Skip to content

Commit

Permalink
Version Update of HapCUT2 and Restructuring of XML file (galaxyprojec…
Browse files Browse the repository at this point in the history 
…t#5975)

* Updating tools/hapcut2 from version 1.3.3 to 1.3.4

* Version bump and restructuring of XML file

* Updated changes as per review

---------

Co-authored-by: planemo-autoupdate <[email protected]>
  • Loading branch information
@SaimMomin12
SaimMomin12 and planemo-autoupdate authored Apr 30, 2024
1 parent 491c6fc commit 908fb91
Show file tree
Hide file tree
Showing 2 changed files with 68 additions and 86 deletions.
124 changes: 38 additions & 86 deletions tools/hapcut2/hapcut2.xml
View file
Original file line number Diff line number Diff line change
@@ -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@">1.3.3</token>
<token name="@TOOL_VERSION@">1.3.4</token>
<token name="@VERSION_SUFFIX@">1</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>
<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
Expand Down Expand Up @@ -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">
Expand All @@ -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 ${on_string}: Fragments">
<filter>output_fragments</filter>
</data>
</outputs>
Expand All @@ -161,7 +103,9 @@ ln -s '$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>

Expand All @@ -171,7 +115,9 @@ ln -s '$input_bam' input.bam
<param name="input_vcf" ftype="vcf" value="input.vcf"/>
<param name="output_fragments" value="1"/>
<param name="output_phased" value="1"/>
<param name="optimization" value="default"/>
<conditional name="optimization">
<param name="choice" value="default"/>
</conditional>
<output name="frags" ftype="txt" file="output_frag.dat"/>
<output name="haplotype" ftype="txt" file="output_haplotype.out"/>
<output name="haplotype_phased" ftype="vcf" file="output_haplotype.out.phased.vcf"/>
Expand All @@ -183,7 +129,9 @@ ln -s '$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"/>
Expand All @@ -195,8 +143,12 @@ ln -s '$input_bam' input.bam
<param name="input_vcf" ftype="vcf" value="input.vcf"/>
<param name="output_fragments" value="1"/>
<param name="output_phased" value="1"/>
<param name="optimization" value="pacbio"/>
<param name="reference_genome" value="history"/>
<conditional name="optimization">
<param name="choice" value="pacbio"/>
</conditional>
<conditional name="reference_genome">
<param name="source" value="history"/>
</conditional>
<param name="fasta" ftype="fasta" value="ref.fasta"/>
<output name="frags" ftype="txt" file="output_frag.dat"/>
<output name="haplotype" ftype="txt" file="output_haplotype.out"/>
Expand All @@ -212,8 +164,12 @@ ln -s '$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>
Expand Down Expand Up @@ -259,13 +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
Quickmerge was wrapped by the Galaxy Australia team.
]]></help>
<citations>
<citation type="doi">10.1101/gr.213462.116</citation>
</citations>
<expand macro="creator"/>
</tool>
30 changes: 30 additions & 0 deletions tools/hapcut2/macros.xml
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,30 @@
<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>

<xml name="creator">
<creator>
<organization name="Galaxy Australia" url="https://site.usegalaxy.org.au"/>
</creator>
</xml>
</macro>

0 comments on commit 908fb91

Please sign in to comment.