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Update clair3 (galaxyproject#6195)
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* Update clair3 to version 1.0.8

* Fix permissions

* Increase lines_diff, bump profile

* Really set lines_diff to 4
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@pvanheus
pvanheus authored Jul 30, 2024
1 parent 9af8730 commit fa0f3ca
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Showing 7 changed files with 23 additions and 19 deletions.
42 changes: 23 additions & 19 deletions tools/clair3/clair3.xml
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@@ -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>
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#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" />
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</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>
Expand All @@ -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." />
Expand All @@ -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"/>
Expand All @@ -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" />
Expand All @@ -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" />
Expand All @@ -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">
Expand All @@ -248,24 +251,25 @@
<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" />
<conditional name="ref_source">
<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[
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