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changeset 5:99650691a26e draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit 07e6d5d6cc0615ea23d18df910ee6b278b9cb5df
author iuc
date Thu, 12 Feb 2026 08:51:36 +0000
parents 09fff9439112
children
files deepvariant.xml macros.xml
diffstat 2 files changed, 18 insertions(+), 14 deletions(-) [+]
line wrap: on
line diff
--- a/deepvariant.xml	Mon Feb 02 12:34:03 2026 +0000
+++ b/deepvariant.xml	Thu Feb 12 08:51:36 2026 +0000
@@ -6,8 +6,12 @@
     <expand macro='edam_ontology' />
     <expand macro='requirements' />
     <command detect_errors='exit_code'><![CDATA[
-        ln -s '${reads}' reads_alignment.bam
-        && ln -s '${reads.metadata.bam_index}' reads_alignment.bam.bai
+        ln -s '${reads}' 'reads_alignment.$reads.ext'
+        #if $reads.is_of_type("bam")
+            && ln -s '${reads.metadata.bam_index}' reads_alignment.bam.bai
+        #elif $reads.is_of_type("cram")
+            && ln -s '${reads.metadata.cram_index}' reads_alignment.cram.crai
+        #end if
         #if $regions_conditional.regions_option == 'bed'
             && ln -s '${regions_conditional.bed_file}' region.bed
         #end if
@@ -29,7 +33,7 @@
         && run_deepvariant
         --model_type=$model_type
         --ref=$ref_genome
-        --reads='reads_alignment.bam'
+        --reads='reads_alignment.$reads.ext'
         #if $sample_name
             --sample_name '$sample_name'
         #end if
@@ -90,7 +94,7 @@
                 <param name="history_item" type="data" format="fasta" label="Reference genome" help="A reference genome in FASTA format" />
             </when>
         </conditional>
-        <param argument="--reads" type="data" format="bam" label="BAM file" help="An aligned reads file in BAM format. The reads must be aligned to the reference genome" />
+        <param argument="--reads" type="data" format="bam,cram" label="BAM file" help="An aligned reads file in BAM format. The reads must be aligned to the reference genome" />
         <param argument="--sample_name" type="text" optional="true" label="Sample name" help="Sample name to use instead of the SM tag in the BAM header. Example: NA12878" />
         <param argument="--model_type" type="select" label="Model type" help="Type of model to use for variant calling">
             <option value="WGS">WGS: Illumina whole genome sequencing</option>
@@ -155,7 +159,7 @@
                 <param name="source" value="history"/>
                 <param name="history_item" value="reference.fasta"/>
             </conditional>
-            <param name="reads" value="reads.bam"/>
+            <param name="reads" value="reads.bam" ftype="bam"/>
             <param name="model_type" value="WGS"/>
             <param name="output_gvcf" value="False"/>
             <conditional name="regions_conditional">
@@ -185,7 +189,7 @@
                 <param name="source" value="history"/>
                 <param name="history_item" value="reference.fasta"/>
             </conditional>
-            <param name="reads" value="reads.bam"/>
+            <param name="reads" value="reads.bam" ftype="bam"/>
             <param name="model_type" value="WGS"/>
             <conditional name="regions_conditional">
                 <param name="regions_option" value="region"/>
@@ -214,7 +218,7 @@
                 <param name="source" value="history"/>
                 <param name="history_item" value="reference.fasta"/>
             </conditional>
-            <param name="reads" value="reads.bam"/>
+            <param name="reads" value="reads.bam" ftype="bam"/>
             <param name="model_type" value="WGS"/>
             <conditional name="regions_conditional">
                 <param name="regions_option" value="bed"/>
@@ -243,7 +247,7 @@
                 <param name="source" value="history"/>
                 <param name="history_item" value="reference.fasta"/>
             </conditional>
-            <param name="reads" value="reads.bam"/>
+            <param name="reads" value="reads.bam" ftype="bam"/>
             <param name="model_type" value="WGS"/>
             <param name="output_gvcf" value="True"/>
             <conditional name="regions_conditional">
@@ -279,7 +283,7 @@
                 <param name="source" value="history"/>
                 <param name="history_item" value="reference.fasta"/>
             </conditional>
-            <param name="reads" value="reads.cram"/>
+            <param name="reads" value="reads.cram" ftype="cram"/>
             <param name="model_type" value="WGS"/>
             <conditional name="regions_conditional">
                 <param name="regions_option" value="disabled"/>
@@ -307,7 +311,7 @@
                 <param name="source" value="indexed"/>
                 <param name="index" value="phix174"/>
             </conditional>
-            <param name="reads" value="reads.bam"/>
+            <param name="reads" value="reads.bam" ftype="bam"/>
             <param name="model_type" value="WGS"/>
             <conditional name="regions_conditional">
                 <param name="regions_option" value="disabled"/>
@@ -335,7 +339,7 @@
                 <param name="source" value="history"/>
                 <param name="history_item" value="reference.fasta"/>
             </conditional>
-            <param name="reads" value="reads.bam"/>
+            <param name="reads" value="reads.bam" ftype="bam"/>
             <param name="model_type" value="WGS"/>
             <conditional name="regions_conditional">
                 <param name="regions_option" value="disabled"/>
@@ -370,7 +374,7 @@
                 <param name="source" value="history"/>
                 <param name="history_item" value="reference.fasta"/>
             </conditional>
-            <param name="reads" value="reads.bam"/>
+            <param name="reads" value="reads.bam" ftype="bam"/>
             <param name="model_type" value="WGS"/>
             <conditional name="regions_conditional">
                 <param name="regions_option" value="disabled"/>
@@ -400,7 +404,7 @@
                 <param name="source" value="history"/>
                 <param name="history_item" value="reference.fasta"/>
             </conditional>
-            <param name="reads" value="reads.bam"/>
+            <param name="reads" value="reads.bam" ftype="bam"/>
             <param name="model_type" value="WGS"/>
             <conditional name="regions_conditional">
                 <param name="regions_option" value="disabled"/>
--- a/macros.xml	Mon Feb 02 12:34:03 2026 +0000
+++ b/macros.xml	Thu Feb 12 08:51:36 2026 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">1.9.0</token>
-    <token name="@SUFFIX_VERSION@">0</token>
+    <token name="@SUFFIX_VERSION@">1</token>
     <token name="@PROFILE@">23.1</token>
     <xml name="edam_ontology">
         <edam_topics>