diff argnorm.xml @ 1:d8e95a03321a draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit 4de98d11ef4e46d92c545f665499be8fd714bac5

--- a/argnorm.xml	Wed Aug 28 20:27:17 2024 +0000
+++ b/argnorm.xml	Wed Apr 23 09:04:24 2025 +0000
@@ -1,7 +1,8 @@
-<tool id="argnorm" name="argNorm" version="@VERSION@+galaxy0" profile="22.05">
+<tool id="argnorm" name="argNorm" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
     <description>a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO)</description>
     <macros>
-        <token name="@VERSION@">0.6.0</token>
+        <token name="@VERSION@">1.0.0</token>
+        <token name="@VERSION_SUFFIX@">0</token>
     </macros>
     <xrefs>
        <xref type="bio.tools">argnorm</xref>
@@ -11,37 +12,60 @@
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
     argnorm
-        '$tool'
+        '$choose_tool.tool'
+        #if $choose_tool.tool == "abricate" or $choose_tool.tool == "groot"
         --db '$db'
+        #end if
         -i '$input' 
         -o '$output'
+        #if $choose_tool.tool == "hamronization"
         $hamronized
+        #end if
     ]]></command>
     <inputs>
         <param type="data" name="input" format="tsv,txt" label="Specify input file" help="-i" />
-        <param type="select" name="tool" label="The tool you used to do ARG annotation" help="[tool]" >
-            <option value="deeparg" selected="true">DeepARG</option>
-            <option value="argsoap">ARGs_OAP</option>
-            <option value="abricate">ABRicate</option>
-            <option value="resfinder">ResFinder</option>
-            <option value="amrfinderplus">AMRFinderPlus</option>
-            <option value="groot">Groot</option>
-        </param>
-        <param type="select" argument="--db" label="The database you used to do ARG annotation">
-            <option value="sarg" selected="true">SARG</option>
-            <option value="ncbi">NCBI</option>
-            <option value="resfinder">ResFinder</option>
-            <option value="deeparg" selected="true">DeepARG</option>
-            <option value="amrfinderplus">AMRFinderPlus</option>
-            <option value="megares">MEGARes</option>
-            <option value="argannot">ARG-ANNOT</option>
-            <option value="groot-resfinder">Groot ResFinder database </option>
-            <option value="groot-argannot">Groot ARG-ANNOT database </option>
-            <option value="groot-card">Groot CARD database </option>
-            <option value="groot-db">Groot DB (combining all sequences in ResFinder, ARG-annot and CARD)</option>
-            <option value="groot-core-db">Groot Core DB (combining sequences that are present in each of ResFinder, ARG-annot and CARD databases)</option>
-        </param> 
-        <param name="hamronized" type="boolean" label="If the input is hamronized" truevalue="--hamronized" falsevalue="" optional="true" help="Use this if the input is hamronized (processed using the hAMRonization tool)" />
+        <conditional name="choose_tool">
+            <param type="select" name="tool" label="The tool used to do ARG annotation" help="" >
+                <option value="deeparg" selected="true">DeepARG</option>
+                <option value="argsoap">ARGs-OAP</option>
+                <option value="abricate">ABRicate</option>
+                <option value="resfinder">ResFinder</option>
+                <option value="amrfinderplus">AMRFinderPlus</option>
+                <option value="groot">Groot</option>
+                <option value="hamronization">hAMRonization</option>
+            </param>
+            <when value="deeparg">
+            </when>
+            <when value="argsoap">
+            </when>
+            <when value="abricate">
+                <param type="select" argument="--db" label="The database you used to do ARG annotation">
+                    <option value="sarg" selected="true">SARG</option>
+                    <option value="ncbi">NCBI</option>
+                    <option value="resfinder">ResFinder</option>
+                    <option value="resfinderfg">ResFinder FG</option>
+                    <option value="deeparg" selected="true">DeepARG</option>
+                    <option value="megares">MEGARes</option>
+                    <option value="argannot">ARG-ANNOT</option>
+                </param>
+            </when>
+            <when value="resfinder">
+            </when>
+            <when value="amrfinderplus">
+            </when>
+            <when value="groot">
+                <param type="select" argument="--db" label="The database you used to do ARG annotation">
+                    <option value="groot-resfinder">Groot ResFinder database </option>
+                    <option value="groot-argannot">Groot ARG-ANNOT database </option>
+                    <option value="groot-card">Groot CARD database </option>
+                    <option value="groot-db">Groot DB (combining all sequences in ResFinder, ARG-annot and CARD)</option>
+                    <option value="groot-core-db">Groot Core DB (combining sequences that are present in each of ResFinder, ARG-annot and CARD databases)</option>
+                </param>
+            </when>
+            <when value="hamronization">
+                <param name="hamronized" type="boolean" label="Skip rows with unsupported tools" truevalue="--hamronization_skip_unsupported_tool" falsevalue="" checked="false" help="Combined hAMRonization results can have ARGs detected by unsupported tools (e.g. staramr), --hamronization_skip_unsupported_tool allows to skip rows with unsupported tools"/>
+            </when>
+        </conditional>
     </inputs>
     <outputs>
         <data name="output" format="tsv" label="${tool.name} on ${on_string} : ARG normalized table" />
@@ -50,23 +74,27 @@
         <!-- Test 1 : input : tsv, output : tsv, tool : groot -->
         <test>
             <param name="input" value="resfinder_PSM7J199_R2.report"/>
-            <param name="tool" value="groot"/>
-            <param name="db" value="groot-resfinder"/>
+            <conditional name="choose_tool">
+                <param name="tool" value="groot"/>
+                <param name="db" value="groot-resfinder"/>
+            </conditional>
             <output name="output" file="groot-resfinder-results.tsv"/>
         </test>
         <!-- Test 2 : input : txt, output : tsv, tool : argsoap -->
         <test>
             <param name="input" value="blastout.filtered.txt"/>
-            <param name="tool" value="argsoap"/>
-            <param name="db" value="sarg"/>
+            <conditional name="choose_tool">
+                <param name="tool" value="argsoap"/>
+            </conditional>
             <output name="output" file="blastout.filtered.argnorm.tsv"/>
         </test>
-        <!-- Test 3 : input : tsv, output : tsv, tool : deeparg, hamronize : true -->
+        <!-- Test 3 : input : tsv, output : tsv, tool : deeparg, hamronize -->
         <test>
             <param name="input" value="deeparg_hamronize.tsv"/>
-            <param name="tool" value="deeparg"/>
-            <param name="db" value="deeparg"/>
-            <param name="hamronized" value="true"/>
+            <conditional name="choose_tool">                
+                <param name="tool" value="hamronization"/>
+                <param name="hamronized" value="true"/>
+            </conditional>
             <output name="output" file="deeparg_hamronize_argnorm_results.tsv"/>
         </test>
     </tests>