| Previous changeset 0:44f6ec903688 (2022-06-15) Next changeset 2:c8ba8286e7c0 (2024-07-30) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 05505898035b41c07461dc0eecec61699ecbcf41 |
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modified:
clair3.xml |
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added:
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 test-data/test1.cram |
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removed:
test-data/full_alignment_1.vcf test-data/merge_output_1.vcf test-data/pileup_1.vcf |
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| diff -r 44f6ec903688 -r 63e02ef6e153 clair3.xml --- a/clair3.xml Wed Jun 15 09:45:05 2022 +0000 +++ b/clair3.xml Fri Oct 28 20:58:30 2022 +0000 |
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| b'@@ -1,8 +1,12 @@\n <tool id="clair3" name="Clair3" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">\n+ <description>germline small variant caller for long-reads</description>\n <macros>\n- <token name="@TOOL_VERSION@">0.1.11</token>\n+ <token name="@TOOL_VERSION@">0.1.12</token>\n <token name="@VERSION_SUFFIX@">0</token>\n </macros>\n+ <xrefs>\n+ <xref type=\'bio.tools\'>clair3</xref>\n+ </xrefs>\n <requirements>\n <requirement type="package" version="@TOOL_VERSION@">clair3</requirement>\n </requirements>\n@@ -18,9 +22,13 @@\n #if $model_source.source == "datatable"\n #set model_path = $model_source.model.fields.path \n #end if\n-\n- ln -s \'${$bam_input}\' input_reads.bam &&\n- ln -s \'${$bam_input.metadata.bam_index}\' input_reads.bai &&\n+ #set $extension = $bam_input.ext\n+ ln -s \'${$bam_input}\' input_reads.$extension &&\n+ #if $extension == \'bam\'\n+ ln -s \'${$bam_input.metadata.bam_index}\' input_reads.bai &&\n+ #else\n+ ln -s \'${$bam_input.metadata.cram_index}\' input_reads.crai &&\n+ #end if\n \n #if $bed_or_vcf.bed_or_vcf_selector == \'bed\'\n ln -s \'$bed_or_vcf.bed_fn\' input.bed &&\n@@ -29,7 +37,7 @@\n #end if\n \n run_clair3.sh\n- --bam_fn=input_reads.bam\n+ --bam_fn=input_reads.$extension\n --ref_fn=reference.fasta\n #if $model_source.source == "datatable"\n --platform=\'${model_source.model.fields.platform}\'\n@@ -43,7 +51,7 @@\n --model_path=\\$(dirname \\$(which run_clair3.sh))/models/$model_source.select_built_in\n #end if\n --output=\'.\'\n- --threads=\\${GALAXY_SLOTS:-1}\n+ --threads=\\${GALAXY_SLOTS:-2}\n #if $bed_or_vcf.bed_or_vcf_selector == \'bed\'\n --bed_fn=input.bed\n #elif $bed_or_vcf.bed_or_vcf_selector == \'vcf\'\n@@ -51,9 +59,7 @@\n #else\n $bed_or_vcf.include_all_ctgs\n #end if\n- #if $output_options.selection_mode == \'advanced\'\n- $output_options.gvcf\n- #end if\n+ $gvcf\n #if $adv.qual\n --qual=$adv.qual\n #end if\n@@ -73,13 +79,14 @@\n \n ]]></command>\n <inputs>\n+ <param type="data" name="bam_input" argument="--bam_fn" format="bam,cram" label="BAM/CRAM file input" />\n <conditional name="ref_source">\n <param type="select" label="Reference genome source" name="source">\n <option value="history" selected="true">History</option>\n <option value="builtin">Built-in</option>\n </param>\n <when value="history">\n- <param type="data" format="fasta" name="ref_fasta" label="Reference genome" />\n+ <param type="data" format="fasta" name="ref_fasta" argument="--ref_fn" label="Reference genome" />\n </when>\n <when value="builtin">\n <param type="select" name="ref_fasta_builtin" label="Reference genome">\n@@ -88,12 +95,12 @@\n </when>\n </conditional>\n <conditional name="model_source">\n- <param type="select" label="Select if you want to use built-in models or your own via datatable." name="source">\n+ <param name="source" type="select" label="Clair3 model" help="Select if you want to use a built-in model shipping with the tool or a model cached on this Galaxy server.">\n <option value="built-in">Built-in</option>\n- <option value="datatable">Datatable</option>\n+ <option value="datatable">Cached</option>\n </param>\n <when value="built-in">\n- <param type="select" name="select_built_in" label="Select built-in model.">\n+ <param type="select" name="select_built_in" label="Built-in model">\n <op'..b'ion_mode\'] == \'advanced\' and output_options[\'phased_bam_check\']</filter>\n+ <data name="phased_bam" format="bam" from_work_dir="./phased_bam.bam" label="${tool.name} on ${on_string}: phased BAM">\n+ <filter>output_files and \'phased_bam\' in output_files</filter>\n </data>\n </outputs>\n <tests>\n@@ -180,10 +179,6 @@\n <param name="bed_or_vcf_selector" value="vcf"/>\n <param name="vcf_fn" value="test1.vcf.gz" />\n </conditional>\n- <conditional name="output_options">\n- <param name="selection_mode" value="advanced"/>\n- <param name="gvcf" value="true" />\n- </conditional>\n <section name="adv">\n <param name="no_phasing_for_fa" value="true"/>\n <param name="print_ref_calls" value="true"/>\n@@ -207,18 +202,14 @@\n <param name="source" value="builtin" />\n <param name="ref_fasta_builtin" value="test1" />\n </conditional>\n- <conditional name="output_options">\n- <param name="selection_mode" value="advanced"/>\n- <param name="pileup_check" value="true"/>\n- <param name="full_alignment_check" value="true"/>\n- <param name="phased_bam_check" value="true"/>\n- </conditional>\n+ <param name="gvcf" value="true"/>\n+ <param name="output_files" value="full_alignment,pileup,phased_bam"/>\n <section name="adv">\n <param name="print_ref_calls" value="true"/>\n </section>\n- <output name="merge_output" decompress="true" file="merge_output_1.vcf" ftype="vcf_bgzip"/>\n- <output name="pileup" decompress="true" file="pileup_1.vcf" ftype="vcf_bgzip"/>\n- <output name="full_alignment" decompress="true" file="full_alignment_1.vcf" ftype="vcf_bgzip"/>\n+ <output name="merge_output" decompress="true" file="merge_output_1.vcf.gz" ftype="vcf_bgzip"/>\n+ <output name="pileup" decompress="true" file="pileup_1.vcf.gz" ftype="vcf_bgzip"/>\n+ <output name="full_alignment" decompress="true" file="full_alignment_1.vcf.gz" ftype="vcf_bgzip"/>\n <output name="phased_bam" file="phased_bam_1.bam" ftype="bam"/>\n </test>\n <test expect_num_outputs="4">\n@@ -235,12 +226,7 @@\n <param name="source" value="builtin" />\n <param name="ref_fasta_builtin" value="test1" />\n </conditional>\n- <conditional name="output_options">\n- <param name="selection_mode" value="advanced"/>\n- <param name="pileup_check" value="true"/>\n- <param name="full_alignment_check" value="true"/>\n- <param name="phased_bam_check" value="true"/>\n- </conditional>\n+ <param name="output_files" value="full_alignment,pileup,phased_bam"/>\n <section name="adv">\n <param name="snp_min_af" value="0.5"/>\n <param name="indel_min_af" value="0.12"/>\n@@ -268,6 +254,19 @@\n </assert_contents>\n </output>\n </test>\n+ <!-- Test input CRAM -->\n+ <test expect_num_outputs="1">\n+ <conditional name="model_source">\n+ <param name="source" value="builtin" />\n+ <param name="select_built_in" value="r941_prom_hac_g360+g422" />\n+ </conditional>\n+ <param name="bam_input" value="test1.cram" />\n+ <conditional name="ref_source">\n+ <param name="source" value="history" />\n+ <param name="ref_fasta" value="test1.fasta" />\n+ </conditional>\n+ <output name="merge_output" file="output_cram_test.vcf.gz" ftype="vcf_bgzip"/>\n+ </test>\n </tests>\n <help><![CDATA[\n Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories:\n' |
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