| Next changeset 1:63e02ef6e153 (2022-10-28) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f |
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added:
clair3.xml test-data/all_fasta.loc test-data/clair3_models.loc test-data/full_alignment_1.vcf test-data/merge_output_1.vcf test-data/phased_bam_1.bam test-data/pileup_1.vcf test-data/test1.bam test-data/test1.bed test-data/test1.fasta test-data/test1.vcf.gz tool-data/all_fasta.loc.sample tool-data/model.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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| diff -r 000000000000 -r 44f6ec903688 clair3.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/clair3.xml Wed Jun 15 09:45:05 2022 +0000 |
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| b'@@ -0,0 +1,311 @@\n+<tool id="clair3" name="Clair3" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">\n+ <macros>\n+ <token name="@TOOL_VERSION@">0.1.11</token>\n+ <token name="@VERSION_SUFFIX@">0</token>\n+ </macros>\n+ <requirements>\n+ <requirement type="package" version="@TOOL_VERSION@">clair3</requirement>\n+ </requirements>\n+ <version_command><![CDATA[run_clair3.sh --version | cut -f2 -d \' \']]></version_command>\n+ <command detect_errors="exit_code"><![CDATA[\n+ #if $ref_source.source == "history"\n+ ln -s \'${ref_source.ref_fasta}\' reference.fasta &&\n+ #elif $ref_source.source == "builtin"\n+ ln -s \'${ref_source.ref_fasta_builtin.fields.path}\' reference.fasta &&\n+ #end if\n+ samtools faidx reference.fasta &&\n+\n+ #if $model_source.source == "datatable"\n+ #set model_path = $model_source.model.fields.path \n+ #end if\n+\n+ ln -s \'${$bam_input}\' input_reads.bam &&\n+ ln -s \'${$bam_input.metadata.bam_index}\' input_reads.bai &&\n+\n+ #if $bed_or_vcf.bed_or_vcf_selector == \'bed\'\n+ ln -s \'$bed_or_vcf.bed_fn\' input.bed &&\n+ #elif $bed_or_vcf.bed_or_vcf_selector == \'vcf\'\n+ ln -s \'$bed_or_vcf.vcf_fn\' input.vcf &&\n+ #end if\n+\n+ run_clair3.sh\n+ --bam_fn=input_reads.bam\n+ --ref_fn=reference.fasta\n+ #if $model_source.source == "datatable"\n+ --platform=\'${model_source.model.fields.platform}\'\n+ --model_path=${model_source.model.fields.path}\n+ #else\n+ #if $model_source.select_built_in == "hifi" or $model_source.select_built_in == "ilmn":\n+ --platform=\'${$model_source.select_built_in}\'\n+ #else\n+ --platform=\'ont\'\n+ #end if\n+ --model_path=\\$(dirname \\$(which run_clair3.sh))/models/$model_source.select_built_in\n+ #end if\n+ --output=\'.\'\n+ --threads=\\${GALAXY_SLOTS:-1}\n+ #if $bed_or_vcf.bed_or_vcf_selector == \'bed\'\n+ --bed_fn=input.bed\n+ #elif $bed_or_vcf.bed_or_vcf_selector == \'vcf\'\n+ --vcf_fn=input.vcf\n+ #else\n+ $bed_or_vcf.include_all_ctgs\n+ #end if\n+ #if $output_options.selection_mode == \'advanced\'\n+ $output_options.gvcf\n+ #end if\n+ #if $adv.qual\n+ --qual=$adv.qual\n+ #end if\n+ #if $adv.snp_min_af\n+ --snp_min_af=$adv.snp_min_af\n+ #end if\n+ #if $adv.indel_min_af\n+ --indel_min_af=$adv.indel_min_af\n+ #end if\n+ $adv.enable_phasing\n+ $adv.no_phasing_for_fa\n+ $adv.print_ref_calls\n+ $adv.ploidity_model\n+ #if $adv.chunk_size\n+ --chunk_size=$adv.chunk_size\n+ #end if\n+\n+ ]]></command>\n+ <inputs>\n+ <conditional name="ref_source">\n+ <param type="select" label="Reference genome source" name="source">\n+ <option value="history" selected="true">History</option>\n+ <option value="builtin">Built-in</option>\n+ </param>\n+ <when value="history">\n+ <param type="data" format="fasta" name="ref_fasta" label="Reference genome" />\n+ </when>\n+ <when value="builtin">\n+ <param type="select" name="ref_fasta_builtin" label="Reference genome">\n+ <options from_data_table="all_fasta" />\n+ </param>\n+ </when>\n+ </conditional>\n+ <conditional name="model_source">\n+ <param type="select" label="Select if you want to use built-in models or your own via datatable." name="source">\n+ <option value="built-in">Built-in</option>\n+ <option value="datatable">Datatable</option>\n+ '..b' <conditional name="ref_source">\n+ <param name="source" value="builtin" />\n+ <param name="ref_fasta_builtin" value="test1" />\n+ </conditional>\n+ <conditional name="output_options">\n+ <param name="selection_mode" value="advanced"/>\n+ <param name="pileup_check" value="true"/>\n+ <param name="full_alignment_check" value="true"/>\n+ <param name="phased_bam_check" value="true"/>\n+ </conditional>\n+ <section name="adv">\n+ <param name="snp_min_af" value="0.5"/>\n+ <param name="indel_min_af" value="0.12"/>\n+ <param name="no_phasing_for_fa" value="true" />\n+ <param name="print_ref_calls" value="true"/>\n+ </section>\n+ <output name="merge_output" ftype="vcf_bgzip">\n+ <assert_contents>\n+ <has_size value="450" delta="50" />\n+ </assert_contents>\n+ </output>\n+ <output name="pileup" ftype="vcf_bgzip">\n+ <assert_contents>\n+ <has_size value="0" />\n+ </assert_contents>\n+ </output>\n+ <output name="full_alignment" ftype="vcf_bgzip">\n+ <assert_contents>\n+ <has_size value="0" />\n+ </assert_contents>\n+ </output>\n+ <output name="phased_bam" ftype="bam">\n+ <assert_contents>\n+ <has_size value="0" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+ Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories:\n+ pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall.\n+ Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration.\n+ \n+ https://github.com/HKU-BAL/Clair3\n+\n+ LICENSE:\n+\n+ Copyright 2021 The University of Hong Kong, Department of Computer Science\n+\n+ Redistribution and use in source and binary forms, with or without modification,\n+ are permitted provided that the following conditions are met:\n+\n+ 1. Redistributions of source code must retain the above copyright notice, this\n+ list of conditions and the following disclaimer.\n+\n+ 2. Redistributions in binary form must reproduce the above copyright notice,\n+ this list of conditions and the following disclaimer in the documentation\n+ and/or other materials provided with the distribution.\n+\n+ 3. Neither the name of the copyright holder nor the names of its contributors\n+ may be used to endorse or promote products derived from this software without\n+ specific prior written permission.\n+\n+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND\n+ ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED\n+ WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\n+ DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR\n+ ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES\n+ (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;\n+ LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON\n+ ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT\n+ (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS\n+ SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.\n+ ]]></help>\n+ <citations>\n+ <citation type="doi">10.1101/2021.12.29.474431</citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r 44f6ec903688 test-data/all_fasta.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/all_fasta.loc Wed Jun 15 09:45:05 2022 +0000 |
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| @@ -0,0 +1,10 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the "genome" directory (a directory that contains a directory +#for each build). The script extract_fasta.py will generate the file +#all_fasta.loc. This file has the format (white space characters are +#TAB characters): +# +#<unique_build_id> <display_name> <file_path> +# +#So, all_fasta.loc could look something like this: +test1 "Test Genome" ${__HERE__}/test1.fasta |
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| diff -r 000000000000 -r 44f6ec903688 test-data/clair3_models.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clair3_models.loc Wed Jun 15 09:45:05 2022 +0000 |
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| @@ -0,0 +1,10 @@ +#Enter the model names in the second column, the platform name in the second and the path in the third. +#This file lists the locations and dbkeys of all the model files +#under the "models" directory (a directory that contains a directory +#for each build). This file has the format (white space characters are +#TAB characters): +# +#<unique_build_id> <display_name> <platform> <file_path> +# +#So, all_model.loc could look something like this: +test_model "the_model_name" ont $(dirname $(which run_clair3.sh))/models/r941_prom_hac_g360+g422 |
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| Binary file test-data/full_alignment_1.vcf has changed |
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| diff -r 000000000000 -r 44f6ec903688 test-data/test1.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1.bed Wed Jun 15 09:45:05 2022 +0000 |
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| @@ -0,0 +1,3 @@ +chr1 14756 15038 JUNC00000001 294 - 14756 15038 255,0,0 2 73,69 0,213 +chr1 14969 15836 JUNC00000002 144 - 14969 15836 255,0,0 2 69,41 0,826 +chr1 15905 16677 JUNC00000003 12 - 15905 16677 255,0,0 2 42,71 0,701 |
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| diff -r 000000000000 -r 44f6ec903688 test-data/test1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1.fasta Wed Jun 15 09:45:05 2022 +0000 |
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| @@ -0,0 +1,85 @@ +>demo20 +TGCCTGCTTTGTGCCAGGTTCTGGGTTGGGAGGTGCTGGGGACAGGGAGATGAGTCAGAC +CTgggaagatttcgtagaggaggtgacagtaagctggaacctgtgtaatgagcaggagtt +gcccagtggagaaggggaaggtgttccaggcggaagaaacagcatatgcaaaggccccaa +ggtaggaagggccctagtgtgtgcagaggacagggcatggggaggggaactaaggctgag +gccaaggagaggaaatgactcacaccgtgagagaggagttgagaccagggaggCTGCTTG +CTGTATGATGCAACTGAGAGGGTAGAACAAGGCTGGCACAGAGAAGGTGGGGAAGGAAAA +GGAGAGACGAAGCTGAGATTTCAGCAGGGCCAAGTCAGCCGTGAGTGCCAGGCTGCGGAG +CCCAGATTCTCTGGGCTGagaaagagcactctgtccagagtgtggaggggggcctggagg +ggatgagactcaaagctgggaggccagagaggaggctgctagagttttctgggagagagt +tactggggcctgaacTCCAGTGAGGCActtcccatttcacagaccaggaaactgaggccc +aagagtgaggcaactggcccaagggcacacagccaggtaaggcagaacCTTCCTTCTTTG +GAGCTCCCTTGGGTGGGAAGCTGTGGGCTCCCCTTCATAGCCCACCCTTTTGGCTGTATC +TCCCTGCTGCCCTGGGCATATGCTCCCTTATTCTGTCCTCCCTTGAAGCTGACTGCTGGC +CTTAAAGGGCCCCTGTTTCTTCCCTCTGGACTACATGAGATCGGGATAGTATTAATGACT +AAAACCTACCAGGGGTTTCTAGGCCTGGCCTGGAAAAAGTGACTGTTGACAAACAAAGTG +CAGAGATTTAAAATCTCCTCTGTCTCAATTAGTGGAATCCAGTTAGAGGTTTGAACTATG +ATTCTACCAGAATCCAATCTCTCTGGGTAGCCAGGTACCCAGGATGGGGCTAAAATTCCA +GATGGATAGGTTGTCAACACCAGTGAGGAACCAGGAGGCTACCACAGGGTGGGACTTCCT +GGTTTGGCTTTACATCTGAACTTCAGGGATCCCAGATCCTGGATCTGGGGCACTTGTCCA +GAGAAGGCTATTGCTCTCATGTCACAAATGAGATGACTAAGACCCCCAAATCAATTCCAG +TTCACTCACAAGCATTTCCTGGGCAGTGGAGACCCCTGCCCCACCTGTTGGCACCCCCTC +AGCTCCCCACAGGGAATTGGAGTCCAGCCAAGCATGAGGAGGCTGTTGGCCTCAAGGTGA +GCAGGGATGGGCTGAACCTCACCCAGTAAGGCAAGGACAGAGCCAGGGTTGGCCTGAGAT +TTCCAGCCACCCTTTCCAAGGCTCTGCTCACTGTTATTTTCCTTAGTCTacaacaatatc +aataacaataacaacaataatatcaacaCAAAAAGTGAAATACTCACCATGTATTGTAGT +GTTTCCAAGGTGTCATGTAATGCCAGGGGTAGTTTGGGGCCAGGAAAAATATTTTTGGGA +GGCATAAGAATAGGATGGACTGATATTGATATGCAACAGTTTGATCTGGTCCTCCTCTGA +ATATCTGGGCTGGTAATTTGTACCAGTTTCCCTCGCTTTtgtgcataggcactgtgctga +acccttttgtatgcatgaactcatccgattctctgtgcaagaactctatgagattattat +tcccgttttacaagtaagaaaaattgaggctctgagaagttaaataaatgacttgtatga +agttccagtgctaattaataagtgaaggagccagggcttgaactccggcccatctgactg +caaagccagtgcccttcctcctacacATCTTCCTTTGGATTTCCACCACTGAGCATATGT +AAGGTTGGGCAAACAGCCTGCATGAACAATCGCTGCTTTTATATCATGCACAAGTTTGGT +CTTTTCTGCCTGTGCCCATGTCCTTGTAACCTTCTGAACCAAACTCCCCAGTGCCTGGGA +ACATCAGAAGACTTGACTCTCTTCTCCTTTCACTAGCCTCCACCTGACTGGGACAAAGCC +ATGCAGAGAGCTAGTGCTCCCTTCCTGCTAGACTTCAAGGATGCCTGGTTCCTGTGCCCC +ATCTCCATCCAGCCCTCTCTTCTACACCTGGTGACTGAGCCTCTCCTTCAGTTTCTCCAT +CCAGAAGGGGGTGAAAGCAACTGCCTAGTGTCCTTCCCTGGTGATAGTGGAGCACGGGGG +ACAGGGTGTTTGGGCAAAAGGTGCCCAAGGTGAGGTGCCCAACACAACCTCCTACTCAGA +CGATTGAGCAGACATTCAGCCTCATCTGGGGACTGGGTTACCAGTGGGTTAGTGGGAGGC +ATTGGGCCCAGGCCCTGTGCCTTGGGCTGAGCTACAAGAAACCCACACATGGGATGAATT +CAGGCAGCTCAAGGCCAGGTCTGTGCATACGCCAGTAATAGGTTCAGGTTAATCCACATG +TCGCGATTTGGAAGGTGTCTACTTTTCCTACCTGTAGCTTCCTTAGGCCTCAAACCCCTA +CTCAGCTGGGTCTGCCAGACTGAGATGGAGCCAGGGTGGAATCTTCTGCCCTCAAATCCC +TGTCAGCCCTGGTGGTGCCGGGAGCGCCATCACTATTGGGTCTTAAAGGCTTTCCAGCCT +TCCACTATGGATCCAGGAGCAGCAGTAGCCCCTTTGGTCTTTCTCTCTCATCAGGACATC +TCCACTCATGGTTCCAGTCAGAGCTTCTTGAAAGTAGTCCCACTCTGTTCAAAAGCCTCC +CATGCCCCCTGCTAGCCTCAGGCTAAGAGCCCTTCTCCTTCGCACAGCCTTTGGACCTGT +CTATTTTTATGGTCTGGAAACTTCAGGAACACTGATAGCTGAGCATCTGGCACATATTAT +GCACTCAAAAACCATGTATTTCTTTCTCCTTCCCTTTGGGACCCGTAAACCAGGGactgg +acatttttgcaagagacaggagctgtgactgtgcattcactgctgtatccccagcaccca +gcactgggcctgccacacagtaagtgcttagtaaatgtttgttgactgagtgaTTGCAGC +TGGGGCCAAGAATGCCTTGGACACCCCAAGTAGGCCGTGTTAGAAGGAGTCAGTGAGAGC +CTGGGAGCCCAGCCCAGAATTGTTTTCTTGACCCAGAAGCCAGGGCCAGGGATGCCTCTT +CACTTCTGTTTGGCCCTCTTGGGCTTAGGGGCAGGGGCATTAAGATGAgagaggtccttg +gggtgcattgagtctaacctcccagttcctcccattctacagccaggaaaactgaggccc +agggaggggtaggacaagcccaagAAAGTGGGGCTGGAGAATGAATCCTGGAGACCAAAC +TTGTCAGTCTGGATTGCTGTTGCCCTCATCCTCGCCTCCAAAACCCatgggtaaactgag +gccaagagaggggcaggggcatgcccaaggtcacccatggaatcaggggacagggcctgg +attgggattgttgttgacgccattattactgtttattgttgtttctatttcacAGATGGT +CGGGGAGGGTGGGGCCCGCAATGGCTCCCAGGCGCCCAGAGACCCTGGAGGGTGAGCAGG +GTCTCCCCTCCCCTCTCCTGCCCGTCTTTAGCCACACTGGGGCGCACACCGCTCACTCAC +CCGGGGCCGAGGCGTTAGCCCTTTCTTGCACCAGGTGCCGCAACAACACCAGCAGCTGGC +GCAGGCTGTGCTGCTGGTCCTGCAGGAGGCTGGAGTTGTGCCTGACACCGCGCAGGCCGC +GCTCGATGTTGGTGAGGGCGGCGCTCTGGCGGCTCAGCGTGTTCAGCAGCTTCGCCTTCT +TGCTGAGGATGCTGGCCAGCTCCTCCTGCTGCTTGGTCTCCAGGGCCTGCAACCGCTTCT +CGAGCGCGCTGCGGGGTAGGGGGCGCACAGAGGTGAGCCTGGCATCCTCGCGAAGCACGC +ACCCCCGCGCGCCTCCCCGGCCCTGGAGTCCCTGCAGCCCGACGATGAGACTCAAGTGTG +GTGGAACGTCCTGTGCCCACTGTAGGCACAGATTGAGGAGGGGAGAAAAGAGATACCCGG +CCCTGGAGTAATATAGATTGAGGTTTAGTGGAAGAAAGAGGTGGTGTGGGAGGGACACCA +GCAACTGGGTAGCTATTATCAAATCCCAACTGTGCTTGCTTTTTGACCCAGCAGTCTACT +CTCAGGAGTTATCCTCTAGGGAGCATGGTCAAGAATGGCCCTGGGGACTTGCTTGTAATA +GAAAAACAAACTAACCAACCAACCAAAAAAGATATAGCCTAGATGCCCAAAAGCCAGGAC +TGGCTGAATCCGTTGCGTTTTGGCGTCCCTGGAAATGTTCCGCAGTCATGAAGGAGGAGG +CATTTGCACAGAATTGGAAAGATGCCCAGGACTTGGGGCACATCAAGCCTAACCCCATGT +GTGGCAAGAGAAGAAAGAAAGTATTAATGTAAATAAAGAGAAATGGGGTGAACATATAGG +AGAAGGCTGGAAAGACCGCAGTGGTGCCTGTGTTTGGGAAGAATATGAAAGAAATTCCCT +CAAGTGCTGTGACTTCTGCAGAGCAGGTTTGAGTGGATGAAGATGGAGAGGAGGAAGATG +GGGGCAGGATGGAGGGCCCAACTTTCACTTTTATTTTGTACAGGTTCCTGTTGTCCGATG +ATATTATAATAATCAAGAGACATTTTTTGTAATGGATTTAGAAGCAAAGAGGAGTTTTTC +AAAAGAAAGCCTTAGACTCAGCTCTTTCTTTTTGGACATTTTATCCTCCAGATTTACTca +catgtgtgtgaaatgagatatggaaatgttactcatcgtatcactggttggattagtaaa +aggctggaagcaacctcaatatccattaactggggactggaggaataaaagcagggacca +catatggtggagcattataa |
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| diff -r 000000000000 -r 44f6ec903688 test-data/test1.vcf.gz |
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| Binary file test-data/test1.vcf.gz has changed |
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| diff -r 000000000000 -r 44f6ec903688 tool-data/all_fasta.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/all_fasta.loc.sample Wed Jun 15 09:45:05 2022 +0000 |
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| @@ -0,0 +1,10 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the "genome" directory (a directory that contains a directory +#for each build). The script extract_fasta.py will generate the file +#all_fasta.loc. This file has the format (white space characters are +#TAB characters): +# +#<unique_build_id> <display_name> <file_path> +# +#So, all_fasta.loc could look something like this: +#test1 Test-Genome ./test-data/test1.fa |
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| diff -r 000000000000 -r 44f6ec903688 tool-data/model.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/model.loc.sample Wed Jun 15 09:45:05 2022 +0000 |
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| @@ -0,0 +1,10 @@ +#Enter the model names in the second column, the platform name in the second and the path in the third. +#This file lists the locations and dbkeys of all the model files +#under the "models" directory (a directory that contains a directory +#for each build). This file has the format (white space characters are +#TAB characters): +# +#<unique_build_id> <display_name> <platform> <file_path> +# +#So, all_model.loc could look something like this: +#test_model "the_model_name" r941_prom_hac_g360+g422 $(dirname $(which run_clair3.sh))/models/r941_prom_hac_g360+g422 |
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| diff -r 000000000000 -r 44f6ec903688 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Wed Jun 15 09:45:05 2022 +0000 |
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| @@ -0,0 +1,12 @@ +<?xml version="1.0"?> +<tables> + <!-- Locations of indexes in the Bowtie mapper format --> + <table name="model" comment_char="#"> + <columns>value, name, platform, path</columns> + <file path="tool-data/model.loc" /> + </table> + <table name="all_fasta" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/all_fasta.loc" /> + </table> +</tables> |
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| diff -r 000000000000 -r 44f6ec903688 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Wed Jun 15 09:45:05 2022 +0000 |
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| @@ -0,0 +1,13 @@ +<?xml version="1.0"?> +<tables> + <!-- Locations of model folders --> + <table name="clair3_models" comment_char="#"> + <columns>value, name, platform, path</columns> + <file path="${__HERE__}/test-data/clair3_models.loc" /> + </table> + <!-- Locations of reference genome files in fasta format --> + <table name="all_fasta" comment_char="#"> + <columns>value, name, path</columns> + <file path="${__HERE__}/test-data/all_fasta.loc" /> + </table> +</tables> |