diff bwa_macros.xml @ 17:23e88ff6c494 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit e953b3b7dac6cbe9509fdc673907a7c2c7183180

--- a/bwa_macros.xml	Fri Aug 19 18:51:11 2022 +0000
+++ b/bwa_macros.xml	Wed Mar 19 17:24:58 2025 +0000
@@ -1,7 +1,7 @@
 <macros>
     <import>read_group_macros.xml</import>
 
-    <token name="@VERSION@">0.7.17</token>
+    <token name="@TOOL_VERSION@">0.7.18</token>
 
     <token name="@pipefail@"><![CDATA[set -o | grep -q pipefail && set -o pipefail;]]></token>
 
@@ -36,11 +36,17 @@
 
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="@VERSION@">bwa</requirement>
-            <requirement type="package" version="1.6">samtools</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">bwa</requirement>
+            <requirement type="package" version="1.20">samtools</requirement>
         </requirements>
     </xml>
 
+    <xml name="bio_tools">
+        <xrefs>
+            <xref type="bio.tools">bwa</xref>
+        </xrefs>
+    </xml>
+
     <xml name="stdio">
         <stdio>
             <exit_code range="1:" />
@@ -103,6 +109,26 @@
         </actions>
     </macro>
 
+    <token name="@ref_genomes@">
+**Indices: Selecting reference genomes for BWA**
+
+The Galaxy wrapper for BWA allows you to select between precomputed and user-defined indices for reference genomes
+using the **Will you select a reference genome from your history or use a built-in index?** select box.
+
+This select box has two options:
+
+  1. **Use a built-in genome index**
+
+     With this option (which is the default), Galaxy provides you with a dropdown select menu populated with genomes that have been pre-indexed with the bwa index utility and are ready to map sequenced reads against.
+
+     The collection of pre-indexed genomes is managed by the administrators of your Galaxy instance. If your genome of interest is missing and its impractical to use the second option below to work with it, consider contacting the support team for the Galaxy server you are working on to let them know that you would like to have an additional genome indexed.
+
+  2. **Use a genome from history and build index**
+
+     With this option, Galaxy provides you with a dropdown select menu populated with all FASTA formatted files listed in your current history. If you have uploaded your genome of interest into your history it will be shown there.
+
+     Selecting a genome from this dropdown will cause Galaxy to index it transparently first using the `bwa index` command, and then map against it with `bwa aln`.
+    </token>
     <token name="@RG@">
 -----
 
@@ -155,19 +181,8 @@
 
 Note the hierarchical relationship between read groups (unique for each lane) to libraries (sequenced on two lanes) and samples (across four lanes, two lanes for each library).
     </token>
-    <token name="@info@">
------
-
-.. class:: infomark
-
-**More info**
-
-To obtain more information about BWA and ask questions use these resources:
-
-  1. https://biostar.usegalaxy.org/
-  2. https://www.biostars.org/
-  3. https://github.com/lh3/bwa
-  4. http://bio-bwa.sourceforge.net/
-
+    <token name="@links@">
+.. _BWA: https://github.com/lh3/bwa
+.. _`BWA manual`: https://bio-bwa.sourceforge.net/bwa.shtml
     </token>
 </macros>