working loc file with dummy data

usegalaxy-au · Jun 11, 2024 · 4f5f155 · 4f5f155
1 parent e1c686c
commit 4f5f155
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Showing 6 changed files with 38 additions and 5 deletions.
diff --git a/tools/dorado/README.md b/tools/dorado/README.md
diff --git a/tools/dorado/dorado.xml b/tools/dorado/dorado.xml
@@ -1,11 +1,9 @@
 <tool id="dorado" name="dorado" version="@CONTAINER_HASH@+galaxy0" python_template_version="3.5" profile="21.05">
     <macros>
-        <!-- TODO: the containers aren't tagged with software versions -->
-        <token name="@CONTAINER_HASH@">c2d8bc91ca2d043fed84d06cca92aaeb62bcc1cd</token>
+        <import>macros.xml</import>
     </macros>
-    <requirements>
-        <container type="docker">nanoporetech/dorado:sha@CONTAINER_HASH@</container>
-    </requirements>
+    <expand macro="xrefs"/>
+    <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
 
 ln -s '$pod5_file' ./reads.pod5 &&
@@ -20,6 +18,12 @@ reads.pod5
     ]]></command>
     <inputs>
         <param name="pod5_file" type="data" format="fast5" label="Raw fast5 file"/>
+        <!-- <param name="model" type="select">
+            <options from_data_table="dorado_models" />
+        </param> -->
+        <param name="index" type="select">
+            <options from_data_table="bowtie_indexes" />
+        </param>
     </inputs>
     <outputs>
         <data format="sam" name="out_sam" label="Output from dorado list-models" from_work_dir="output.sam"/>

diff --git a/tools/dorado/macros.xml b/tools/dorado/macros.xml
@@ -0,0 +1,14 @@
+<macros>
+    <!-- TODO: the containers aren't tagged with software versions -->
+    <token name="@CONTAINER_HASH@">c2d8bc91ca2d043fed84d06cca92aaeb62bcc1cd</token>
+    <xml name="requirements">
+        <requirements>
+            <container type="docker">nanoporetech/dorado:sha@CONTAINER_HASH@</container>
+        </requirements>
+    </xml>
+    <xml name="xrefs">
+        <xrefs>
+            <xref type="bio.tools">dorado</xref>
+        </xrefs>
+    </xml>
+</macros>
diff --git a/tools/dorado/test-data/bowtie_indices.loc b/tools/dorado/test-data/bowtie_indices.loc
@@ -0,0 +1 @@
+../tool-data/bowtie_indices.loc.sample
diff --git a/tools/dorado/tool_data_table_conf.xml.sample b/tools/dorado/tool_data_table_conf.xml.sample
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Locations of indexes in the Bowtie mapper format -->
+    <table name="bowtie_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/bowtie_indices.loc" />
+    </table>
+</tables>
diff --git a/tools/dorado/tool_data_table_conf.xml.test b/tools/dorado/tool_data_table_conf.xml.test
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Locations of indexes in the Bowtie mapper format -->
+    <table name="bowtie_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="${__HERE__}/test-data/bowtie_indices.loc" />
+    </table>
+</tables>