| Next changeset 1:f4ec47f1a8da (2023-03-13) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbmm2 commit b9fe99d8335825c6c23f569034354323b794127a |
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added:
macros.xml pbmm2.xml test-data/All4mer.V2.01_Insert.fa test-data/all_fasta.loc test-data/bnd-ref.fasta test-data/bnd.bam test-data/out.aligned_subreads.bam tool_data_table_conf.xml.test |
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| diff -r 000000000000 -r 29eec6c7bab2 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Mar 08 12:00:46 2023 +0000 |
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| @@ -0,0 +1,20 @@ +<macros> + <token name="@TOOL_VERSION@">1.10.0</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">20.09</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">pbmm2</requirement> + </requirements> + </xml> + <xml name="xrefs"> + <xrefs> + <xref type="bio.tools">pbmm2</xref> + </xrefs> + </xml> + <xml name="creator"> + <creator> + <organization name="Galaxy Australia" url="https://site.usegalaxy.org.au"/> + </creator> + </xml> +</macros> |
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| diff -r 000000000000 -r 29eec6c7bab2 pbmm2.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pbmm2.xml Wed Mar 08 12:00:46 2023 +0000 |
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| @@ -0,0 +1,112 @@ +<tool id="pbmm2" name="pbmm2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>map PacBio reads to a reference genome.</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="xrefs"/> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ + ## set up files + #set reads_fn = 'reads.' + $reads.ext + ln -s '$reads' '$reads_fn' && + + #if $reference_source.reference_source_selector == 'history': + #set ref_fn = 'reference.fa' + ln -f -s '$reference_source.ref_file' '$ref_fn' && + #else: + #set ref_fn = $reference_source.ref_file.fields.path + #end if + + ## run pbmm2 + pbmm2 align + -j \${GALAXY_SLOTS:-4} + '$reads_fn' + '$ref_fn' + out.aligned.bam + --sort + ]]></command> + <inputs> + <!-- from tools-iuc minimap2 wrapper --> + <conditional name="reference_source"> + <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a built-in index?"> + <option value="cached">Use a built-in genome index</option> + <option value="history">Use a genome from history and build index</option> + </param> + <when value="cached"> + <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list"> + <options from_data_table="all_fasta"> + <filter type="sort_by" column="2" /> + <validator type="no_options" message="No reference genomes are available" /> + </options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> + </param> + </when> + <when value="history"> + <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="You can upload a FASTA sequence to the history and use it as reference" /> + </when> + </conditional> + <param type="data" name="reads" format="fastq,fastq.gz,fasta,fasta.gz,bam" label="reads" help="PacBio reads in BAM or [gzipped] fasta or fastq format." /> + </inputs> + <outputs> + <data name="bam" format="bam" from_work_dir="out.aligned.bam" label="${tool.name} on ${on_string} (BAM file)" /> + </outputs> + <tests> + <!-- test1: basic test --> + <test expect_num_outputs="1"> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" ftype="fasta" value="bnd-ref.fasta"/> + <param name="reads" value="bnd.bam"/> + <output name="bam"> + <assert_contents> + <has_size value="2778" delta="200" /> + </assert_contents> + </output> + </test> + <!-- test2: map some reads for use with pbgcpp --> + <test expect_num_outputs="1"> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" ftype="fasta" value="All4mer.V2.01_Insert.fa"/> + <param name="reads" value="out.aligned_subreads.bam"/> + <output name="bam"> + <assert_contents> + <has_size value="539464" delta="50000" /> + </assert_contents> + </output> + </test> + <!-- test3: cached genome --> + <test> + <param name="reference_source_selector" value="cached" /> + <param name="ref_file" value="bnd-ref"/> + <param name="reads" value="bnd.bam"/> + <output name="bam"> + <assert_contents> + <has_size value="2778" delta="200" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +**What it does** + +A minimap2 wrapper for PacBio data: native PacBio data in ⇨ native +PacBio BAM out. + +-------------- + +pbmm2 is Pacific Biosciences’ wrapper for +`minimap2 <https://github.com/lh3/minimap2>`__\ ’s C API. It supports +native PacBio input. Output can be used directly for polishing using +`pbgcpp <root?tool_id=pbgcpp>`__. + +**Input**: PacBio reads in bam or [gzipped] fasta or fastq format. +**NOTE**: to use the output of pbmm2 for pbgcpp (GenomicConsensus), you +have to provide PacBio CLR reads in bam format. You can use pbmm2 to +align other types of PacBio reads in [gzipped] fasta or fastq format, +but you can’t use the output for pbgcpp (GenomicConsensus). + +**Output**: A **sorted** PacBio BAM file, suitable for use with +pbgcpp (previously known as GenomicConsensus). + + ]]></help> + <expand macro="creator"/> +</tool> |
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| diff -r 000000000000 -r 29eec6c7bab2 test-data/All4mer.V2.01_Insert.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/All4mer.V2.01_Insert.fa Wed Mar 08 12:00:46 2023 +0000 |
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| @@ -0,0 +1,5 @@ +>All4mer.V2.01_Insert +CATCAGGTAAGAAAGTACGATGCTACAGCTTGTGACTGGTGCGGCACTTTTGGCTGAGTTTCCTGTCCAC +CTCATGTATTCTGCCCTAACGTCGGTCTTCACGCCATTACTAGACCGACAAAATGGAAGCCGGGGCCTTA +AACCCCGTTCGAGGCGTAGCAAGGAGATAGGGTTATGAACTCTCCCAGTCAATATACCAACACATCGTGG +GACGGATTGCAGAGCGAATCTATCCGCGCTCGCATAATTTAGTGTTGATC |
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| diff -r 000000000000 -r 29eec6c7bab2 test-data/all_fasta.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/all_fasta.loc Wed Mar 08 12:00:46 2023 +0000 |
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| @@ -0,0 +1,1 @@ +bnd-ref bnd-ref bnd-ref ${__HERE__}/bnd-ref.fasta \ No newline at end of file |
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| diff -r 000000000000 -r 29eec6c7bab2 test-data/bnd-ref.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bnd-ref.fasta Wed Mar 08 12:00:46 2023 +0000 |
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| b'@@ -0,0 +1,208 @@\n+>indel_ref whatever\n+GGAGACTGCGGCTGGGTCTCGGGGCGCGGAGCCTCGGCGGGAGGAGGCGGACACGCTGGC\n+AGCGGCGGCGGCAGCGGCCAGCAGCAGCGGCGGCAGCAGCGGCGGCCTCGGTCCGGGGCG\n+CCGGCCGTCCTCCTCCTTCCTCCGGCGGCAGCCCTAGTTCCGCCTCTCGGCTCCCCCCGG\n+CTCCACTCTCCCCAGCCGGGAGCTGCTCTCTCCTCTTTCTAGTCTCGCCAACATGACCCG\n+GCGCGGGCCCGCAGCGCCGCCACCATGGGGAAGGGGGTTGACGAGACAAGTATGAGCCCG\n+CAGCTGGTATCAGAACATGGGGACAAGACGAGCAAAAGGCGAAGAAGGAAAGGGACATGG\n+ACGAACTCAAGAAGGAAGTGTCTATGGACGACCATAAACTCAGCCATGGATGAACTCCAT\n+CGTAAATACGGAACAGATTTGAGCCGAGGCTAACACCCGCAAGGGCCGCTGAGATCCTGG\n+CTCGGGATGGCCCAACGCCCTCACGCCCCTCTCCCACTACTCCCGAGTGGGTCAAATTCT\n+GTAGGCAGCTGTTCGGTGGCTTCTCCATGTTACTGTGGATTGGAGCCATTCTTGGTTTCT\n+TGGCTTATGGCATCCGAAGTGGCTACAGGAAGAGGAACCACCAAATGATGATCTGTACCA\n+TCGGGGTCGTGCTGTCTGCTGTCTCGATCCATTAACTGGCTGTTTCTCCTATTATCAAGA\n+AGCAAAAAAGCTCCAAGTCAATGGAATTCCTTCAAGAACATGGGTCCCTCAGCAAGCCCT\n+CGTGATTCGAAATGGAGAGAAGATGAGCATCAACGGCAGAGGAGTTCGTCGTTGGTGATC\n+TGGTGGAGGTGAAGGGCGGAGACCGAATCCCTGCTGATCTCAGAATCATATCTGCAAATG\n+GGCTGCAAGGTGGATAACTCCTCACTCACTGGTGAATCAGAACCCCAGACTCCGGTCCCC\n+GGATTTCACAAACGAGAACCCTTGGAGACAAGGAACATTGCCTCTTCTCAACCAACTGTG\n+TTGAAGGAACTGCACGTGGCATCGTTGTGTACACTGGGGATCGCACCGTGATGGGCAGGA\n+TCGCCACACCCTTGCTTCTGGGCTGGAATGCGGCCAGACCCCCATTGCTGAAGAAATCGA\n+GCACTTTCATCCACCTCATCACGGGGTGGCCGTGTTCCTGGGGGGTGTCTTTCTTCATGT\n+CTCTCTCTGATCCTTGAGTACACCTGGCTCGAGGCTGTTCATCTTTCCCCATTGGTATCA\n+>bnd_ref_U [moreinfo]\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+GATGCCGACTTTAGCAAAAAATGAGAATGAGTTGATCGATAGTTGTGATTACTCCTGCGA\n+AACATCATCCCACGCGTCCGGAGAAAGCTGGCGACCGATATCCGGATAACGCAATGGATC\n+AAACACCGGGCGCACGCCGAGTTTACGCTGGCGTAGATAATCACTGGCAATGGTATGAAC\n+CACAGGCGAGAGCAGTAAAATGGCGGTCAAATTGGTAATAGCCATGCAGGCCATTATGAT\n+ATCTGCCAGTTGCCACATCAGCGGAAGGCTTAGCAAGGTGCCGCCGATGACCGTTGCGAA\n+GGTGCAGATCCGCAAACACCAGATCGCTTTAGGGTTGTTCAGGCGTAAAAAGAAGAGATT\n+GTTTTCGGCATAAATGTAGTTGGCAACGATGGAGCTGAAGGCAAACAGAATAACCACAAG\n+GGTAACAAACTCAGCACCCCAGGAACCCATTAGCACCCGCATCGCCTTCTGGATAAGCTG\n+AATACCTTCCAGCGGCATGTAGGTTGTGCCGTTACCCGCCAGTAATATCAGCATGGCGCT\n+TGCCGTACAGATGACCAGGGTGTCGATAAAAATGCCAATCATCTGGACAATCCCTTGCGC\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+>bnd_ref_V\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+GACTGACATTGCTTTTGCACTTGGTGTACTGGCGCTGTTGGGAAGTCGTGTTCCGTTAGC\n+GCTGAAGATCTTTTTGATGGCTCTGGCTATTATCGACGATCTTGGGGCCATCATTATCAT\n+CGCATTGTTCTACACTAA'..b'AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+>bnd_ref_X\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+GGAATACCCAGCACATCGGCGATCGCGTGGATCGCACCATCCGGCACCCAGCCACGCTGC\n+TTCTGAACGATTTTCAGCGCTTCAATGGACGCCGCACGCGGGTCTTCGTAGTGGTGCATC\n+TCGTGCTCGATCGCTTCACGCTCTGCCGCACTCAGCTCAAAAGCCTCGGTTTGTGGTTGT\n+TGATTCTCGTGCATAATTAGCGGTCCACATCTGACATAACAAAATCGATACTGCCCAGAT\n+AAACAATCAGGTCAGACACCAGGCTGCCGCGGATCGCCGCCGGAATTTGCTGCAAATGCG\n+CAAAGCTCGGGGTACGAACACGGGTGCGGTAACTCATGGTGCTGCCGTCGCTGGTCAGGT\n+AGTAACTGTTGATCCCTTTGGTCGCCTCAATCATCTGGAAAGATTCATTGGCAGGCATCA\n+CCGGACCCCACGACACTTGCAGGAAGTGGGTGATCAGGGTTTCGATATGTTGCAGCGTGC\n+GCTCTTTCGGCGGCGGCGTGGTCAGCGGGTGATCCGCTTTGAACGGGCCTTCCGGCATGT\n+TGTTGAGGCACTGCTCAAGAATGCGCAGACTCTGGCGCAGCTCTTCCACTTTAAGCATTG\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+>bnd_ref_Z #appendix\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+CTAAAAACGTGGCGAACGGTTTGCTTTTCAGATCCTGCAATGCGCCGTGGAAGGCATAGC\n+GCACCTGTTCGTTGAAAACGTTGGTTTTGCGATTTACCGGTTTTGGCGAGGATTTCGCGC\n+GTTTTGGTGCGTTACGACCGCCGTCGCCTGAGCCGCCGACCGATTTACGGAAGCGATCAA\n+GACGCCCGCCAAACTGCCGAATATGATTGATTGCATCGCGCTTATTCATGGCCCACGCCT\n+CCATGCAAGTGACCATCGCTCAGGGTGAGCATGCGATAGGAACGCCGCGAGATCAGGTTG\n+ATGTCGTGCGTTGCCATCAATACGGTTACCCCAACGCGGTTAAACTCTTCAAACAGACGT\n+AAAATGCCTTCCGACAGCGCGTCGTCCAGGTTACCAGTCGGTTCGTCCGCCAGCAGTACC\n+GCGGGCTTGTTCACCACCGCGCGGGCAATGCCAACACGCTGTTGTTCACCGCCCGAAAGC\n+TGAATAGGGAAGTTCTTCGCTTTGTCCAGTAGCCCGACTTTATCCAGCGCCGCCGACACC\n+CGGCGACGAATATCGTCACCGCTGGCACCGGCGATAATCAGCGGGATCGCCACGTTATCG\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n' 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| diff -r 000000000000 -r 29eec6c7bab2 test-data/bnd.bam |
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| Binary file test-data/bnd.bam has changed |
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| diff -r 000000000000 -r 29eec6c7bab2 test-data/out.aligned_subreads.bam |
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| Binary file test-data/out.aligned_subreads.bam has changed |
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| diff -r 000000000000 -r 29eec6c7bab2 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Wed Mar 08 12:00:46 2023 +0000 |
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| @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/all_fasta.loc" /> + </table> +</tables> |