Mercurial > repos > iuc > pangolin

changeset 28:9d61d3fa046c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit f93f921e3c2d0002ff0c152d90b9221533ad22e9
author iuc
date Tue, 11 Jul 2023 22:32:30 +0000
parents 03ed9524dcd1
children 2f1019071464
files pangolin.xml
diffstat 1 files changed, 66 insertions(+), 56 deletions(-) [+]
line wrap: on
line diff
--- a/pangolin.xml	Sun Jan 15 12:35:01 2023 +0000
+++ b/pangolin.xml	Tue Jul 11 22:32:30 2023 +0000
@@ -1,21 +1,23 @@
 <tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy0" profile="20.01">
     <description>Phylogenetic Assignment of Outbreak Lineages</description>
     <macros>
-        <token name="@TOOL_VERSION@">4.2</token>
-        <token name="@PANGOLIN_DATA_VERSION@">1.17</token>
-        <token name="@CONSTELLATIONS_VERSION@">0.1.10</token>
-        <token name="@MIN_COMPATIBLE_PANGOLIN_DATA_FORMAT@">4</token>
+        <token name="@TOOL_VERSION@">4.3</token>
+        <token name="@PANGOLIN_DATA_VERSION@">1.21</token>
+        <token name="@CONSTELLATIONS_VERSION@">0.1.12</token>
+        <!-- a regex describing the pangolin-data versions that this wrapper version
+        is backwards-compatible with; can be used with the min_pangolin_version
+        column of the pangolin_data and pangolin_assignment data table to offer
+        only compatible versions of that data. -->
+        <token name="@MIN_COMPATIBLE_PANGOLIN_DATA_FORMAT@"><![CDATA[^4$|^4\.3$]]></token>
+        <!-- pangolin-data versions >=1.20 do not contain pangoLEARN models anymore.
+        This version of pangolin still supports pangolearn analysis mode, but only when using
+        older versions of pangolin-data. -->
+        <token name="@MIN_COMPATIBLE_PANGOLIN_DATA_FORMAT_FOR_PANGOLEARN@">4></token>
         <!-- a regex describing the scorpio versions that this wrapper version
         is backwards-compatible with; can be used with the min_scorpio_version
-        column of the constellations data table to offer only compatible
+        column of the pangolin_constellations data table to offer only compatible
         versions of constellations data. -->
         <token name="@COMPATIBLE_SCORPIO_DATA_FORMAT@"><![CDATA[(^0\.[1-3]$|^0\.[0-2]\.\d+$|^0\.3\.\d$|^0\.3\.1[0-7]$|^0$)]]></token>
-        <xml name="usher_download_option">
-            <when value="download">
-                <param argument="--use-assignment-cache" type="boolean" truevalue="--use-assignment-cache" falsevalue="" label="Download and use also latest UShER assignment cache?"
-                help="Get the latest UShER assignment cache from the pangolin-assignment online repository and use it to speed up UShER lineage assignment. Note: Downloading the cached assignments will only pay off for large numbers of input samples." />
-            </when>
-        </xml>
         <xml name="cached_usher_assignment_cache">
             <param name="assignment_cache_release" type="select" optional="true" label="Use corresponding UShER assignment cache?"
             help="If the server offers a copy of the UShER assignment cache along with the specified version of pangolin-data, you can select it here to speed up UShER lineage assignment. If no suitable assignment cache is available, it is perfectly fine to proceed without one, and the performance difference will only become obvious with very large numbers of samples.">
@@ -23,38 +25,11 @@
                     <column name="value" index="0" />
                     <column name="description" index="1" />
                     <column name="path" index="4" />
-                    <filter type="static_value" column="2" value="@MIN_COMPATIBLE_PANGOLIN_DATA_FORMAT@" />
+                    <filter type="regexp" column="2" value="@MIN_COMPATIBLE_PANGOLIN_DATA_FORMAT@" />
                     <filter type="param_value" ref="release" column="0" />
                 </options>
             </param>
         </xml>
-        <xml name="cached_pangolin_data">
-            <when value="cached">
-                <param name="release" label="Cached release of pangolin-data" type="select">
-                    <options from_data_table="pangolin_data">
-                        <column name="value" index="0" />
-                        <column name="description" index="1" />
-                        <column name="date" index="3" />
-                        <column name="path" index="4" />
-                        <filter type="sort_by" column="3" />
-                        <filter type="static_value" column="2" value="@MIN_COMPATIBLE_PANGOLIN_DATA_FORMAT@" />
-                        <validator type="no_options" message="No cached constellations release available" />
-                    </options>
-                </param>
-                <yield />
-            </when>
-        </xml>
-        <xml name="pangolin_data_sources">
-            <conditional name="pangolin_data">
-                <param name="source" type="select" label="Version of pangolin-data to use">
-                    <option value="default">Use pangolin-data version (v@PANGOLIN_DATA_VERSION@) shipped with this version of the tool</option>
-                    <option value="cached">Use specific pangolin-data version cached on this Galaxy server</option>
-                    <option value="download">Download latest available pangolin-data version from web</option>
-                </param>
-                <when value="default" />
-                <yield />
-            </conditional>
-        </xml>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">pangolin</requirement>
@@ -74,14 +49,14 @@
         <requirement type="package" version="@PANGOLIN_DATA_VERSION@">pangolin-data</requirement>
         <requirement type="package" version="@CONSTELLATIONS_VERSION@">constellations</requirement>
         <requirement type="package" version="0.6.2">usher</requirement>
-        <requirement type="package" version="1.1.0">gofasta</requirement>
-        <requirement type="package" version="426">ucsc-fatovcf</requirement>
-        <requirement type="package" version="2.24">minimap2</requirement>
+        <requirement type="package" version="1.2.0">gofasta</requirement>
+        <requirement type="package" version="448">ucsc-fatovcf</requirement>
+        <requirement type="package" version="2.26">minimap2</requirement>
         <!-- wrapper-specific requirements to turn pangolin's native
         comma-separated output into tab-separated one and to truncate
         pangolin's all-versions output. -->
-        <requirement type="package" version="0.25.0">csvtk</requirement>
-        <requirement type="package" version="3.4">grep</requirement>
+        <requirement type="package" version="0.26.0">csvtk</requirement>
+        <requirement type="package" version="3.11">grep</requirement>
     </requirements>
     <version_command><![CDATA[pangolin --version]]></version_command>
     <command detect_errors="exit_code"><![CDATA[
@@ -179,7 +154,7 @@
     #end if
 #end if
 #if $alignment:
-    $alignment --alignment-file '$align1'
+    $alignment --alignment-file aln.fa
 #end if
 --outfile report.csv
 --max-ambig $max_ambig
@@ -201,18 +176,53 @@
                 <option value="pangolearn">pangoLEARN</option>
             </param>
             <when value="usher">
-                <expand macro="pangolin_data_sources">
-                    <expand macro="cached_pangolin_data">
+                <conditional name="pangolin_data">
+                    <param name="source" type="select" label="Version of pangolin-data to use">
+                        <option value="default">Use pangolin-data version (v@PANGOLIN_DATA_VERSION@) shipped with this version of the tool</option>
+                        <option value="cached">Use specific pangolin-data version cached on this Galaxy server</option>
+                        <option value="download">Download latest available pangolin-data version from web</option>
+                    </param>
+                    <when value="default" />
+                    <when value="cached">
+                        <param name="release" label="Cached release of pangolin-data" type="select">
+                            <options from_data_table="pangolin_data">
+                                <column name="value" index="0" />
+                                <column name="description" index="1" />
+                                <column name="date" index="3" />
+                                <column name="path" index="4" />
+                                <filter type="sort_by" column="3" />
+                                <filter type="regexp" column="2" value="@MIN_COMPATIBLE_PANGOLIN_DATA_FORMAT@" />
+                                <validator type="no_options" message="No compatible cached pangolin-data release available" />
+                            </options>
+                        </param>
                         <expand macro="cached_usher_assignment_cache" />
-                    </expand>
-                    <expand macro="usher_download_option" />
-                </expand>
+                    </when>
+                    <when value="download">
+                        <param argument="--use-assignment-cache" type="boolean" truevalue="--use-assignment-cache" falsevalue="" label="Download and use also latest UShER assignment cache?"
+                        help="Get the latest UShER assignment cache from the pangolin-assignment online repository and use it to speed up UShER lineage assignment. Note: Downloading the cached assignments will only pay off for large numbers of input samples." />
+                    </when>
+                </conditional>
             </when>
             <when value="pangolearn">
-                <expand macro="pangolin_data_sources">
-                    <expand macro="cached_pangolin_data" />
-                    <when value="download" />
-                </expand>
+                <conditional name="pangolin_data">
+                    <param name="source" type="select" label="Version of pangolin-data to use"
+                    help="Please note: pangoLEARN mode is considered deprecated and the underlying machine learning model has been removed from recent versions of pangolin-data. If you really still want to use this mode, you are restricted to the compatible historic pangolin-data versions cached on this Galaxy server.">
+                        <option value="cached">Use specific pangolin-data version cached on this Galaxy server</option>
+                    </param>
+                    <when value="cached">
+                        <param name="release" label="Cached release of pangolin-data" type="select">
+                            <options from_data_table="pangolin_data">
+                                <column name="value" index="0" />
+                                <column name="description" index="1" />
+                                <column name="date" index="3" />
+                                <column name="path" index="4" />
+                                <filter type="sort_by" column="3" />
+                                <filter type="static_value" column="2" value="@MIN_COMPATIBLE_PANGOLIN_DATA_FORMAT_FOR_PANGOLEARN@" />
+                                <validator type="no_options" message="No compatible cached pangolin-data release available" />
+                            </options>
+                        </param>
+                    </when>
+                </conditional>
             </when>
         </conditional>
         <conditional name="constellations">
@@ -231,7 +241,7 @@
                         <column name="path" index="4" />
                         <filter type="sort_by" column="3" />
                         <filter type="regexp" column="2" value="@COMPATIBLE_SCORPIO_DATA_FORMAT@" />
-                        <validator type="no_options" message="No cached constellations release available" />
+                        <validator type="no_options" message="No compatible cached constellations release available" />
                     </options>
                 </param>
             </when>
@@ -257,7 +267,7 @@
                 </conditional>
             </actions>
         </data>
-        <data name="align1" format="fasta" label="pangolin alignment on ${on_string}">
+        <data name="align1" format="fasta" from_work_dir="aln.fa" label="pangolin alignment on ${on_string}">
             <filter>alignment</filter>
         </data>
     </outputs>