diff data_manager/kma_build_index.xml @ 3:b221a6c2ed00 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit d0b3d69f25fe8419e5b98165ae53b59651d711b1

--- a/data_manager/kma_build_index.xml	Sun Nov 22 12:45:39 2020 +0000
+++ b/data_manager/kma_build_index.xml	Fri Oct 10 12:03:10 2025 +0000
@@ -1,47 +1,70 @@
 <?xml version="1.0"?>
-<tool id="kma_build_index" name="KMA Index Builder" tool_type="manage_data" version="1.2.21+galaxy0" profile="19.01">
+<tool id="kma_build_index" name="KMA Index Builder" tool_type="manage_data" version="1.6.6+galaxy0" profile="24.1">
     <description>kma index builder</description>
     <requirements>
-        <requirement type="package" version="1.2.21">kma</requirement>
-        <requirement type="package" version="3.7">python</requirement>
+        <requirement type="package" version="1.6.6">kma</requirement>
     </requirements>
     <version_command>kma -v</version_command>
     <command detect_errors="exit_code">
     <![CDATA[
-        python '${__tool_directory__}/kma_build_index.py'
-          '${out_file}'
-          --k ${k}
-          --k_t ${k_t}
-          --k_i ${k_i}
-	  --ML ${ML}
-	  --ht ${ht}
-	  --hq ${hq}
-          --name '${name}'
-	  '${fasta}'
-    ]]>
-    </command>
+mkdir -p '${out_file.extra_files_path}'/index_folder &&
+kma_index
+  -i '$fasta'
+  -o '${out_file.extra_files_path}'/index_folder/index
+  ## index options
+  -k $k
+  -k_t $k_t
+  -k_i $k_i
+  -ML $ML
+  -ht $ht
+  -hq $hq
+    ]]></command>
+    <configfiles>
+        <configfile filename="dm.json"><![CDATA[#slurp
+#from datetime import datetime
+#from hashlib import md5
+#set value=datetime.now().strftime("%Y-%m-%d") + "_" + md5($name.encode()).hexdigest()
+{"data_tables": {"kma_index": [{"value": "$value", "name": "$name", "path": "index_folder"}]}}
+]]></configfile>
+    </configfiles>
     <inputs>
-        <param name="k" type="integer" value="16" min="8" max="32" label="kmer size used for indexing the database." />
-        <param name="k_t" type="integer" value="16" min="8" max="32" label="kmer size used to identify template candidates when running KMA." />
-        <param name="k_i" type="integer" value="16" min="8" max="32" label="kmer size used when performing alignments between two sequences." />
-        <param name="ML" type="integer" value="16" label="Minimum length of templates" />
-        <param name="ht" type="float" value="1.0" min="0.0" max="1.0" label="Homology template" />
-        <param name="hq" type="float" value="1.0" min="0.0" max="1.0" label="Homology query" />
-	<param name="name" type="text" label="Name for index" />
-	<param name="fasta" type="data" format="fasta" label="Sequence to index (fasta)" />
+        <param argument="-k" type="integer" value="16" min="8" max="32" label="kmer size used for indexing the database." />
+        <param argument="-k_t" type="integer" value="16" min="8" max="32" label="kmer size used to identify template candidates when running KMA." />
+        <param argument="-k_i" type="integer" value="16" min="8" max="32" label="kmer size used when performing alignments between two sequences." />
+        <param argument="-ML" type="integer" value="16" label="Minimum length of templates" />
+        <param argument="-ht" type="float" value="1.0" min="0.0" max="1.0" label="Homology template" />
+        <param argument="-hq" type="float" value="1.0" min="0.0" max="1.0" label="Homology query" />
+        <param name="fasta" type="data" format="fasta" label="Sequence to index (fasta)" />
+        <param name="name" type="text" optional="false" label="Name for index" help="Choose a name that describes the indexed sequence and possibly any non-default indexing parameters.">
+            <validator type="empty_field"/>
+        </param>
     </inputs>
     <outputs>
-        <data name="out_file" format="data_manager_json" />
+        <data name="out_file" format="data_manager_json" from_work_dir="dm.json"/>
     </outputs>
     <tests>
         <test>
             <param name="fasta" value="phiX174.fasta"/>
             <param name="name" value="index"/>
-            <output name="out_file" value="kma_data_manager.json" compare="sim_size" />
+            <output name="out_file" ftype="data_manager_json">
+                <assert_contents>
+                    <has_text text='"kma_index":' />
+                    <has_text text='"name": "index"' />
+                    <has_text text='"path": "index_folder"' />
+                    <has_text_matching expression='"value": "\d{4}-\d{2}-\d{2}_6a992d5529f459a44fee58c733255e86"' />
+                </assert_contents>
+            </output>
         </test>
     </tests>
-    <help>
-    </help>
+    <help><![CDATA[
+**Data manager for building an index for the kma aligner**
+
+Runs the kma index command on the input sequence with the chosen options.
+
+.. class:: infomark
+
+   You may want to capture details about the reference sequence and any non-default indexing parameters in the name of the index so that users have a better idea what they are selecting for tool runs.
+    ]]></help>
     <citations>
         <citation type="doi">10.1186/s12859-018-2336-6</citation>
     </citations>