# HG changeset patch
# User iuc
# Date 1690816997 0
# Node ID f193fef5b19da0635bcafb25a159ef36d490a33a
# Parent  d04ea6b052c555715de846d3e7320b1a391ad6e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6

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
@@ -1,69 +1,131 @@
 <tool id="cooc_pubmut" name="Cojac: pubmut" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
       profile="@PROFILE@">
     <description>
-        render a JSON or YAML file to a pretty table
+        pretty-prints cojac mutbamscan co-occurrence results
     </description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="biotools"/>
     <expand macro="requirements">
-        <requirement type="package" version="2.12">pandoc</requirement>
+        <requirement type="package" version="3.1.3">pandoc</requirement>
+        <requirement type="package" version="6.2.1">gmp</requirement>
     </expand>
     <expand macro="version"/>
     <command detect_errors="exit_code"><![CDATA[
-@VOCDIR_COMMAND@
-#for $input_file in $cooc_file
-    #set $cooc_ext = $input_file.ext
-#end for
-cooc-pubmut
-    -m '$vocdir'
-    -a '$amplicons'
-    #if $cooc_ext == 'json'
-        -j '$cooc_file'
-    #else if $cooc_ext == 'yaml'
-        -y '$cooc_file'
+#if $annotations.availability == 'full':
+  #set $voc_config = $annotations.voc_source
+  @VOCDIR_COMMAND@
+#end if
+cojac cooc-pubmut
+    #if $annotations.availability == 'full':
+      -m voc/
+    #end if
+    #if $annotations.availability != 'none':
+      -a '$annotations.in_amp'
     #end if
-    -o cooc-table.csv
+    #if $cooc_data.ext == 'json':
+      -j '$cooc_data'
+    #else
+      -y '$cooc_data'
+    #end if
     -q
-    $escape
-    #if $add_html
+    #if $out_opts.format == 'tsv':
+      -o cooc-table.tsv
+    #else:
+      -o cooc-table.csv
+      #if $out_opts.format == 'html':
         && pandoc cooc-table.csv -o cooc-table.html
-        && mkdir -p '$html.files_path'
-        && cp cooc-table.html '$html.files_path'
+      #end if
     #end if
     ]]></command>
     <inputs>
-        <expand macro="vocdir_input"/>
-        <param name="amplicons" type="data" format="yaml" label="List of query amplicons"
-               help="File generated by the Cojac mutbamscan tool"/>
-        <param name="cooc_file" type="data" format="json,yaml" multiple="true"
-               label="Results generated by mutbamscan"/>
-        <param argument="--escape" type="boolean" truevalue="--escape" falsevalue=""
-               checked="false" label="Use escape characters for newlines"/>
-        <param name="add_html" type="boolean" checked="false"
-               label="Convert CSV output table to HTML format"/>
+        <param name="cooc_data" type="data" format="json,yaml" label="Co-occurrence results generated by mutbamscan"
+        help="The tool can work with json- or yaml-formatted output of cojac mutbamscan."/>
+        <conditional name="annotations">
+            <param name="availability" type="select" label="Available amplicon and lineage annotations"
+            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.">
+                <option value="full">per-lineage amplicon info and original lineage definitions</option>
+                <option value="amplicon">per-lineage amplicon info only</option>
+                <option value="none">no annotations</option>
+            </param>
+            <when value="full">
+                <param name="in_amp" type="data" format="yaml" label="Combined cojac per-amplicon lineage definitions"/>
+                <expand macro="vocdir_input"/>
+            </when>
+            <when value="amplicon">
+                <param name="in_amp" type="data" format="yaml" label="Combined per-amplicon lineage definitions"/>
+            </when>
+            <when value="none" />
+        </conditional>
+        <section name="out_opts" title="Output formatting" expanded="true">
+            <param name="format" type="select" label="Type of output to produce">
+                <option value="tsv">Tab-separated (TSV)</option>
+                <option value="csv">Comma-separated (CSV)</option>
+                <option value="html">HTML (for display in browsers)</option>
+            </param>
+        </section>
     </inputs>
     <outputs>
-        <data name="table" format="csv"
-              label="${tool.name} on ${on_string}: Mutation cooccurrence (CSV table)"
-              from_work_dir="cooc-table.csv">
+        <data name="table_tsv" format="tsv" label="${tool.name} on ${on_string}: Mutation co-occurrence (TSV table)" from_work_dir="cooc-table.tsv">
+            <filter>out_opts['format'] == 'tsv'</filter>
         </data>
-        <data name="html" format="html"
-              label="${tool.name} on ${on_string}: Mutation cooccurrence (HTML)"
-              from_work_dir="cooc-table.html">
-            <filter>add_html</filter>
+        <data name="table_csv" format="csv" label="${tool.name} on ${on_string}: Mutation co-occurrence (CSV table)" from_work_dir="cooc-table.csv">
+            <filter>out_opts['format'] == 'csv'</filter>
+        </data>
+        <data name="table_html" format="html" label="${tool.name} on ${on_string}: Mutation co-occurrence (HTML)" from_work_dir="cooc-table.html">
+            <filter>out_opts['format'] == 'html'</filter>
         </data>
     </outputs>
     <tests>
         <test expect_num_outputs="1">
-            <conditional name="vocdir_option">
-                <param name="choice" value="custom"/>
-                <param name="voc_file" value="omicron_ba1_mutations.yaml"/>
+            <param name="cooc_data" value="cooc-test111.json"/>
+            <conditional name="annotations">
+                <conditional name="vocdir_option">
+                    <param name="choice" value="custom"/>
+                    <param name="voc_file" value="omicron_ba1_mutations.yaml"/>
+                </conditional>
+                <param name="in_amp" value="amplicons111.yaml"/>
+            </conditional>
+            <output name="table_tsv" ftype="tsv">
+                <assert_contents>
+                    <has_text text="Amplicon 76"/>
+                    <has_text text="Amplicon 81"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="cooc_data" value="cooc-test111.json"/>
+            <conditional name="annotations">
+                <conditional name="vocdir_option">
+                    <param name="choice" value="custom"/>
+                    <param name="voc_file" value="omicron_ba1_mutations.yaml"/>
+                </conditional>
+                <param name="in_amp" value="amplicons111.yaml"/>
             </conditional>
-            <param name="amplicons" value="amplicons111.yaml"/>
-            <param name="cooc_file" value="cooc-test111.json"/>
-            <output name="table" ftype="csv">
+            <section name="out_opts">
+                <param name="format" value="csv"/>
+            </section>
+            <output name="table_csv" ftype="csv">
+                <assert_contents>
+                    <has_text text="Amplicon 76"/>
+                    <has_text text="Amplicon 81"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="cooc_data" value="cooc-test111.json"/>
+            <conditional name="annotations">
+                <conditional name="vocdir_option">
+                    <param name="choice" value="custom"/>
+                    <param name="voc_file" value="omicron_ba1_mutations.yaml"/>
+                </conditional>
+                <param name="in_amp" value="amplicons111.yaml"/>
+            </conditional>
+            <section name="out_opts">
+                <param name="format" value="html"/>
+            </section>
+            <output name="table_html" ftype="html">
                 <assert_contents>
                     <has_text text="Amplicon 76"/>
                     <has_text text="Amplicon 81"/>
@@ -74,12 +136,12 @@
     <help><![CDATA[
 @HELP_HEADER@
 
-Information about **cooc-pubmut** method
-========================================
+Information about **cojac cooc-pubmut**
+=======================================
 
-The method renders a JSON or YAML file to a table as in the publication.
-You need to open the output CSV in a spreadsheet that understands linebreaks.
+The tool pretty-prints json or yaml output of cojac cooc-mutbamscan.
 
+Hint: The output (unless you select html format) is best viewed in spreadsheet software that understands linebreaks.
     ]]></help>
     <expand macro="citations"/>
 </tool>
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>
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
@@ -0,0 +1,99 @@
+SARS-CoV-2_1_LEFT	SARS-CoV-2_1_RIGHT
+SARS-CoV-2_2_LEFT	SARS-CoV-2_2_RIGHT
+SARS-CoV-2_3_LEFT	SARS-CoV-2_3_RIGHT
+SARS-CoV-2_4_LEFT	SARS-CoV-2_4_RIGHT
+SARS-CoV-2_5_LEFT	SARS-CoV-2_5_RIGHT
+SARS-CoV-2_6_LEFT	SARS-CoV-2_6_RIGHT
+SARS-CoV-2_7_LEFT	SARS-CoV-2_7_RIGHT
+SARS-CoV-2_8_LEFT	SARS-CoV-2_8_RIGHT
+SARS-CoV-2_9_LEFT	SARS-CoV-2_9_RIGHT
+SARS-CoV-2_10_LEFT	SARS-CoV-2_10_RIGHT
+SARS-CoV-2_11_LEFT	SARS-CoV-2_11_RIGHT
+SARS-CoV-2_12_LEFT	SARS-CoV-2_12_RIGHT
+SARS-CoV-2_13_LEFT	SARS-CoV-2_13_RIGHT
+SARS-CoV-2_14_LEFT	SARS-CoV-2_14_RIGHT
+SARS-CoV-2_15_LEFT	SARS-CoV-2_15_RIGHT
+SARS-CoV-2_16_LEFT	SARS-CoV-2_16_RIGHT
+SARS-CoV-2_17_LEFT	SARS-CoV-2_17_RIGHT
+SARS-CoV-2_18_LEFT	SARS-CoV-2_18_RIGHT
+SARS-CoV-2_19_LEFT	SARS-CoV-2_19_RIGHT
+SARS-CoV-2_20_LEFT	SARS-CoV-2_20_RIGHT
+SARS-CoV-2_21_LEFT	SARS-CoV-2_21_RIGHT
+SARS-CoV-2_22_LEFT	SARS-CoV-2_22_RIGHT
+SARS-CoV-2_23_LEFT	SARS-CoV-2_23_RIGHT
+SARS-CoV-2_24_LEFT	SARS-CoV-2_24_RIGHT
+SARS-CoV-2_25_LEFT	SARS-CoV-2_25_RIGHT
+SARS-CoV-2_26_LEFT	SARS-CoV-2_26_RIGHT
+SARS-CoV-2_27_LEFT	SARS-CoV-2_27_RIGHT
+SARS-CoV-2_28_LEFT	SARS-CoV-2_28_RIGHT
+SARS-CoV-2_29_LEFT	SARS-CoV-2_29_RIGHT
+SARS-CoV-2_30_LEFT	SARS-CoV-2_30_RIGHT
+SARS-CoV-2_31_LEFT	SARS-CoV-2_31_RIGHT
+SARS-CoV-2_32_LEFT	SARS-CoV-2_32_RIGHT
+SARS-CoV-2_33_LEFT	SARS-CoV-2_33_RIGHT
+SARS-CoV-2_34_LEFT	SARS-CoV-2_34_RIGHT
+SARS-CoV-2_35_LEFT	SARS-CoV-2_35_RIGHT
+SARS-CoV-2_36_LEFT	SARS-CoV-2_36_RIGHT
+SARS-CoV-2_37_LEFT	SARS-CoV-2_37_RIGHT
+SARS-CoV-2_38_LEFT	SARS-CoV-2_38_RIGHT
+SARS-CoV-2_39_LEFT	SARS-CoV-2_39_RIGHT
+SARS-CoV-2_40_LEFT	SARS-CoV-2_40_RIGHT
+SARS-CoV-2_41_LEFT	SARS-CoV-2_41_RIGHT
+SARS-CoV-2_42_LEFT	SARS-CoV-2_42_RIGHT
+SARS-CoV-2_43_LEFT	SARS-CoV-2_43_RIGHT
+SARS-CoV-2_44_LEFT	SARS-CoV-2_44_RIGHT
+SARS-CoV-2_45_LEFT	SARS-CoV-2_45_RIGHT
+SARS-CoV-2_46_LEFT	SARS-CoV-2_46_RIGHT
+SARS-CoV-2_47_LEFT	SARS-CoV-2_47_RIGHT
+SARS-CoV-2_48_LEFT	SARS-CoV-2_48_RIGHT
+SARS-CoV-2_49_LEFT	SARS-CoV-2_49_RIGHT
+SARS-CoV-2_50_LEFT	SARS-CoV-2_50_RIGHT
+SARS-CoV-2_51_LEFT	SARS-CoV-2_51_RIGHT
+SARS-CoV-2_52_LEFT	SARS-CoV-2_52_RIGHT
+SARS-CoV-2_53_LEFT	SARS-CoV-2_53_RIGHT
+SARS-CoV-2_54_LEFT	SARS-CoV-2_54_RIGHT
+SARS-CoV-2_55_LEFT	SARS-CoV-2_55_RIGHT
+SARS-CoV-2_56_LEFT	SARS-CoV-2_56_RIGHT
+SARS-CoV-2_57_LEFT	SARS-CoV-2_57_RIGHT
+SARS-CoV-2_58_LEFT	SARS-CoV-2_58_RIGHT
+SARS-CoV-2_59_LEFT	SARS-CoV-2_59_RIGHT
+SARS-CoV-2_60_LEFT	SARS-CoV-2_60_RIGHT
+SARS-CoV-2_61_LEFT	SARS-CoV-2_61_RIGHT
+SARS-CoV-2_62_LEFT	SARS-CoV-2_62_RIGHT
+SARS-CoV-2_63_LEFT	SARS-CoV-2_63_RIGHT
+SARS-CoV-2_64_LEFT	SARS-CoV-2_64_RIGHT
+SARS-CoV-2_65_LEFT	SARS-CoV-2_65_RIGHT
+SARS-CoV-2_66_LEFT	SARS-CoV-2_66_RIGHT
+SARS-CoV-2_67_LEFT	SARS-CoV-2_67_RIGHT
+SARS-CoV-2_68_LEFT	SARS-CoV-2_68_RIGHT
+SARS-CoV-2_69_LEFT	SARS-CoV-2_69_RIGHT
+SARS-CoV-2_70_LEFT	SARS-CoV-2_70_RIGHT
+SARS-CoV-2_71_LEFT	SARS-CoV-2_71_RIGHT
+SARS-CoV-2_72_LEFT	SARS-CoV-2_72_RIGHT
+SARS-CoV-2_73_LEFT	SARS-CoV-2_73_RIGHT
+SARS-CoV-2_74_LEFT	SARS-CoV-2_74_RIGHT
+SARS-CoV-2_75_LEFT	SARS-CoV-2_75_RIGHT
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+SARS-CoV-2_77_LEFT	SARS-CoV-2_77_RIGHT
+SARS-CoV-2_78_LEFT	SARS-CoV-2_78_RIGHT
+SARS-CoV-2_79_LEFT	SARS-CoV-2_79_RIGHT
+SARS-CoV-2_80_LEFT	SARS-CoV-2_80_RIGHT
+SARS-CoV-2_81_LEFT	SARS-CoV-2_81_RIGHT
+SARS-CoV-2_82_LEFT	SARS-CoV-2_82_RIGHT
+SARS-CoV-2_83_LEFT	SARS-CoV-2_83_RIGHT
+SARS-CoV-2_84_LEFT	SARS-CoV-2_84_RIGHT
+SARS-CoV-2_85_LEFT	SARS-CoV-2_85_RIGHT
+SARS-CoV-2_86_LEFT	SARS-CoV-2_86_RIGHT
+SARS-CoV-2_87_LEFT	SARS-CoV-2_87_RIGHT
+SARS-CoV-2_88_LEFT	SARS-CoV-2_88_RIGHT
+SARS-CoV-2_89_LEFT	SARS-CoV-2_89_RIGHT
+SARS-CoV-2_90_LEFT	SARS-CoV-2_90_RIGHT
+SARS-CoV-2_91_LEFT	SARS-CoV-2_91_RIGHT
+SARS-CoV-2_92_LEFT	SARS-CoV-2_92_RIGHT
+SARS-CoV-2_93_LEFT	SARS-CoV-2_93_RIGHT
+SARS-CoV-2_94_LEFT	SARS-CoV-2_94_RIGHT
+SARS-CoV-2_95_LEFT	SARS-CoV-2_95_RIGHT
+SARS-CoV-2_96_LEFT	SARS-CoV-2_96_RIGHT
+SARS-CoV-2_97_LEFT	SARS-CoV-2_97_RIGHT
+SARS-CoV-2_98_LEFT	SARS-CoV-2_98_RIGHT
+SARS-CoV-2_99_LEFT	SARS-CoV-2_99_RIGHT
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
@@ -0,0 +1,99 @@
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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
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