# HG changeset patch
# User iuc
# Date 1722349416 0
# Node ID c8ba8286e7c092e630b598313baf1c781a4b2c5c
# Parent  63e02ef6e1531e5429184fde1c73b41ee6846afa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c

diff -r 63e02ef6e153 -r c8ba8286e7c0 clair3.xml
--- a/clair3.xml	Fri Oct 28 20:58:30 2022 +0000
+++ b/clair3.xml	Tue Jul 30 14:23:36 2024 +0000
@@ -1,7 +1,7 @@
-<tool id="clair3" name="Clair3" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
+<tool id="clair3" name="Clair3" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.2">
     <description>germline small variant caller for long-reads</description>
     <macros>
-        <token name="@TOOL_VERSION@">0.1.12</token>
+        <token name="@TOOL_VERSION@">1.0.8</token>
         <token name="@VERSION_SUFFIX@">0</token>
     </macros>
     <xrefs>
@@ -76,7 +76,6 @@
             #if $adv.chunk_size
                 --chunk_size=$adv.chunk_size
             #end if
-
     ]]></command>
     <inputs>
         <param type="data" name="bam_input" argument="--bam_fn" format="bam,cram" label="BAM/CRAM file input" />
@@ -116,7 +115,7 @@
             </when>
         </conditional>
         <conditional name="bed_or_vcf">
-            <param type="select" name="bed_or_vcf_selector" label="Restict variant calling to:">
+            <param type="select" name="bed_or_vcf_selector" label="Restrict variant calling to:">
                 <option value="unrestricted" selected="true">Whole reference (unrestricted)</option>
                 <option value="bed" selected="true">Regions defined in BED dataset</option>
                 <option value="vcf">Sites defined in VCF dataset</option>
@@ -135,7 +134,7 @@
         <param name="output_files" type="select" display="checkboxes" multiple="true" label="Optional additional output files">
             <option value="full_alignment">Full alignment file</option>
             <option value="pileup">Pileup file</option>
-            <option value="phased_bam">Phased BAM file</option>
+            <option value="phased_vcf">Phased VCF file</option>
         </param>
         <section name="adv" title="Advanced parameters" expanded="false">
             <param type="integer" argument="--qual" value="0" min="0" label="Qual" help="If set, variants with >qual will be marked PASS, or LowQual otherwise." />
@@ -160,11 +159,12 @@
         <data name="full_alignment" format="vcf_bgzip" from_work_dir="./full_alignment.vcf.gz" label="${tool.name} on ${on_string}: full alignment">
             <filter>output_files and 'full_alignment' in output_files</filter>
         </data>
-        <data name="phased_bam" format="bam" from_work_dir="./phased_bam.bam" label="${tool.name} on ${on_string}: phased BAM">
-            <filter>output_files and 'phased_bam' in output_files</filter>
+        <data name="phased_vcf" format="vcf_bgzip" from_work_dir="./phased_merge_output.vcf.gz" label="${tool.name} on ${on_string}: phased VCF">
+            <filter>output_files and 'phased_vcf' in output_files</filter>
         </data>
     </outputs>
     <tests>
+        <!-- test1 -->
         <test expect_num_outputs="1">
             <conditional name="model_source">
                 <param name="source" value="built-in"/>  
@@ -188,9 +188,10 @@
               <has_text text="[WARNING] No contig intersection found, output header only in" />
             </assert_stdout>
         </test>
+        <!-- test2 -->
         <test expect_num_outputs="4">
             <conditional name="model_source">
-                <param name="source" value="builtin" />
+                <param name="source" value="built-in" />
                 <param name="select_built_in" value="r941_prom_hac_g360+g422" />
             </conditional>
             <param name="bam_input" value="test1.bam" />
@@ -203,15 +204,17 @@
                 <param name="ref_fasta_builtin" value="test1" />
             </conditional>
             <param name="gvcf" value="true"/>
-            <param name="output_files" value="full_alignment,pileup,phased_bam"/>
+            <param name="output_files" value="full_alignment,pileup,phased_vcf"/>
             <section name="adv">
                 <param name="print_ref_calls" value="true"/>
+                <param name="enable_phasing" value="true"/>
             </section>
-            <output name="merge_output" decompress="true" file="merge_output_1.vcf.gz" ftype="vcf_bgzip"/>
-            <output name="pileup" decompress="true" file="pileup_1.vcf.gz" ftype="vcf_bgzip"/>
-            <output name="full_alignment" decompress="true" file="full_alignment_1.vcf.gz" ftype="vcf_bgzip"/>
-            <output name="phased_bam" file="phased_bam_1.bam" ftype="bam"/>
+            <output name="merge_output" decompress="true" file="merge_output_1.vcf.gz" ftype="vcf_bgzip" lines_diff="4"/>
+            <output name="pileup" decompress="true" file="pileup_1.vcf.gz" ftype="vcf_bgzip" lines_diff="4"/>
+            <output name="full_alignment" decompress="true" file="full_alignment_1.vcf.gz" ftype="vcf_bgzip" lines_diff="4"/>
+            <output name="phased_vcf" decompress="true" file="phased_vcf_1.vcf.gz" ftype="vcf_bgzip" lines_diff="4"/>
         </test>
+        <!-- test3 -->
         <test expect_num_outputs="4">
             <conditional name="model_source">
                 <param name="source" value="datatable" />
@@ -226,16 +229,16 @@
                 <param name="source" value="builtin" />
                 <param name="ref_fasta_builtin" value="test1" />
             </conditional>
-            <param name="output_files" value="full_alignment,pileup,phased_bam"/>
+            <param name="output_files" value="full_alignment,pileup,phased_vcf"/>
             <section name="adv">
                 <param name="snp_min_af" value="0.5"/>
                 <param name="indel_min_af" value="0.12"/>
                 <param name="no_phasing_for_fa" value="true" />
                 <param name="print_ref_calls" value="true"/>
             </section>
-            <output name="merge_output" ftype="vcf_bgzip">
+            <output name="merge_output" decompress="true" ftype="vcf_bgzip">
                 <assert_contents>
-                    <has_size value="450" delta="50" />
+                    <has_text text="#CHROM" />
                 </assert_contents>
             </output>
             <output name="pileup" ftype="vcf_bgzip">
@@ -248,16 +251,17 @@
                     <has_size value="0" />
                 </assert_contents>
             </output>
-            <output name="phased_bam" ftype="bam">
+            <output name="phased_vcf" ftype="vcf_bgzip">
                 <assert_contents>
                     <has_size value="0" />
                 </assert_contents>
             </output>
         </test>
+        <!-- test4 -->
         <!-- Test input CRAM -->
         <test expect_num_outputs="1">
             <conditional name="model_source">
-                <param name="source" value="builtin" />
+                <param name="source" value="built-in" />
                 <param name="select_built_in" value="r941_prom_hac_g360+g422" />
             </conditional>
             <param name="bam_input" value="test1.cram" />
@@ -265,7 +269,7 @@
                 <param name="source" value="history" />
                 <param name="ref_fasta" value="test1.fasta" />
             </conditional>
-            <output name="merge_output" file="output_cram_test.vcf.gz" ftype="vcf_bgzip"/>
+            <output name="merge_output" decompress="true" file="output_cram_test.vcf.gz" ftype="vcf_bgzip" lines_diff="4"/>
         </test>
     </tests>
     <help><![CDATA[
diff -r 63e02ef6e153 -r c8ba8286e7c0 test-data/full_alignment_1.vcf.gz
Binary file test-data/full_alignment_1.vcf.gz has changed
diff -r 63e02ef6e153 -r c8ba8286e7c0 test-data/merge_output_1.vcf.gz
Binary file test-data/merge_output_1.vcf.gz has changed
diff -r 63e02ef6e153 -r c8ba8286e7c0 test-data/output_cram_test.vcf.gz
Binary file test-data/output_cram_test.vcf.gz has changed
diff -r 63e02ef6e153 -r c8ba8286e7c0 test-data/phased_bam_1.bam
diff -r 63e02ef6e153 -r c8ba8286e7c0 test-data/phased_vcf_1.vcf.gz
Binary file test-data/phased_vcf_1.vcf.gz has changed
diff -r 63e02ef6e153 -r c8ba8286e7c0 test-data/pileup_1.vcf.gz
Binary file test-data/pileup_1.vcf.gz has changed