| Previous changeset 0:d04ea6b052c5 (2022-08-11) Next changeset 2:0349d8981030 (2023-10-02) |
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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_pubmut.xml macros.xml |
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added:
test-data/ampl_info.tsv test-data/bed_cojac.bed test-data/primers.bed |
| b |
| diff -r d04ea6b052c5 -r f193fef5b19d cooc_pubmut.xml --- a/cooc_pubmut.xml Thu Aug 11 13:49:40 2022 +0000 +++ b/cooc_pubmut.xml Mon Jul 31 15:23:17 2023 +0000 |
| [ |
| b'@@ -1,69 +1,131 @@\n <tool id="cooc_pubmut" name="Cojac: pubmut" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"\n profile="@PROFILE@">\n <description>\n- render a JSON or YAML file to a pretty table\n+ pretty-prints cojac mutbamscan co-occurrence results\n </description>\n <macros>\n <import>macros.xml</import>\n </macros>\n <expand macro="biotools"/>\n <expand macro="requirements">\n- <requirement type="package" version="2.12">pandoc</requirement>\n+ <requirement type="package" version="3.1.3">pandoc</requirement>\n+ <requirement type="package" version="6.2.1">gmp</requirement>\n </expand>\n <expand macro="version"/>\n <command detect_errors="exit_code"><![CDATA[\n-@VOCDIR_COMMAND@\n-#for $input_file in $cooc_file\n- #set $cooc_ext = $input_file.ext\n-#end for\n-cooc-pubmut\n- -m \'$vocdir\'\n- -a \'$amplicons\'\n- #if $cooc_ext == \'json\'\n- -j \'$cooc_file\'\n- #else if $cooc_ext == \'yaml\'\n- -y \'$cooc_file\'\n+#if $annotations.availability == \'full\':\n+ #set $voc_config = $annotations.voc_source\n+ @VOCDIR_COMMAND@\n+#end if\n+cojac cooc-pubmut\n+ #if $annotations.availability == \'full\':\n+ -m voc/\n+ #end if\n+ #if $annotations.availability != \'none\':\n+ -a \'$annotations.in_amp\'\n #end if\n- -o cooc-table.csv\n+ #if $cooc_data.ext == \'json\':\n+ -j \'$cooc_data\'\n+ #else\n+ -y \'$cooc_data\'\n+ #end if\n -q\n- $escape\n- #if $add_html\n+ #if $out_opts.format == \'tsv\':\n+ -o cooc-table.tsv\n+ #else:\n+ -o cooc-table.csv\n+ #if $out_opts.format == \'html\':\n && pandoc cooc-table.csv -o cooc-table.html\n- && mkdir -p \'$html.files_path\'\n- && cp cooc-table.html \'$html.files_path\'\n+ #end if\n #end if\n ]]></command>\n <inputs>\n- <expand macro="vocdir_input"/>\n- <param name="amplicons" type="data" format="yaml" label="List of query amplicons"\n- help="File generated by the Cojac mutbamscan tool"/>\n- <param name="cooc_file" type="data" format="json,yaml" multiple="true"\n- label="Results generated by mutbamscan"/>\n- <param argument="--escape" type="boolean" truevalue="--escape" falsevalue=""\n- checked="false" label="Use escape characters for newlines"/>\n- <param name="add_html" type="boolean" checked="false"\n- label="Convert CSV output table to HTML format"/>\n+ <param name="cooc_data" type="data" format="json,yaml" label="Co-occurrence results generated by mutbamscan"\n+ help="The tool can work with json- or yaml-formatted output of cojac mutbamscan."/>\n+ <conditional name="annotations">\n+ <param name="availability" type="select" label="Available amplicon and lineage annotations"\n+ help="For best readability of its report the tool requires a per-lineage amplicon info dataset (in yaml format) produced by the mutbamscan tool and the original lineage definitions. If all you have is the per-lineage amplicon info, you can use it to obtain a nearly identical report, but cojac-internal lineage identifiers won\'t be translated into standard lineage names. With no available annotations a limited report can still be generated, but this is not recommended.">\n+ <option value="full">per-lineage amplicon info and original lineage definitions</option>\n+ <option value="amplicon">per-lineage amplicon info only</option>\n+ <option value="none">no annotations</option>\n+ </param>\n+ <when value="full">\n+ <param name="in_amp" type="data" format="yaml" label="Combined cojac per-amplicon lineage definitions"/>\n+ <expand macro="vocdir_input"/>\n+ </when>\n+ <when value="amplicon">\n+ <param name="in_amp" type="data" format="yaml" label="Combined per-amplicon lineage definitions"/>\n+ </when>\n+ <when value="none" />\n+ '..b'="html"\n- label="${tool.name} on ${on_string}: Mutation cooccurrence (HTML)"\n- from_work_dir="cooc-table.html">\n- <filter>add_html</filter>\n+ <data name="table_csv" format="csv" label="${tool.name} on ${on_string}: Mutation co-occurrence (CSV table)" from_work_dir="cooc-table.csv">\n+ <filter>out_opts[\'format\'] == \'csv\'</filter>\n+ </data>\n+ <data name="table_html" format="html" label="${tool.name} on ${on_string}: Mutation co-occurrence (HTML)" from_work_dir="cooc-table.html">\n+ <filter>out_opts[\'format\'] == \'html\'</filter>\n </data>\n </outputs>\n <tests>\n <test expect_num_outputs="1">\n- <conditional name="vocdir_option">\n- <param name="choice" value="custom"/>\n- <param name="voc_file" value="omicron_ba1_mutations.yaml"/>\n+ <param name="cooc_data" value="cooc-test111.json"/>\n+ <conditional name="annotations">\n+ <conditional name="vocdir_option">\n+ <param name="choice" value="custom"/>\n+ <param name="voc_file" value="omicron_ba1_mutations.yaml"/>\n+ </conditional>\n+ <param name="in_amp" value="amplicons111.yaml"/>\n+ </conditional>\n+ <output name="table_tsv" ftype="tsv">\n+ <assert_contents>\n+ <has_text text="Amplicon 76"/>\n+ <has_text text="Amplicon 81"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test expect_num_outputs="1">\n+ <param name="cooc_data" value="cooc-test111.json"/>\n+ <conditional name="annotations">\n+ <conditional name="vocdir_option">\n+ <param name="choice" value="custom"/>\n+ <param name="voc_file" value="omicron_ba1_mutations.yaml"/>\n+ </conditional>\n+ <param name="in_amp" value="amplicons111.yaml"/>\n </conditional>\n- <param name="amplicons" value="amplicons111.yaml"/>\n- <param name="cooc_file" value="cooc-test111.json"/>\n- <output name="table" ftype="csv">\n+ <section name="out_opts">\n+ <param name="format" value="csv"/>\n+ </section>\n+ <output name="table_csv" ftype="csv">\n+ <assert_contents>\n+ <has_text text="Amplicon 76"/>\n+ <has_text text="Amplicon 81"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test expect_num_outputs="1">\n+ <param name="cooc_data" value="cooc-test111.json"/>\n+ <conditional name="annotations">\n+ <conditional name="vocdir_option">\n+ <param name="choice" value="custom"/>\n+ <param name="voc_file" value="omicron_ba1_mutations.yaml"/>\n+ </conditional>\n+ <param name="in_amp" value="amplicons111.yaml"/>\n+ </conditional>\n+ <section name="out_opts">\n+ <param name="format" value="html"/>\n+ </section>\n+ <output name="table_html" ftype="html">\n <assert_contents>\n <has_text text="Amplicon 76"/>\n <has_text text="Amplicon 81"/>\n@@ -74,12 +136,12 @@\n <help><![CDATA[\n @HELP_HEADER@\n \n-Information about **cooc-pubmut** method\n-========================================\n+Information about **cojac cooc-pubmut**\n+=======================================\n \n-The method renders a JSON or YAML file to a table as in the publication.\n-You need to open the output CSV in a spreadsheet that understands linebreaks.\n+The tool pretty-prints json or yaml output of cojac cooc-mutbamscan.\n \n+Hint: The output (unless you select html format) is best viewed in spreadsheet software that understands linebreaks.\n ]]></help>\n <expand macro="citations"/>\n </tool>\n' |
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| diff -r d04ea6b052c5 -r f193fef5b19d macros.xml --- a/macros.xml Thu Aug 11 13:49:40 2022 +0000 +++ b/macros.xml Mon Jul 31 15:23:17 2023 +0000 |
| [ |
| @@ -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 d04ea6b052c5 -r f193fef5b19d test-data/ampl_info.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ampl_info.tsv Mon Jul 31 15:23:17 2023 +0000 |
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| diff -r d04ea6b052c5 -r f193fef5b19d test-data/bed_cojac.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bed_cojac.bed Mon Jul 31 15:23:17 2023 +0000 |
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| diff -r d04ea6b052c5 -r f193fef5b19d test-data/primers.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/primers.bed Mon Jul 31 15:23:17 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' |