diff macros.xml @ 11:5a326a6fa105 draft default tip

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
author artbio
date Fri, 17 Oct 2025 17:21:17 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Fri Oct 17 17:21:17 2025 +0000
@@ -0,0 +1,57 @@
+<macros>
+    <token name="@TOOL_VERSION@">0.2.8</token>
+    <token name="@GALAXY_VERSION@">4</token>
+
+    <!-- Requirements for lumpy_smoove (Python 2.7 environment) -->
+    <xml name="lumpy_smoove_requirements">
+        <requirements>
+            <requirement type="package" version="0.2.8">smoove</requirement>
+            <requirement type="package" version="0.7.1">svtyper</requirement>
+            <requirement type="package" version="2.7">python</requirement>
+        </requirements>
+    </xml>
+
+    <!-- Requirements for vcf2hrdetect (Python 3.9 environment) -->
+    <xml name="vcf2hrdetect_requirements">
+        <requirements>
+            <requirement type="package" version="3.9">python</requirement>
+        </requirements>
+    </xml>
+
+    <xml name="stdio">
+        <stdio>
+            <exit_code range="1:" level="fatal" description="Tool exception" />
+        </stdio>
+    </xml>
+    <token name="@pipefail@"><![CDATA[set -o | grep -q pipefail && set -o pipefail;]]></token>
+    <token name="@set_fasta_index@"><![CDATA[
+    #if str( $reference_source.reference_source_selector ) == "history":
+        ln -s '${reference_source.ref_file}' reference.fa &&
+        samtools faidx 'reference.fa' 2>&1 || echo "Error running samtools faidx for lumpy_smoove" >&2 &&
+    #else:
+        ln -s '${reference_source.index.fields.path}' reference.fa &&
+        ln -s '${reference_source.index.fields.path}.fai' reference.fa.fai &&
+    #end if
+    ]]></token>
+    <macro name="reference_source_conditional">
+        <conditional name="reference_source">
+            <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options.">
+                <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="index" type="select" label="Using built-in genome" help="Select genome from the list">
+                    <options from_data_table="fasta_indexes">
+                        <filter type="sort_by" column="2" />
+                        <validator type="no_options" message="No indexes are available" />
+                    </options>
+                </param>
+            </when>
+            <when value="history">
+                <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" />
+            </when>
+        </conditional>
+    </macro>
+</macros>
+
+