTTTCGTCTGGGGGGTATGCACGCGATAGCATTGCGAGACGCTG\n+GAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATC\n+CTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTA\n+AAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATAACAATTGAAT\n+GTCTGCACAGCCACTTTCCACACAGACATCATAACAAAAAATTTCCACCA\n+AACCCCCCCTCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCA\n+AACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTT\n+TATCTTTTGGCGGTATGCACTTTTAACAGTCACCCCCCAACTAACACATT\n+ATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATACAACCCCCGC\n+CCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAACCA\n+ACCAAACCCCAAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCAAA\n+GCAATACACTGAAAATGTTTAGACGGGCTCACATCACCCCATAAACAAAT\n+AGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAA\n+GCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGA\n+ACAAGCATCAAGCACGCAGCAATGCAGCTCAAAACGCTTAGCCTAGCCAC\n+ACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAAACGAAAGTTT\n+AACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGC\n+GGTCACACGATTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTA\n+GATCACCCCCTCCCCAATAAAGCTAAAACTCACCTGAGTTGTAAAAAACT\n+CCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAACAC\n+ACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCC\n+TAAACCTCAACAGTTAAATCAACAAAACTGCTCGCCAGAACACTACGAGC\n+CACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATCCCTCTAGAGG\n+AGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTC\n+AGCCTATATACCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAA\n+GCGCAAGTACCCACGTAAAGACGTTAGGTCAAGGTGTAGCCCATGAGGTG\n+GCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTAT\n+GAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTAAGAGTAGAGTGC\n+TTAGTTGAACAGGGCCCTGAAGCGCGTACACACCGCCCGTCACCCTCCTC\n+AAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCATTTATATAGA\n+GGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAA\n+CCAGAGTGTAGCTTAACACAAAGCACCCAACTTACACTTAGGAGATTTCA\n+ACTTAACTTGACCGCTCTGAGCTAAACCTAGCCCCAAACCCACTCCACCT\n+TACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCG\n+ATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGATG\n+AAAAATTATAACCAAGCATAATATAGCAAGGACTAACCCCTATACCTTCT\n+GCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCCAAAGCTAAGA\n+CCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGT\n+CTATGTAGCAAAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTAC\n+CGAGCCTGGTGATAGCTGGTTGTCCAAGATAGAATCTTAGTTCAACTTTA\n+AATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTC\n+CAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGT\n+AAAAAATTTAACACCCATAGTAGGCCTAAAAGCAGCCACCAATTAAGAAA\n+GCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAACATATAACTGA\n+ACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATG\n+TTAGTATAAGTAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGA\n+TTAAAACACTGAACTGACAATTAACAGCCCAATATCTACAATCAACCAAC\n+AAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGA\n+AAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTA\n+CCAAAAACATCACCTCTAGCATCACCAGTATTAGAGGCACCGCCTGCCCA\n+GTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAaaggtagcata\n+atcacttgttccttaaatagggacctgtatgaatggctccacgagggttc\n+agctgtctcttacttttaaccagtgaaattgacctgcccgtgaagaggcg\n+ggcataacacagcaagacgagaagaccctatggagctttaatttaTTAAT\n+GCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATT\n+AAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCAGT\n+ACATGCTAAGACTTCACCAGTCAAAGCGAACTACTATACTCAATTGATCC\n+AATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACAGCGCAATCCT\n+ATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCA\n+GGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATT\n+AAAGTCCTACGTGATCTGAGTTCAGACCGGAGTAATCCAGGTCGGTTTCT\n+ATCTACNTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCCT\n+ACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTATT\n+ATACCCACACCCACCCAAGAACAGGGTTTgttaagatggcagagcccggt\n+aatcgcataaaacttaaaactttacagtcagaggttcaattcctcttctt\n+aacaacaTACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAAT\n+CGCAATGGCATTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATAC\n+AACTACGCAAAGGCCCCAACGTTGTAGGCCCCTACGGGCTACTACAACCC\n+TTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCAC\n+ATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCG\n+CTCTTCTACTATGAACCCCCCTCCCCATACCCAACCCCCTGGTCAACCTC\n+AACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAGCCGTTTACTC\n+AATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCG\n+CACTGCGAGCAGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCATC\n+ATTCTACTATCAACATTACTAATAAGTGGCTCCTTTAACCTCTCCACCCT\n+TATCACAACACAAGAACACCT'..b'CTTAGTTACCGCTAACAACCTATTC\n+CAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCAT\n+CAGTTGATGATACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCAA\n+TCCTATACAACCGTATCGGCGATATCGGTTTCATCCTCGCCTTAGCATGA\n+TTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAA\n+CGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAG\n+GCAAATCAGCCCAATTAGGTCTCCACCCCTGACTCCCCTCAGCCATAGAA\n+GGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTATAGTTGTAGC\n+AGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCAC\n+TAATCCAAACTCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCA\n+GCAGTCTGCGCCCTTACACAAAATGACATCAAAAAAATCGTAGCCTTCTC\n+CACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAAC\n+CACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCATA\n+CTATTTATGTGCTCCGGGTCCATCATCCACAACCTTAACAATGAACAAGA\n+TATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTCACTTCAACCT\n+CCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGGT\n+TTCTACTCCAAAGACCACATCATCGAAACCGCAAACATATCATACACAAA\n+CGCCTGAGCCCTATCTATTACTCTCATCGCTACCTCCCTGACAAGCGCCT\n+ATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCCC\n+ACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTAA\n+ACGCCTGGCAGCCGGAAGCCTATTCGCAGGATTTCTCATTACTAACAACA\n+TTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTACCTAAAACTC\n+ACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAA\n+CTACCTAACCAACAAACTTAAAATAAAATCCCCACTATGCACATTTTATT\n+TCTCCAACATACTCGGATTCTACCCTAGCATCACACACCGCACAATCCCC\n+TATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACCT\n+AACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATCT\n+CCACCTCCATCATCACCTCAACCCAAAAAGGCATAATTAAACTTTACTTC\n+CTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAATCACATAACC\n+TATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGTT\n+CAACCAGTAACTACTACTAATCAACGCCCATAATCATACAAAGCCCCCGC\n+ACCAATAGGATCCTCCCGAATCAACCCTGACCCCTCTCCTTCATAAATTA\n+TTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATAC\n+TCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAAC\n+ACTCACCAAGACCTCAACCCCTGACCCCCATGCCTCAGGATACTCCTCAA\n+TAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCCCCCTAAATAA\n+ATTAAAAAAACTATTAAACCCATATAACCTCCCCCAAAATTCAGAATAAT\n+AACACACCCGACCACACCGCTAACAATCAATACTAAACCCCCATAAATAG\n+GAGAAGGCTTAGAAGAAAACCCCACAAACCCCATTACTAAACCCACACTC\n+AACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGAC\n+CAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGA\n+CCCCAATACGCAAAACTAACCCCCTAATAAAATTAATTAACCACTCATTC\n+ATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAAACTTCGGCTC\n+ACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGGACTATTCCTAG\n+CCATGCACTACTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCAC\n+ATCACTCGAGACGTAAATTATGGCTGAATCATCCGCTACCTTCACGCCAA\n+TGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCC\n+TATATTACGGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATC\n+CTCCTGCTTGCAACTATAGCAACAGCCTTCATAGGCTATGTCCTCCCGTG\n+AGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAACTTACTATCCG\n+CCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTAC\n+TCAGTAGACAGTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCTT\n+GCCCTTCATTATTGCAGCCCTAGCAACACTCCACCTCCTATTCTTGCACG\n+AAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATC\n+ACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCTT\n+CCTTCTCTCCTTAATGACATTAACACTATTCTCACCAGACCTCCTAGGCG\n+ACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCCTCCCCACATC\n+AAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCCC\n+TAACAAACTAGGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAG\n+CAATAATCCCCATCCTCCATATATCCAAACAACAAAGCATAATATTTCGC\n+CCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTCT\n+AACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGAC\n+AAGTAGCATCCGTACTATACTTCACAACAATCCTAATCCTAATACCAACT\n+ATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTCCTTGTAGTAT\n+AAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCAAGG\n+ACAAATCAGAGAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAG\n+ATTCTAATTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGT\n+ACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACA\n+TTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCAC\n+CTGTAGTACATAAAAACCCAATCCACATCAAAACCCCCTCCCCATGCTTA\n+CAAGcaagtacagcaatcaaccctcaactatcacacatcaactgcaactC\n+CAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAA\n+CAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAA\n+ATCCCTTCTCGTCCCCATGGATGACCCCCCTCAGATAGGGGTCCCTTGAC\n+CACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCTCG\n+CTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACAT\n+CTGGTTCCTACTTCAGGGTCATAAAGCCTAAATAGCCCACACGTTCCCCT\n+TAAATAAGACATCACGATG\n' |
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| diff -r 000000000000 -r 8745321ccc3e test-data/chrM.fa.fai --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chrM.fa.fai Mon Oct 24 15:19:04 2022 +0000 |
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| @@ -0,0 +1,1 @@ +chrM 16569 6 50 51 |
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| diff -r 000000000000 -r 8745321ccc3e test-data/fasta_indexes.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fasta_indexes.loc Mon Oct 24 15:19:04 2022 +0000 |
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| @@ -0,0 +1,1 @@ +chrM hg19 human mitochondrial genome ${__HERE__}/chrM.fa |
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| diff -r 000000000000 -r 8745321ccc3e test-data/input.cool |
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| Binary file test-data/input.cool has changed |
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| diff -r 000000000000 -r 8745321ccc3e test-data/input.validPairs.tabix |
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| Binary file test-data/input.validPairs.tabix has changed |
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| diff -r 000000000000 -r 8745321ccc3e test-data/input.validPairs.tabix.tbi |
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| Binary file test-data/input.validPairs.tabix.tbi has changed |
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| diff -r 000000000000 -r 8745321ccc3e test-data/input.validPairs.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.validPairs.txt Mon Oct 24 15:19:04 2022 +0000 |
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| b'@@ -0,0 +1,20000 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| diff -r 000000000000 -r 8745321ccc3e test-data/output.cool |
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| diff -r 000000000000 -r 8745321ccc3e tool-data/fasta_indexes.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/fasta_indexes.loc.sample Mon Oct 24 15:19:04 2022 +0000 |
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| @@ -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 |
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| diff -r 000000000000 -r 8745321ccc3e tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Mon Oct 24 15:19:04 2022 +0000 |
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| @@ -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> |
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| diff -r 000000000000 -r 8745321ccc3e tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Mon Oct 24 15:19:04 2022 +0000 |
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| @@ -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> |
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| diff -r 000000000000 -r 8745321ccc3e workflow_cooler.pdf |
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