From f637f04ab0e00cb84208c7bd891db429d6552c7e Mon Sep 17 00:00:00 2001
From: planemo-autoupdate <planemo-autoupdate@users.noreply.github.com>
Date: Mon, 29 Apr 2024 04:21:27 +0000
Subject: [PATCH 1/3] Updating tools/hapcut2 from version 1.3.3 to 1.3.4

---
 tools/hapcut2/hapcut2.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/hapcut2/hapcut2.xml b/tools/hapcut2/hapcut2.xml
index 9790c09e60d..e16e7817794 100644
--- a/tools/hapcut2/hapcut2.xml
+++ b/tools/hapcut2/hapcut2.xml
@@ -2,8 +2,8 @@
   <description>haplotype assembly for diploid organisms</description>
 
   <macros>
-    <token name="@TOOL_VERSION@">1.3.3</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@TOOL_VERSION@">1.3.4</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <xml name="reference_genome_input">
       <conditional name="reference_genome">
         <param name="source" type="select" label="Source for the reference genome" help="Built-in references were created using default options.">

From 7328403dfd81edaa8776b5eb027de698b00f939b Mon Sep 17 00:00:00 2001
From: Saim Momin <mominsaim12@gmail.com>
Date: Mon, 29 Apr 2024 17:09:27 +0200
Subject: [PATCH 2/3] Version bump and restructuring of XML file

---
 tools/hapcut2/hapcut2.xml | 120 ++++++++++++--------------------------
 tools/hapcut2/macros.xml  |  24 ++++++++
 2 files changed, 62 insertions(+), 82 deletions(-)
 create mode 100644 tools/hapcut2/macros.xml

diff --git a/tools/hapcut2/hapcut2.xml b/tools/hapcut2/hapcut2.xml
index e16e7817794..cf97344a4c5 100644
--- a/tools/hapcut2/hapcut2.xml
+++ b/tools/hapcut2/hapcut2.xml
@@ -1,40 +1,16 @@
-<tool id="hapcut2" name="Hapcut2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+<tool id="hapcut2" name="Hapcut2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.2">
   <description>haplotype assembly for diploid organisms</description>
-
   <macros>
     <token name="@TOOL_VERSION@">1.3.4</token>
-    <token name="@VERSION_SUFFIX@">0</token>
-    <xml name="reference_genome_input">
-      <conditional name="reference_genome">
-        <param name="source" type="select" label="Source for the reference genome" help="Built-in references were created using default options.">
-          <option value="indexed" selected="true">Use a built-in genome</option>
-          <option value="history">Use a genome from history</option>
-        </param>
-        <when value="indexed">
-          <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team.">
-              <options from_data_table="fasta_indexes">
-                  <filter type="sort_by" column="2" />
-                  <validator type="no_options" message="No genomes are available for the selected input dataset" />
-              </options>
-          </param>
-        </when>
-        <when value="history">
-          <param name="fasta" type="data" format="fasta,fasta.gz"
-            label="Reference genome fasta file"
-            help="The reference genome is required for long-read optimization."
-          />
-        </when>
-      </conditional>
-    </xml>
+    <token name="@VERSION_SUFFIX@">1</token>
+    <import>macros.xml</import>   
   </macros>
-
   <xrefs>
     <xref type="bio.tools">hapcut2</xref>
   </xrefs>
   <requirements>
     <requirement type="package" version="@TOOL_VERSION@">hapcut2</requirement>
   </requirements>
-
   <command detect_errors="exit_code"><![CDATA[
 
 ## Prep inputs
@@ -78,27 +54,11 @@ ln -s '$input_bam' input.bam
 #if $optimization.choice == 'hic':
   --HiC 1
 #end if
-
   ]]></command>
 
   <inputs>
-    <param
-      name="input_bam"
-      argument="--bam"
-      type="data"
-      format="bam"
-      label="Input BAM file"
-      help="Coordinate-sorted BAM file"
-    />
-    <param
-      name="input_vcf"
-      argument="--VCF"
-      type="data"
-      format="vcf"
-      label="Input VCF file"
-      help="Variant file with genotypes for a single individual"
-    />
-
+    <param name="input_bam" argument="--bam" type="data" format="bam" label="Input BAM file" help="Coordinate-sorted BAM file"/>
+    <param name="input_vcf" argument="--VCF" type="data" format="vcf" label="Input VCF file" help="Variant file with genotypes for a single individual"/>
     <conditional name="optimization">
       <!-- TODO: include 10X (requires extra processing step) -->
       <param name="choice" type="select" display="radio" label="Optimization">
@@ -107,49 +67,31 @@ ln -s '$input_bam' input.bam
         <option value="ont">Oxford Nanopore</option>
         <option value="hic">Hi-C</option>
       </param>
-
+      <when value="default"></when>
       <when value="pacbio">
-        <expand macro="reference_genome_input" />
+        <expand macro="reference_genome_input"/>
       </when>
-
       <when value="ont">
-        <expand macro="reference_genome_input" />
+        <expand macro="reference_genome_input"/>
       </when>
+      <when value="hic"></when>
     </conditional>
 
-    <param name="output_phased" type="boolean" label="Output phased VCF file?"
-      checked="true"
-      help="Output variant calls on the haplotype assembly"
-    />
-    <param name="output_fragments" type="boolean" label="Output fragments file?"
-      help="Output fragments collected by extractHAIRS"
-    />
+    <param name="output_phased" type="boolean" label="Output phased VCF file?" checked="true" help="Output variant calls on the haplotype assembly"/>
+    <param name="output_fragments" type="boolean" label="Output fragments file?" help="Output fragments collected by extractHAIRS"/>
 
     <section name="advanced" title="Advanced parameters">
-      <param argument="--maxIS" type="integer" label="Maximum insert size"
-        optional="true" value="1000" min="0"
-        help="Maximum insert size for a paired-end read to be considered as a single fragment for phasing"
-      />
-
-      <param argument="--minIS" type="integer" label="Minimum insert size"
-        optional="true" value="0" min="0"
-        help="Minimum insert size for a paired-end read to be considered as a single fragment for phasing"
-      />
+      <param argument="--maxIS" type="integer" label="Maximum insert size" optional="true" value="1000" min="0" help="Maximum insert size for a paired-end read to be considered as a single fragment for phasing"/>
+      <param argument="--minIS" type="integer" label="Minimum insert size" optional="true" value="0" min="0" help="Minimum insert size for a paired-end read to be considered as a single fragment for phasing"/>
     </section>
   </inputs>
 
   <outputs>
-    <data name="haplotype" format="txt" from_work_dir="haplotype.out"
-      label="${tool.name} on ${on_string}: Haplotype block"
-    />
-    <data name="haplotype_phased" format="vcf" from_work_dir="haplotype.out.phased.VCF"
-      label="${tool.name} on ${on_string}: Phased haplotype VCF"
-    >
+    <data name="haplotype" format="txt" from_work_dir="haplotype.out" label="${tool.name} on ${on_string}: Haplotype block"/>
+    <data name="haplotype_phased" format="vcf" from_work_dir="haplotype.out.phased.VCF" label="${tool.name} on ${on_string}: Phased haplotype VCF">
       <filter>output_phased</filter>
     </data>
-    <data name="frags" format="txt" from_work_dir="frags.dat"
-      label="${tool.name} on ${on_string}: Fragments"
-    >
+    <data name="frags" format="txt" from_work_dir="frags.dat" label="${tool.name} on ${on_string}: Fragments">
       <filter>output_fragments</filter>
     </data>
   </outputs>
@@ -161,7 +103,9 @@ ln -s '$input_bam' input.bam
       <param name="input_vcf" ftype="vcf" value="input.vcf"/>
       <param name="output_fragments" value="0"/>
       <param name="output_phased" value="0"/>
-      <param name="optimization" value="default"/>
+      <conditional name="optimization">
+        <param name="choice" value="default"/>
+      </conditional>
       <output name="haplotype" ftype="txt" file="output_haplotype.out"/>
     </test>
 
@@ -171,7 +115,9 @@ ln -s '$input_bam' input.bam
       <param name="input_vcf" ftype="vcf" value="input.vcf"/>
       <param name="output_fragments" value="1"/>
       <param name="output_phased" value="1"/>
-      <param name="optimization" value="default"/>
+      <conditional name="optimization">
+        <param name="choice" value="default"/>
+      </conditional>
       <output name="frags" ftype="txt" file="output_frag.dat"/>
       <output name="haplotype" ftype="txt" file="output_haplotype.out"/>
       <output name="haplotype_phased" ftype="vcf" file="output_haplotype.out.phased.vcf"/>
@@ -183,7 +129,9 @@ ln -s '$input_bam' input.bam
       <param name="input_vcf" ftype="vcf" value="input.vcf"/>
       <param name="output_fragments" value="1"/>
       <param name="output_phased" value="1"/>
-      <param name="optimization" value="default"/>
+      <conditional name="optimization">
+        <param name="choice" value="default"/>
+      </conditional>
       <output name="frags" ftype="txt" file="output_frag.dat"/>
       <output name="haplotype" ftype="txt" file="output_haplotype.out"/>
       <output name="haplotype_phased" ftype="vcf" file="output_haplotype.out.phased.vcf"/>
@@ -195,8 +143,12 @@ ln -s '$input_bam' input.bam
       <param name="input_vcf" ftype="vcf" value="input.vcf"/>
       <param name="output_fragments" value="1"/>
       <param name="output_phased" value="1"/>
-      <param name="optimization" value="pacbio"/>
-      <param name="reference_genome" value="history"/>
+      <conditional name="optimization">
+        <param name="choice" value="pacbio"/>
+      </conditional>
+      <conditional name="reference_genome">
+        <param name="source" value="history"/>
+      </conditional>
       <param name="fasta" ftype="fasta" value="ref.fasta"/>
       <output name="frags" ftype="txt" file="output_frag.dat"/>
       <output name="haplotype" ftype="txt" file="output_haplotype.out"/>
@@ -212,8 +164,12 @@ ln -s '$input_bam' input.bam
       <output name="frags" ftype="txt" file="output_frag.dat"/>
       <output name="haplotype" ftype="txt" file="output_haplotype.out"/>
       <output name="haplotype_phased" ftype="vcf" file="output_haplotype.out.phased.vcf"/>
-      <param name="optimization" value="ont"/>
-      <param name="reference_genome" value="history"/>
+      <conditional name="optimization">
+        <param name="optimization" value="ont"/>
+      </conditional>
+      <conditional name="reference_genome">
+        <param name="source" value="history"/>
+      </conditional>
       <param name="fasta" ftype="fasta" value="ref.fasta"/>
     </test>
   </tests>
@@ -262,7 +218,7 @@ See `HapCUT2 on GitHib <https://github.com/vibansal/HapCUT2>`_ for more detailed
 
 .. class:: infomark
 
-Quickmerge was wrapped by the Galaxy Australia team.
+HapCUT2 was wrapped by the Galaxy Australia team.
 
   ]]></help>
   <citations>
diff --git a/tools/hapcut2/macros.xml b/tools/hapcut2/macros.xml
new file mode 100644
index 00000000000..6b7400953eb
--- /dev/null
+++ b/tools/hapcut2/macros.xml
@@ -0,0 +1,24 @@
+<macro>
+    <xml name="reference_genome_input">
+        <conditional name="reference_genome">
+          <param name="source" type="select" label="Source for the reference genome" help="Built-in references were created using default options.">
+            <option value="indexed" selected="true">Use a built-in genome</option>
+            <option value="history">Use a genome from history</option>
+          </param>
+          <when value="indexed">
+            <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team.">
+                <options from_data_table="fasta_indexes">
+                    <filter type="sort_by" column="2" />
+                    <validator type="no_options" message="No genomes are available for the selected input dataset" />
+                </options>
+            </param>
+          </when>
+          <when value="history">
+            <param name="fasta" type="data" format="fasta,fasta.gz"
+              label="Reference genome fasta file"
+              help="The reference genome is required for long-read optimization."
+            />
+          </when>
+        </conditional>
+      </xml>
+</macro>
\ No newline at end of file

From 55df8a0517ccafe859440bf5009e058e25a03163 Mon Sep 17 00:00:00 2001
From: Saim Momin <mominsaim12@gmail.com>
Date: Tue, 30 Apr 2024 10:10:29 +0200
Subject: [PATCH 3/3] Updated changes as per review

---
 tools/hapcut2/hapcut2.xml | 6 +-----
 tools/hapcut2/macros.xml  | 6 ++++++
 2 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/tools/hapcut2/hapcut2.xml b/tools/hapcut2/hapcut2.xml
index cf97344a4c5..16e1d879e18 100644
--- a/tools/hapcut2/hapcut2.xml
+++ b/tools/hapcut2/hapcut2.xml
@@ -215,13 +215,9 @@ Input data should reference a single diploid individual mapped to a reference ge
 
 See `HapCUT2 on GitHib <https://github.com/vibansal/HapCUT2>`_ for more detailed information.
 
-
-.. class:: infomark
-
-HapCUT2 was wrapped by the Galaxy Australia team.
-
   ]]></help>
   <citations>
       <citation type="doi">10.1101/gr.213462.116</citation>
   </citations>
+  <expand macro="creator"/>
 </tool>
diff --git a/tools/hapcut2/macros.xml b/tools/hapcut2/macros.xml
index 6b7400953eb..703448893da 100644
--- a/tools/hapcut2/macros.xml
+++ b/tools/hapcut2/macros.xml
@@ -21,4 +21,10 @@
           </when>
         </conditional>
       </xml>
+
+    <xml name="creator">
+        <creator>
+            <organization name="Galaxy Australia" url="https://site.usegalaxy.org.au"/>
+        </creator>
+    </xml>
 </macro>
\ No newline at end of file