| Previous changeset 1:63e02ef6e153 (2022-10-28) Next changeset 3:3843a30053ee (2024-09-09) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c |
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modified:
clair3.xml test-data/full_alignment_1.vcf.gz test-data/merge_output_1.vcf.gz test-data/output_cram_test.vcf.gz test-data/pileup_1.vcf.gz |
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added:
test-data/phased_vcf_1.vcf.gz |
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removed:
test-data/phased_bam_1.bam |
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| 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 |
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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> @@ -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[ |
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