| Previous changeset 0:373c1735d31f (2022-08-11) Next changeset 2:d58a57db7a96 (2023-08-25) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6 |
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modified:
cooc_mutbamscan.xml macros.xml |
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added:
test-data/ampl_info.tsv test-data/bed_cojac.bed test-data/primers.bed |
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| diff -r 373c1735d31f -r 9f1660129403 cooc_mutbamscan.xml --- a/cooc_mutbamscan.xml Thu Aug 11 13:50:37 2022 +0000 +++ b/cooc_mutbamscan.xml Mon Jul 31 15:23:23 2023 +0000 |
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| b'@@ -1,96 +1,150 @@\n <tool id="cooc_mutbamscan" name="Cojac: mutbamscan" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"\n profile="@PROFILE@">\n <description>\n- scan an alignment file for mutation co-occurrences\n+ scans an alignment file for mutation co-occurrences\n </description>\n <macros>\n <import>macros.xml</import>\n </macros>\n <expand macro="biotools"/>\n- <expand macro="requirements"/>\n+ <expand macro="requirements">\n+ <requirement type="package" version="0.1.0">viramp-hub</requirement>\n+ </expand>\n <expand macro="version"/>\n <command detect_errors="exit_code"><![CDATA[\n-ln -s \'$bed_file\' \'bed_file\' &&\n-@VOCDIR_COMMAND@\n-#import re\n-#set identifier = re.sub(\'[^\\s\\w\\-\\\\.]\', \'_\', str($bam_file.element_identifier))\n-ln -s \'$bam_file\' ${identifier}.bam &&\n-ln -s \'${bam_file.metadata.bam_index}\' ${identifier}.bai &&\n-cooc-mutbamscan\n- -a \'${identifier}.bam\'\n- -b \'bed_file\'\n- -m \'$vocdir\'\n- -y cooc.yaml\n- -j cooc.json\n- #if $amplicons_file.choice == \'build\'\n- -A amplicons.yaml\n+## arrange BAM inputs and index files into a V-pipe-style folder structure\n+## that cojac understands\n+sh arrange_samples.sh &&\n+\n+#if $spec_layout.mode == \'separate\':\n+ #set $voc_config = $spec_layout.voc_source\n+ @VOCDIR_COMMAND@\n+ ## prepare amplicon information\n+ #if $spec_layout.amplicon_definitions.choice == \'insert_scheme\':\n+ ln -s \'$spec_layout.amplicon_definitions.insert_bed\' bed_cojac.bed &&\n+ #else if $spec_layout.amplicon_definitions.choice == \'primer_scheme\':\n+ scheme-convert \'$spec_layout.amplicon_definitions.primer_bed\' -t bed -b cojac -o bed_cojac.bed &&\n+ #else:\n+ scheme-convert \'$spec_layout.amplicon_definitions.primer_bed\' -t bed -b cojac -a \'$spec_layout.amplicon_definitions.amplicon_info\' -o bed_cojac.bed &&\n+ #end if\n+#end if\n+\n+## run cojac\n+cojac cooc-mutbamscan\n+ ## use a sample list file to tell cojac to look for the inputs in the\n+ ## V-pipe-style folder stucture we\'ve created earlier.\n+ -s samples_list.tsv\n+ -p inputs\n+ -b bed_cojac.bed\n+ #if $spec_layout.mode == \'separate\':\n+ -m voc/\n+ -A amplicons.yaml\n+ --cooc $spec_layout.cooc\n #else\n- -Q \'$amplicons_file.in_amp\'\n+ -Q \'$spec_layout.in_amp\'\n+ #end if\n+ #if \'yaml\' in $out_opts.output_formats:\n+ -y cooc.yaml\n+ #end if\n+ #if \'json\' in $out_opts.output_formats:\n+ -j cooc.json\n+ #end if\n+ #if \'tabular\' in $out_opts.output_formats:\n+ -t cooc.tsv\n #end if\n- -t cooc.tsv\n- --cooc $cooc\n ]]></command>\n+ <configfiles>\n+ <configfile filename="arrange_samples.sh"><![CDATA[#for $dataset in $mapped_input:\n+ #set $sample_id = $dataset.element_identifier.replace("\'", \'_\').replace(\'/\', \'_\')\n+mkdir -p \'inputs/$sample_id/1/alignments/\' &&\n+ln -s \'$dataset\' \'inputs/$sample_id/1/alignments/REF_aln.bam\' &&\n+ln -s \'$dataset.metadata.bam_index\' \'inputs/$sample_id/1/alignments/REF_aln.bam.bai\' &&\n+#end for\n+#set $num_samples = len($mapped_input)\n+echo "Gathered $num_samples sample and index files for cojac to discover from a samples list."\n+ ]]></configfile>\n+ <configfile filename="samples_list.tsv"><![CDATA[#for $dataset in $mapped_input:\n+ #set $line = \'\\t\'.join([$dataset.element_identifier.replace("\'", \'_\').replace(\'/\', \'_\'), \'1\', str($dataset)])\n+$line\n+#end for]]></configfile>\n+ </configfiles>\n <inputs>\n- <expand macro="vocdir_input"/>\n- <param name="bed_file" type="data" format="bed"\n- label="BED file defining the amplicons"/>\n- <param name="bam_file" type="data" format="bam,cram,sam"\n- label="Alignment BAM/CRAM/SAM file"/>\n- <param argument="--cooc" type="integer" min="1" value="2"\n- label="Minimum number of cooccurence mutations on the same amplicon"/>\n- <conditional name="amplicons_file">\n- <param name="choice" type="select" label="Source of amplicons YAML file">\n- '..b'd_file" value="nCoV-2019.insert.V3.bed"/>\n- <conditional name="amplicons_file">\n- <param name="choice" value="custom"/>\n+ <param name="mapped_input" value="tbam11.bam"/>\n+ <conditional name="spec_layout">\n+ <param name="mode" value="combined"/>\n <param name="in_amp" value="amplicons111.yaml"/>\n </conditional>\n- <param name="output_files" value="yaml,tabular"/>\n+ <section name="out_opts">\n+ <param name="output_formats" value="yaml,tabular"/>\n+ </section>\n+ <output name="cooc_yaml" ftype="yaml">\n+ <assert_contents>\n+ <has_text text="76_om1"/>\n+ <has_text text="81_om1"/>\n+ </assert_contents>\n+ </output>\n+ <output name="cooc_tsv" ftype="tabular">\n+ <assert_contents>\n+ <has_text text="76_om1"/>\n+ <has_text text="81_om1"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <!-- Test 3: use computed cojac format amplicon definitions from 2 files -->\n+ <test expect_num_outputs="2">\n+ <param name="mapped_input" value="tbam11.bam"/>\n+ <conditional name="spec_layout">\n+ <conditional name="voc_source">\n+ <param name="choice" value="builtin"/>\n+ </conditional>\n+ <conditional name="amplicon_definitions">\n+ <param name="choice" value="primer_scheme_plus"/>\n+ <param name="primer_bed" value="primers.bed" ftype="bed"/>\n+ <param name="amplicon_info" value="ampl_info.tsv"/>\n+ </conditional>\n+ <param name="output_cojac_ampl" value="false"/>\n+ </conditional>\n+ <section name="out_opts">\n+ <param name="output_formats" value="yaml,tabular"/>\n+ </section>\n+ <output name="cooc_yaml" ftype="yaml">\n+ <assert_contents>\n+ <has_text text="76_om1"/>\n+ <has_text text="81_om1"/>\n+ </assert_contents>\n+ </output>\n+ <output name="cooc_tsv" ftype="tabular">\n+ <assert_contents>\n+ <has_text text="76_om1"/>\n+ <has_text text="81_om1"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <!-- Test 4: test primer scheme as input -->\n+ <test expect_num_outputs="2">\n+ <param name="mapped_input" value="tbam11.bam"/>\n+ <conditional name="spec_layout">\n+ <conditional name="voc_source">\n+ <param name="choice" value="builtin"/>\n+ </conditional>\n+ <conditional name="amplicon_definitions">\n+ <param name="choice" value="primer_scheme"/>\n+ <param name="primer_bed" value="primers.bed" ftype="bed"/>\n+ </conditional>\n+ <param name="output_cojac_ampl" value="false"/>\n+ </conditional>\n+ <section name="out_opts">\n+ <param name="output_formats" value="yaml,tabular"/>\n+ </section>\n <output name="cooc_yaml" ftype="yaml">\n <assert_contents>\n <has_text text="76_om1"/>\n@@ -145,11 +256,11 @@\n <help><![CDATA[\n @HELP_HEADER@\n \n-Information about **cooc-mutbamscan** method\n-============================================\n+Information about **cojac cooc-mutbamscan**\n+===========================================\n \n-The method scans an alignment BAM/CRAM/SAM file for mutation co-occurrences and output a JSON or YAML file.\n-\n+The tool scans an alignment BAM/CRAM/SAM file for mutation co-occurrences.\n+It can report its findings in json, yaml and/or tabular format.\n ]]></help>\n <expand macro="citations"/>\n </tool>\n' |
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| diff -r 373c1735d31f -r 9f1660129403 macros.xml --- a/macros.xml Thu Aug 11 13:50:37 2022 +0000 +++ b/macros.xml Mon Jul 31 15:23:23 2023 +0000 |
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| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">0.2</token> + <token name="@TOOL_VERSION@">0.9</token> <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">21.01</token> <xml name="biotools"> @@ -18,34 +18,28 @@ <version_command>echo @TOOL_VERSION@</version_command> </xml> <xml name="vocdir_input"> - <conditional name="vocdir_option"> + <conditional name="voc_source"> <param name="choice" type="select" - label="Source of YAML files with definition of the variant of concerns" - help="Cojac ships with a directory with variant definitions yaml files (https://github.com/cbg-ethz/cojac/tree/master/voc), which the tool can access internally. You can also download the latest version of the yaml files from https://github.com/phe-genomics/variant_definitions and use it as a custom yamls defining the variant of concerns."> - <option value="cache">Definitions shipped with the tool (can be outdated)</option> - <option value="custom">From history</option> + label="Source of lineage definitions" + help="Cojac detects lineage evidence based on lineage mutation patterns deined in tool-specific yaml format. You can choose between the (possibly outdated) definitions shipped with the tool or definitions provided as a collection of yaml datasets in your history. See the tool help below for more details."> + <option value="builtin">Lineage definitions shipped with the tool</option> + <option value="custom">YAML dataset collection in history</option> </param> - <when value="cache"/> + <when value="builtin"/> <when value="custom"> - <param name="voc_file" type="data" format="yaml" multiple="true" - label="YAML defining the variant of concern"/> + <param name="collection" type="data_collection" collection_type="list" format="yaml" label="Collection of lineage definitions" /> </when> </conditional> </xml> <token name="@VOCDIR_COMMAND@"><![CDATA[ -#if $vocdir_option.choice == 'custom' - #set vocdir = 'voc/' - #set file_paths1 = [] +#if $voc_config.choice == 'custom' mkdir -p voc && - #for $input_file in $voc_file - #set $file_path = $vocdir + $input_file.element_identifier - ln -s '$input_file' '$file_path' && - $file_paths1.append($file_path) + #for $input_file in $voc_config.collection + ln -s '$input_file' 'voc/$input_file.element_identifier' && #end for #else - DB_PATH="\$(dirname "\$(dirname "\$(which cooc-mutbamscan)")")/share/cojac" && - ln -s "\$DB_PATH" db && - #set $vocdir = 'db/voc' + DB_PATH="\$(dirname "\$(dirname "\$(which cojac)")")/share/cojac/voc" && + ln -s "\$DB_PATH" voc && #end if ]]></token> <token name="@HELP_HEADER@"><![CDATA[ @@ -59,4 +53,4 @@ <citation type="doi">10.1101/2021.01.08.21249379</citation> </citations> </xml> -</macros> \ No newline at end of file +</macros> |
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| diff -r 373c1735d31f -r 9f1660129403 test-data/ampl_info.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ampl_info.tsv Mon Jul 31 15:23:23 2023 +0000 |
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| diff -r 373c1735d31f -r 9f1660129403 test-data/bed_cojac.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bed_cojac.bed Mon Jul 31 15:23:23 2023 +0000 |
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| diff -r 373c1735d31f -r 9f1660129403 test-data/primers.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/primers.bed Mon Jul 31 15:23:23 2023 +0000 |
| b |
| b'@@ -0,0 +1,198 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MN908947.3\t20186\t20216\tSARS-CoV-2_66_RIGHT\tpool_2\t-\n+MN908947.3\t20090\t20117\tSARS-CoV-2_67_LEFT\tpool_1\t+\n+MN908947.3\t20472\t20497\tSARS-CoV-2_67_RIGHT\tpool_1\t-\n+MN908947.3\t20377\t20405\tSARS-CoV-2_68_LEFT\tpool_2\t+\n+MN908947.3\t20766\t20792\tSARS-CoV-2_68_RIGHT\tpool_2\t-\n+MN908947.3\t20677\t20699\tSARS-CoV-2_69_LEFT\tpool_1\t+\n+MN908947.3\t21050\t21080\tSARS-CoV-2_69_RIGHT\tpool_1\t-\n+MN908947.3\t20988\t21013\tSARS-CoV-2_70_LEFT\tpool_2\t+\n+MN908947.3\t21358\t21387\tSARS-CoV-2_70_RIGHT\tpool_2\t-\n+MN908947.3\t21294\t21316\tSARS-CoV-2_71_LEFT\tpool_1\t+\n+MN908947.3\t21675\t21700\tSARS-CoV-2_71_RIGHT\tpool_1\t-\n+MN908947.3\t21532\t21561\tSARS-CoV-2_72_LEFT\tpool_2\t+\n+MN908947.3\t21904\t21933\tSARS-CoV-2_72_RIGHT\tpool_2\t-\n+MN908947.3\t21865\t21889\tSARS-CoV-2_73_LEFT\tpool_1\t+\n+MN908947.3\t22247\t22274\tSARS-CoV-2_73_RIGHT\tpool_1\t-\n+MN908947.3\t22091\t22113\tSARS-CoV-2_74_LEFT\tpool_2\t+\n+MN908947.3\t22474\t22503\tSARS-CoV-2_74_RIGHT\tpool_2\t-\n+MN908947.3\t22402\t22428\tSARS-CoV-2_75_LEFT\tpool_1\t+\n+MN908947.3\t22785\t22805\tSARS-CoV-2_75_RIGHT\tpool_1\t-\n+MN908947.3\t22648\t22677\tSARS-CoV-2_76_LEFT\tpool_2\t+\n+MN908947.3\t23028\t23057\tSARS-CoV-2_76_RIGHT\tpool_2\t-\n+MN908947.3\t22944\t22974\tSARS-CoV-2_77_LEFT\tpool_1\t+\n+MN908947.3\t23327\t23351\tSARS-CoV-2_77_RIGHT\tpool_1\t-\n+MN908947.3\t23219\t23246\tSARS-CoV-2_78_LEFT\tpool_2\t+\n+MN908947.3\t23611\t23635\tSARS-CoV-2_78_RIGHT\tpool_2\t-\n+MN908947.3\t23553\t23575\tSARS-CoV-2_79_LEFT\tpool_1\t+\n+MN908947.3\t23927\t23955\tSARS-CoV-2_79_RIGHT\tpool_1\t-\n+MN908947.3\t23853\t23876\tSARS-CoV-2_80_LEFT\tpool_2\t+\n+MN908947.3\t24233\t24258\tSARS-CoV-2_80_RIGHT\tpool_2\t-\n+MN908947.3\t24171\t24194\tSARS-CoV-2_81_LEFT\tpool_1\t+\n+MN908947.3\t24545\t24567\tSARS-CoV-2_81_RIGHT\tpool_1\t-\n+MN908947.3\t24426\t24448\tSARS-CoV-2_82_LEFT\tpool_2\t+\n+MN908947.3\t24814\t24836\tSARS-CoV-2_82_RIGHT\tpool_2\t-\n+MN908947.3\t24750\t24772\tSARS-CoV-2_83_LEFT\tpool_1\t+\n+MN908947.3\t25122\t25150\tSARS-CoV-2_83_RIGHT\tpool_1\t-\n+MN908947.3\t25051\t25076\tSARS-CoV-2_84_LEFT\tpool_2\t+\n+MN908947.3\t25438\t25461\tSARS-CoV-2_84_RIGHT\tpool_2\t-\n+MN908947.3\t25331\t25353\tSARS-CoV-2_85_LEFT\tpool_1\t+\n+MN908947.3\t25711\t25740\tSARS-CoV-2_85_RIGHT\tpool_1\t-\n+MN908947.3\t25645\t25672\tSARS-CoV-2_86_LEFT\tpool_2\t+\n+MN908947.3\t26026\t26050\tSARS-CoV-2_86_RIGHT\tpool_2\t-\n+MN908947.3\t25951\t25979\tSARS-CoV-2_87_LEFT\tpool_1\t+\n+MN908947.3\t26338\t26360\tSARS-CoV-2_87_RIGHT\tpool_1\t-\n+MN908947.3\t26255\t26277\tSARS-CoV-2_88_LEFT\tpool_2\t+\n+MN908947.3\t26635\t26661\tSARS-CoV-2_88_RIGHT\tpool_2\t-\n+MN908947.3\t26564\t26587\tSARS-CoV-2_89_LEFT\tpool_1\t+\n+MN908947.3\t26956\t26979\tSARS-CoV-2_89_RIGHT\tpool_1\t-\n+MN908947.3\t26873\t26895\tSARS-CoV-2_90_LEFT\tpool_2\t+\n+MN908947.3\t27256\t27283\tSARS-CoV-2_90_RIGHT\tpool_2\t-\n+MN908947.3\t27152\t27177\tSARS-CoV-2_91_LEFT\tpool_1\t+\n+MN908947.3\t27534\t27560\tSARS-CoV-2_91_RIGHT\tpool_1\t-\n+MN908947.3\t27447\t27473\tSARS-CoV-2_92_LEFT\tpool_2\t+\n+MN908947.3\t27826\t27855\tSARS-CoV-2_92_RIGHT\tpool_2\t-\n+MN908947.3\t27700\t27726\tSARS-CoV-2_93_LEFT\tpool_1\t+\n+MN908947.3\t28082\t28104\tSARS-CoV-2_93_RIGHT\tpool_1\t-\n+MN908947.3\t27996\t28021\tSARS-CoV-2_94_LEFT\tpool_2\t+\n+MN908947.3\t28394\t28416\tSARS-CoV-2_94_RIGHT\tpool_2\t-\n+MN908947.3\t28190\t28214\tSARS-CoV-2_95_LEFT\tpool_1\t+\n+MN908947.3\t28572\t28598\tSARS-CoV-2_95_RIGHT\tpool_1\t-\n+MN908947.3\t28512\t28536\tSARS-CoV-2_96_LEFT\tpool_2\t+\n+MN908947.3\t28893\t28914\tSARS-CoV-2_96_RIGHT\tpool_2\t-\n+MN908947.3\t28827\t28849\tSARS-CoV-2_97_LEFT\tpool_1\t+\n+MN908947.3\t29206\t29227\tSARS-CoV-2_97_RIGHT\tpool_1\t-\n+MN908947.3\t29136\t29161\tSARS-CoV-2_98_LEFT\tpool_2\t+\n+MN908947.3\t29512\t29534\tSARS-CoV-2_98_RIGHT\tpool_2\t-\n+MN908947.3\t29452\t29475\tSARS-CoV-2_99_LEFT\tpool_1\t+\n+MN908947.3\t29827\t29854\tSARS-CoV-2_99_RIGHT\tpool_1\t-\n' |