Add tool argNorm (#6282)

* Add argNorm + test files * Rename .shed.yml * Update tools/argnorm/argnorm.xml Add argument instead of name Co-authored-by: Björn Grüning <[email protected]> * Update tools/argnorm/argnorm.xml Add argument instead of name Co-authored-by: Björn Grüning <[email protected]> * Update tools/argnorm/argnorm.xml Add argument instead of name Co-authored-by: Björn Grüning <[email protected]> * Update tools/argnorm/argnorm.xml Add argument instead of name Co-authored-by: Björn Grüning <[email protected]> * Update tools/argnorm/argnorm.xml Add argument instead of name Co-authored-by: Björn Grüning <[email protected]> * remove xref * Added xref since the tool was added to biotools --------- Co-authored-by: Björn Grüning <[email protected]>
galaxyproject · Aug 28, 2024 · cc4c7a0 · cc4c7a0
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diff --git a/tools/argnorm/.shed.yml b/tools/argnorm/.shed.yml
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+categories:
+-  Genome annotation
+description: argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database
+long_description: | 
+  argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database. The tool takes as input a list of ARGs and returns the normalized ARGs, which are the ARO identifiers.
+  argNorm also enhances antibiotic resistance gene annotations by providing drug categorization of the drugs that antibiotic resistance genes confer resistance to.
+name: argnorm
+owner: iuc
+homepage_url: https://github.com/BigDataBiology/argNorm
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm
+type: unrestricted
diff --git a/tools/argnorm/argnorm.xml b/tools/argnorm/argnorm.xml
@@ -0,0 +1,83 @@
+<tool id="argnorm" name="argNorm" version="@VERSION@+galaxy0" profile="22.05">
+    <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>
+    </macros>
+    <xrefs>
+       <xref type="bio.tools">argnorm</xref>
+    </xrefs>
+    <requirements>
+        <requirement type="package" version="@VERSION@">argnorm</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+    argnorm
+        '$tool'
+        --db '$db'
+        -i '$input' 
+        -o '$output'
+        $hamronized
+    ]]></command>
+    <inputs>
+        <param type="data" name="input" format="tsv,txt" label="Specify input file" help="-i" />
+        <param type="select" name="tool" label="The tool you used to do ARG annotation" help="[tool]" >
+            <option value="deeparg" selected="true">DeepARG</option>
+            <option value="argsoap">ARGs_OAP</option>
+            <option value="abricate">ABRicate</option>
+            <option value="resfinder">ResFinder</option>
+            <option value="amrfinderplus">AMRFinderPlus</option>
+            <option value="groot">Groot</option>
+        </param>
+        <param type="select" argument="--db" label="The database you used to do ARG annotation">
+            <option value="sarg" selected="true">SARG</option>
+            <option value="ncbi">NCBI</option>
+            <option value="resfinder">ResFinder</option>
+            <option value="deeparg" selected="true">DeepARG</option>
+            <option value="amrfinderplus">AMRFinderPlus</option>
+            <option value="megares">MEGARes</option>
+            <option value="argannot">ARG-ANNOT</option>
+            <option value="groot-resfinder">Groot ResFinder database </option>
+            <option value="groot-argannot">Groot ARG-ANNOT database </option>
+            <option value="groot-card">Groot CARD database </option>
+            <option value="groot-db">Groot DB (combining all sequences in ResFinder, ARG-annot and CARD)</option>
+            <option value="groot-core-db">Groot Core DB (combining sequences that are present in each of ResFinder, ARG-annot and CARD databases)</option>
+        </param> 
+        <param name="hamronized" type="boolean" label="If the input is hamronized" truevalue="--hamronized" falsevalue="" optional="true" help="Use this if the input is hamronized (processed using the hAMRonization tool)" />
+    </inputs>
+    <outputs>
+        <data name="output" format="tsv" label="${tool.name} on ${on_string} : ARG normalized table" />
+    </outputs>
+    <tests>
+        <!-- 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"/>
+            <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"/>
+            <output name="output" file="blastout.filtered.argnorm.tsv"/>
+        </test>
+        <!-- Test 3 : input : tsv, output : tsv, tool : deeparg, hamronize : true -->
+        <test>
+            <param name="input" value="deeparg_hamronize.tsv"/>
+            <param name="tool" value="deeparg"/>
+            <param name="db" value="deeparg"/>
+            <param name="hamronized" value="true"/>
+            <output name="output" file="deeparg_hamronize_argnorm_results.tsv"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database.
+
+argNorm also enhances antibiotic resistance gene annotations by providing drug categorization of the drugs that antibiotic resistance genes confer resistance to.
+
+    ]]></help>
+    <citations>
+        <citation type="doi">https://github.com/BigDataBiology/argNorm</citation>
+    </citations>
+</tool>