diff nextclade.xml @ 5:0c46b95d60c3 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit b565283c946796dfb3f613f52db6008d234ecedb"

--- a/nextclade.xml	Mon Aug 23 12:26:05 2021 +0000
+++ b/nextclade.xml	Wed Sep 01 17:56:32 2021 +0000
@@ -1,17 +1,16 @@
 <tool id="nextclade" name="Nextclade" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
-    <description></description>
+    <description>Viral genome clade assignment, mutation calling, and sequence quality checks</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@TOOL_VERSION@">1.2.3</token>
         <token name="@VERSION_SUFFIX@">0</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">nextclade</requirement>
         <requirement type="package">coreutils</requirement>
     </requirements>
+    <version_command>nextclade --version-detailed</version_command>
     <command detect_errors="exit_code"><![CDATA[
-        export DB_PATH="\$(dirname "\$(dirname "\$(which nextclade)")")/share/nextclade" &&
-        ln -s "\$DB_PATH" db &&
+        nextclade dataset get -n '${organism}' -o db &&
         #set $input_qc_config = "db/qc.json"
         #set $input_root_seq = "db/reference.fasta"
         #set $input_tree = "db/tree.json"
@@ -73,7 +72,14 @@
             <option value="output_fasta">Aligned sequences (FASTA format)</option>
         </param>
         <param name="include_header" type="boolean" label="Include header line in output file" 
-            truevalue="true" falsevalue="false" />        
+            truevalue="true" falsevalue="false" />
+        <param name="organism" type="select" label="Organism">
+            <option value="sars-cov-2" selected="true">SARS-CoV-2</option>
+            <option value="flu_h1n1pdm_ha">Influenza A H1N1pdm HA</option>
+            <option value="flu_h3n2_ha">Influenza A H3N2 HA</option>
+            <option value="flu_vic_ha">Influenza B Victoria HA</option>
+            <option value="flu_yam_ha">Influenza B Yamagata HA</option>
+        </param>   
         <conditional name="adv">
             <param name="advanced_options" type="select" label="Use advanced options" >
                 <option value="yes">Yes</option>
@@ -112,6 +118,7 @@
         <test expect_num_outputs="1">
             <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" />
             <param name="outputs" value="report_tsv" />
+            <param name="organism" value="sars-cov-2" />
             <output name="report_tsv">
                 <assert_contents>
                     <has_n_columns n="48" />
@@ -122,6 +129,7 @@
         <test expect_num_outputs="3">
             <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" />
             <param name="outputs" value="report_tsv,report_json,output_tree" />
+            <param name="organism" value="sars-cov-2" />
             <output name="report_tsv">
                 <assert_contents>
                     <has_n_columns n="48" />
@@ -142,6 +150,7 @@
         <test expect_num_outputs="1">
             <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" />
             <param name="outputs" value="report_tsv" />
+            <param name="organism" value="sars-cov-2" />
             <conditional name="adv">
                 <param name="advanced_options" value="yes" />
                 <param name="input_qc_config" value="strict_qc.json" ftype="json" />