diff diamond_makedb.xml @ 20:0729ae1533e5 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 62db819c1db857d3fba94dc4e290ee0f50f7928d

--- a/diamond_makedb.xml	Fri Apr 22 13:50:54 2022 +0000
+++ b/diamond_makedb.xml	Mon Feb 03 16:00:43 2025 +0000
@@ -1,18 +1,16 @@
-<tool id="bg_diamond_makedb" name="Diamond makedb" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="19.01">
+<tool id="bg_diamond_makedb" name="Diamond makedb" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.2" license="GPL-3.0">
     <description>Build database from a FASTA file</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-
-    <expand macro="requirements" />
-    <expand macro="stdio" />
-    <expand macro="version_command" />
-
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
     <command detect_errors="aggressive">
-    <!-- DB has two files, *.dmnd and *.tx -->
+        <!-- DB has two files, *.dmnd and *.tx -->
     <![CDATA[
     diamond makedb
-        --threads "\${GALAXY_SLOTS:-12}"
+        --threads \${GALAXY_SLOTS:-12}
         --in '$infile'
         --db ./database
 
@@ -23,30 +21,24 @@
       #end if
     ]]>
     </command>
-
     <inputs>
-      <param name="infile" type="data" format="fasta" label="Input reference file in FASTA format" />
-      <conditional name="tax_cond">
-        <param name="tax_select" type="select" label="Add taxonomic data?" help="Needs to be supplied in order to provide taxonomy features of the aligner">
-          <option value="yes">Yes</option>
-          <option value="no" selected="true">No</option>
-        </param>
-        <when value="yes">
-          <param argument="--taxonmap" type="data" format="tabular" 
-            label="Protein accession to taxid mapping file" 
-            help="Path to mapping file that maps NCBI protein accession numbers to taxon ids (gzip compressed). This parameter is optional and needs to be supplied in order to provide taxonomy features. 
-              A custom file following the same format may be supplied here. Note that the first line of this file is assumed to contain headings and will be ignored" />
-          <param argument="--taxonnodes" type="data" format="tabular" label="Taxonomy nodes.dmp from NCBI" help="This parameter is optional and needs to be supplied in order to provide taxonomy features" />
-          <param argument="--taxonnames" type="data" format="tabular" label="Taxonomy names.dmp from NCBI" help="This parameter is optional and needs to be supplied in order to provide taxonomy features" />
-        </when>
-        <when value="no"/>
-      </conditional>
+        <param name="infile" type="data" format="fasta" label="Input reference file in FASTA format"/>
+        <conditional name="tax_cond">
+            <param name="tax_select" type="select" label="Add taxonomic data?" help="Needs to be supplied in order to provide taxonomy features of the aligner">
+                <option value="yes">Yes</option>
+                <option value="no" selected="true">No</option>
+            </param>
+            <when value="yes">
+                <param argument="--taxonmap" type="data" format="tabular" label="Protein accession to taxid mapping file" help="Path to mapping file that maps NCBI protein accession numbers to taxon ids (gzip compressed). This parameter is optional and needs to be supplied in order to provide taxonomy features.                A custom file following the same format may be supplied here. Note that the first line of this file is assumed to contain headings and will be ignored"/>
+                <param argument="--taxonnodes" type="data" format="tabular" label="Taxonomy nodes.dmp from NCBI" help="This parameter is optional and needs to be supplied in order to provide taxonomy features"/>
+                <param argument="--taxonnames" type="data" format="tabular" label="Taxonomy names.dmp from NCBI" help="This parameter is optional and needs to be supplied in order to provide taxonomy features"/>
+            </when>
+            <when value="no"/>
+        </conditional>
     </inputs>
-
     <outputs>
         <data format="dmnd" name="outfile" from_work_dir="database.dmnd" label="${tool.name} on ${on_string}"/>
     </outputs>
-
     <tests>
         <test>
             <param name="infile" value="db.fasta" ftype="fasta"/>
@@ -56,14 +48,13 @@
             <param name="infile" value="db.fasta" ftype="fasta"/>
             <conditional name="tax_cond">
                 <param name="tax_select" value="yes"/>
-                <param name="taxonmap" ftype="tabular" value="prot.accession2taxid" />
-                <param name="taxonnodes" ftype="tabular" value="nodes.dmp" />
-                <param name="taxonnames" ftype="tabular" value="names.dmp" />
+                <param name="taxonmap" ftype="tabular" value="prot.accession2taxid"/>
+                <param name="taxonnodes" ftype="tabular" value="nodes.dmp"/>
+                <param name="taxonnames" ftype="tabular" value="names.dmp"/>
             </conditional>
             <output name="outfile" value="db-wtax.dmnd" compare="sim_size" delta="2"/>
         </test>
     </tests>
-
     <help>
 <![CDATA[
 
@@ -86,6 +77,5 @@
 - taxonnodes: Path to the nodes.dmp file from the NCBI taxonomy. This parameter is optional and needs to be supplied in order to provide taxonomy features. The file is contained within this archive downloadable at NCBI: ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdmp.zip
 ]]>
     </help>
-
-    <expand macro="citations" />
+    <expand macro="citations"/>
 </tool>