diff basil.xml @ 1:77fc7640abc7 draft default tip

planemo upload commit 49a2861a9b3480ea25f1e5526d2edf9dc8cb5334

--- a/basil.xml	Thu May 30 21:14:58 2019 -0400
+++ b/basil.xml	Sun Aug 11 21:06:14 2024 +0000
@@ -1,11 +1,19 @@
-<tool id="basil" name="basil" version="1.2.0">
+<tool id="basil" name="basil" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
     <description>Breakpoint detection, including large insertions</description>
+    <macros>
+        <token name="@TOOL_VERSION@">1.2.0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
+    </macros>
     <requirements>
-        <requirement type="package" version="1.2.0">anise_basil</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">anise_basil</requirement>
     </requirements>
-    <version_command>basil --version 2>&amp;1 | grep 'basil version' | cut -f 3 -d ' '</version_command>
+    <version_command>basil --version 2&gt;&amp;1 | grep 'basil version' | cut -f 3 -d ' '</version_command>
     <command detect_errors="aggressive"><![CDATA[
-        ln -s '$ref' 'ref.fa' &&
+        #if $reference_source.reference_source_selector == 'history':
+            ln -f -s '$reference_source.ref' ref.fa &&
+        #else:
+            ln -f -s '$reference_source.ref.fields.path' ref.fa &&
+        #end if
         ln -s '$bam' 'in.bam' &&
         ln -s '$vcf' 'out.vcf' &&
         basil
@@ -15,18 +23,48 @@
         --oea-min-support-each-side '$min_oea_each_side'
     ]]></command>
     <inputs>
-        <param name="ref" argument="--input-reference" type="data" format="Fasta" label="Reference Sequence File" help="FASTA file with the reference."/>
+        <conditional name="reference_source">
+            <param name="reference_source_selector" type="select" label="Select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below. If you would like to perform self-mapping select `history` here, then choose your input file as reference.">
+                <option value="cached">Use a built-in genome index</option>
+                <option value="history">Use a genome from history and build index</option>
+            </param>
+            <when value="cached">
+                <param name="ref" type="select" label="Using reference genome" help="Select genome from the list">
+                    <options from_data_table="all_fasta">
+                        <filter type="sort_by" column="2"/>
+                        <validator type="no_options" message="No reference genomes are available"/>
+                    </options>
+                    <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
+                </param>
+            </when>
+            <when value="history">
+                <param name="ref" argument="--input-reference" type="data" format="Fasta" label="Reference Sequence File" help="FASTA file with the reference."/>
+            </when>
+        </conditional>
         <param name="bam" argument="--input-mapping" type="data" format="sam,bam" label="Alignment File" help="SAM/BAM file to use as the input."/>
-        <param name="min_oea_each_side" argument="--oea-min-support-each-side" type="integer" value="2" label="Minimum supporting reads, each side" help="Smallest number of OEA (one-end-anchor) reads on each side to support an insertion.  In range [1..inf].  This is the minimum number of supporting reads (without mapped partners) on each side of an insertion breakpoint required to not be filtered." />
+        <param name="min_oea_each_side" argument="--oea-min-support-each-side" type="integer" value="2" label="Minimum supporting reads, each side" help="Smallest number of OEA (one-end-anchor) reads on each side to support an insertion.  In range [1..inf].  This is the minimum number of supporting reads (without mapped partners) on each side of an insertion breakpoint required to not be filtered."/>
     </inputs>
     <outputs>
-        <data name="vcf" format="vcf" />
+        <data name="vcf" format="vcf"/>
     </outputs>
     <tests>
         <test>
+            <conditional name="reference_source">
+                <param name="reference_source_selector" value="history" />
+                <param name="ref" ftype="fasta" value="ref.fa"/>
+            </conditional>
             <param name="ref" value="ref.fa"/>
             <param name="bam" value="simulated.bam"/>
-            <param name="min_oea_each_side"  value="2"/>
+            <param name="min_oea_each_side" value="2"/>
+            <output name="vcf" file="basil.vcf"/>
+        </test>
+        <test>
+            <conditional name="reference_source">
+                <param name="reference_source_selector" value="cached" />
+                <param name="ref" value="genome"/>
+            </conditional>
+            <param name="bam" value="simulated.bam"/>
+            <param name="min_oea_each_side" value="2"/>
             <output name="vcf" file="basil.vcf"/>
         </test>
     </tests>