diff data_manager/bowtie2_index_builder.xml @ 13:8bf75f813413 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 57d05675396f0b44265fb4dbc8f9f891c6073219

--- a/data_manager/bowtie2_index_builder.xml	Sun Apr 16 08:25:58 2023 +0000
+++ b/data_manager/bowtie2_index_builder.xml	Thu Dec 05 06:46:58 2024 +0000
@@ -1,26 +1,57 @@
-<tool id="bowtie2_index_builder_data_manager" name="Bowtie2 index" tool_type="manage_data" version="@WRAPPER_VERSION@+galaxy0" profile="18.09">
+<tool id="bowtie2_index_builder_data_manager" name="Bowtie2 index" tool_type="manage_data" version="@WRAPPER_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
     <description>builder</description>
+    <macros>
+        <token name="@WRAPPER_VERSION@">2.5.4</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
     <requirements>
         <requirement type="package" version="@WRAPPER_VERSION@">bowtie2</requirement>
     </requirements>
-    <macros>
-        <token name="@WRAPPER_VERSION@">2.4.4</token>
-    </macros>
     <command detect_errors="exit_code"><![CDATA[
-        python '$__tool_directory__/bowtie2_index_builder.py'
-        '${out_file}'
-        --fasta_filename '${all_fasta_source.fields.path}'
-        --fasta_dbkey '${all_fasta_source.fields.dbkey}'
-        --fasta_description '${all_fasta_source.fields.name}'
-        --data_table_name bowtie2_indexes ${tophat2}
+        #set $value = $sequence_id or $all_fasta_source.fields.dbkey
+        #set $fasta_file_name = str($all_fasta_source.fields.path).split('/')[-1]
+        mkdir -p '${out_file.extra_files_path}' &&
+        ln -s '${all_fasta_source.fields.path}' '${out_file.extra_files_path}/${fasta_file_name}' &&
+        cd '${out_file.extra_files_path}' &&
+        bowtie2-build --threads \${GALAXY_SLOTS:-1} '${out_file.extra_files_path}/${fasta_file_name}' '${value}' &&
+        cp '$dmjson' '$out_file'
     ]]></command>
+    <configfiles>
+        <configfile name="dmjson"><![CDATA[#slurp
+#set $fasta_file_name = str($all_fasta_source.fields.path).split('/')[-1]
+#set $value = $sequence_id or $all_fasta_source.fields.dbkey
+#set $name = $sequence_name or $all_fasta_source.fields.name
+{
+  "data_tables":{
+    "bowtie2_indexes":[
+      {
+        "value": "${value}",
+        "dbkey": "${all_fasta_source.fields.dbkey}",
+        "name": "${name}",
+        "path": "${fasta_file_name}"
+      }
+#if $tophat2:
+    ],
+    "tophat2_indexes":[
+      {
+        "value": "${value}",
+        "dbkey": "${all_fasta_source.fields.dbkey}",
+        "name": "${name}",
+        "path": "${fasta_file_name}"
+      }
+#end if
+    ]
+  }
+}
+]]></configfile>
+    </configfiles>
     <inputs>
         <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
             <options from_data_table="all_fasta"/>
         </param>
         <param name="sequence_name" type="text" value="" label="Name of sequence" />
         <param name="sequence_id" type="text" value="" label="ID for sequence" />
-        <param name="tophat2" type="boolean" truevalue="--data_table_name tophat2_indexes" falsevalue="" checked="True" label="Also make available for TopHat" help="Adds values to tophat2_indexes tool data table" />
+        <param name="tophat2" type="boolean" checked="True" label="Also make available for TopHat" help="Adds values to tophat2_indexes tool data table" />
     </inputs>
     <outputs>
         <data name="out_file" format="data_manager_json"/>
@@ -28,7 +59,14 @@
     <tests>
         <test>
             <param name="all_fasta_source" value="phiX174"/>
-            <output name="out_file" value="bowtie2_data_manager.json"/>
+            <output name="out_file" value="bowtie2_data_manager.1.json"/>
+        </test>
+        <test>
+            <param name="all_fasta_source" value="phiX174"/>
+            <param name="sequence_name" value="Galeocerdo cuvier"/>
+            <param name="sequence_id" value="tigHai1"/>
+            <param name="tophat2" value="False"/>
+            <output name="out_file" file="bowtie2_data_manager.2.json"/>
         </test>
     </tests>