Mercurial > repos > iuc > cooc_tabmut

changeset 1:74328ad6bb70 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
author iuc
date Mon, 31 Jul 2023 15:23:01 +0000
parents ab84c87e56f7
children a2963e79f4d7
files cooc_tabmut.xml macros.xml test-data/ampl_info.tsv test-data/bed_cojac.bed test-data/primers.bed
diffstat 5 files changed, 448 insertions(+), 41 deletions(-) [+]
line wrap: on
line diff
--- a/cooc_tabmut.xml	Thu Aug 11 13:47:51 2022 +0000
+++ b/cooc_tabmut.xml	Mon Jul 31 15:23:01 2023 +0000
@@ -1,7 +1,7 @@
 <tool id="cooc_tabmut" name="Cojac: tabmut" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
       profile="@PROFILE@">
     <description>
-        export cooccurrence mutations as a table
+        exports co-occurrence results from mutbamscan as a table
     </description>
     <macros>
         <import>macros.xml</import>
@@ -10,26 +10,26 @@
     <expand macro="requirements"/>
     <expand macro="version"/>
     <command detect_errors="exit_code"><![CDATA[
-#for $input_file in $cooc_file
-    #set $cooc_ext = $input_file.ext
-#end for
-cooc-tabmut
-    #if $cooc_ext == 'json'
-        -j '$cooc_file'
-    #else if $cooc_ext == 'yaml'
-        -y '$cooc_file'
+cojac cooc-tabmut
+    #if $cooc_data.ext == 'json'
+        -j '$cooc_data'
+    #else
+        -y '$cooc_data'
     #end if
-    -o cooc-table.csv
     #if $table_orientation.choice == 'lines'
         -l
     #else if $table_orientation.choice == 'multiindex'
         -m
     #end if
+    #if $out_format == 'tsv':
+        -o cooc-table.tsv
+    #else:
+        -o cooc-table.csv
+    #end if
     -q
     ]]></command>
     <inputs>
-        <param name="cooc_file" type="data" format="json,yaml" multiple="true"
-               label="Results generated by mutbamscan"/>
+        <param name="cooc_data" type="data" format="json,yaml" label="Results generated by mutbamscan"/>
         <conditional name="table_orientation">
             <param name="choice" type="select" label="Output table orientation">
                 <option value="columns">Column-oriented table (default)</option>
@@ -42,23 +42,40 @@
             <when value="lines"/>
             <when value="multiindex"/>
         </conditional>
+        <param name="out_format" type="select" label="Type of output to produce">
+            <option value="tsv">Tab-separated (TSV)</option>
+            <option value="csv">Comma-separated (CSV)</option>
+        </param>
     </inputs>
     <outputs>
-        <data name="table" format="csv"
-              label="${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 ${on_string}: Mutation coo-ccurrence (TSV table)" from_work_dir="cooc-table.tsv">
+            <filter>out_format == 'tsv'</filter>
+        </data>
+        <data name="table_csv" format="csv" label="${tool.name} on ${on_string}: Mutation coo-ccurrence (CSV table)" from_work_dir="cooc-table.csv">
+            <filter>out_format == 'csv'</filter>
         </data>
     </outputs>
     <tests>
         <test expect_num_outputs="1">
-            <param name="cooc_file" value="cooc-test111.json"/>
+            <param name="cooc_data" value="cooc-test111.json"/>
             <conditional name="table_orientation">
                 <param name="choice" value="columns"/>
             </conditional>
-            <output name="table" ftype="csv">
+            <output name="table_tsv" ftype="tsv">
                 <assert_contents>
-                    <has_text text="A76_om1.count"/>
-                    <has_text text="A76_om1.mut_oneless"/>
+                    <has_text text="A76"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="cooc_data" value="cooc-test111.json"/>
+            <conditional name="table_orientation">
+                <param name="choice" value="columns"/>
+            </conditional>
+            <param name="out_format" value="csv"/>
+            <output name="table_csv" ftype="csv">
+                <assert_contents>
+                    <has_text text="A76"/>
                 </assert_contents>
             </output>
         </test>
@@ -66,8 +83,8 @@
     <help><![CDATA[
 @HELP_HEADER@
 
-Information about **cooc_tabmut** method
-========================================
+Information about **cojac cooc_tabmut** method
+==============================================
 
 The method exports a JSON or YAML file as a CSV/TSV table for downstream analysis (e.g.: RStudio).
 
--- a/macros.xml	Thu Aug 11 13:47:51 2022 +0000
+++ b/macros.xml	Mon Jul 31 15:23:01 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>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ampl_info.tsv	Mon Jul 31 15:23:01 2023 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bed_cojac.bed	Mon Jul 31 15:23:01 2023 +0000
@@ -0,0 +1,99 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/primers.bed	Mon Jul 31 15:23:01 2023 +0000
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