| Previous changeset 1:b040adcfeefd (2022-01-04) |
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Commit message:
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 commit 9c42369510cce59bf0dcb0edb440322d17b18339 |
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modified:
FilterMutectCalls.xml MergeMutectStats.xml Mutect2.xml macros.xml macros_filtermutectcalls.xml |
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| diff -r b040adcfeefd -r 646e6943bcd2 FilterMutectCalls.xml --- a/FilterMutectCalls.xml Tue Jan 04 15:10:59 2022 +0000 +++ b/FilterMutectCalls.xml Sun Oct 15 12:06:24 2023 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="filtermutectcalls" name="gatk4 FilterMutectCalls" version="@WRAPPER_VERSION@" profile="18.05"> +<tool id="filtermutectcalls" name="gatk4 FilterMutectCalls" version="@WRAPPER_VERSION@" profile="21.01"> <description>Filter variants in a GATK4 Mutect2 VCF callset</description> <macros> <import>macros.xml</import> @@ -91,7 +91,7 @@ </data> </outputs> <tests> - <test> + <test expect_num_outputs="2"> <param name="reference_source_selector" value="history" /> <param name="reference_sequence" ftype="fasta" value="reference.fa" /> <conditional name="input_options"> @@ -101,7 +101,7 @@ <output name="output_vcf" file="filtered_Mutect2-out1.vcf" lines_diff="2" /> <output name="output_vcf_stats" file="filtered_Mutect2-out1_stats.tsv" /> </test> - <test> + <test expect_num_outputs="2"> <param name="reference_source_selector" value="history" /> <param name="reference_sequence" ftype="fasta" value="chr20.fa" /> <conditional name="input_options"> @@ -112,7 +112,7 @@ <output name="output_vcf" file="filtered_Mutect2-out6.vcf_bgzip" compare="sim_size" /> <output name="output_vcf_stats" file="filtered_Mutect2-out6_stats.tsv" /> </test> - <test> + <test expect_num_outputs="2"> <param name="reference_source_selector" value="history" /> <param name="reference_sequence" ftype="fasta" value="chr20.fa" /> <conditional name="input_options"> |
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| diff -r b040adcfeefd -r 646e6943bcd2 MergeMutectStats.xml --- a/MergeMutectStats.xml Tue Jan 04 15:10:59 2022 +0000 +++ b/MergeMutectStats.xml Sun Oct 15 12:06:24 2023 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="mergemutectstats" name="gatk4 MergeMutectStats" version="@WRAPPER_VERSION@" profile="18.05"> +<tool id="mergemutectstats" name="gatk4 MergeMutectStats" version="@WRAPPER_VERSION@" profile="21.01"> <description>Merge the stats output by scatters of a single Mutect2 job</description> <macros> <import>macros.xml</import> |
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| diff -r b040adcfeefd -r 646e6943bcd2 Mutect2.xml --- a/Mutect2.xml Tue Jan 04 15:10:59 2022 +0000 +++ b/Mutect2.xml Sun Oct 15 12:06:24 2023 +0000 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="mutect2" name="gatk4 Mutect2" version="@WRAPPER_VERSION@" profile="18.05">\n+<tool id="mutect2" name="gatk4 Mutect2" version="@WRAPPER_VERSION@" profile="21.01">\n <description>- Call somatic SNVs and indels via local assembly of haplotypes</description>\n <macros>\n <import>macros.xml</import>\n@@ -25,12 +25,10 @@\n #set ref_flag=\'\'\n #end if\n \n- #if str($mode.mode_parameters) == \'tumor_only\'\n- ln -s $mode.tumor tumor.bam &&\n- ln -s $mode.tumor.metadata.bam_index tumor.bam.bai &&\n- #else\n- ln -s $mode.tumor tumor.bam &&\n- ln -s $mode.tumor.metadata.bam_index tumor.bam.bai &&\n+ ln -s $tumor tumor.bam &&\n+ ln -s $tumor.metadata.bam_index tumor.bam.bai &&\n+\n+ #if str($mode.mode_parameters) == \'somatic\'\n ln -s $mode.normal normal.bam &&\n ln -s $mode.normal.metadata.bam_index normal.bam.bai &&\n #end if\n@@ -288,16 +286,15 @@\n ]]>\n </command>\n <inputs>\n+ <param name="tumor" argument="--tumor" type="data" format="bam" label="Input Tumor BAM file" />\n <conditional name="mode">\n <param name="mode_parameters" type="select" label="Type of analysis">\n <option value="tumor_only">Tumor-only</option>\n <option value="somatic">Somatic</option>\n </param>\n <when value="tumor_only">\n- <param name="tumor" argument="--tumor" type="data" format="bam" label="Input Tumor BAM file" />\n </when>\n <when value="somatic">\n- <param name="tumor" argument="--tumor" type="data" format="bam" label="Input Tumor BAM file" />\n <param name="normal" argument="--normal" type="data" format="bam" label="Input Normal BAM file" />\n </when>\n </conditional>\n@@ -504,7 +501,6 @@\n <option value="STRICT">Strict</option>\n <option value="LENIENT">Lenient</option>\n </param>\n- <param name="sites_only_vcf_output" argument="--sites-only-vcf-output" type="boolean" truevalue="--sites-only-vcf-output" falsevalue="" optional="true" checked="false" label="Sites Only Vcf Output" help="If true, don&apos;t emit genotype fields when writing vcf file output."/>\n <param name="tumor_lod_to_emit" argument="--tumor-lod-to-emit" type="float" optional="true" value="3.0" label="Tumor Lod To Emit" help="LOD threshold to emit tumor variant to VCF."/>\n </when>\n <when value="no" />\n@@ -602,10 +598,10 @@\n </data>\n </outputs>\n <tests>\n- <test>\n+ <test expect_num_outputs="2">\n+ <param name="tumor" ftype="bam" value="Mutect2-in1.bam" />\n <conditional name="mode">\n <param name="mode_parameters" value="tumor_only"/>\n- <param name="tumor" ftype="bam" value="Mutect2-in1.bam" />\n </conditional>\n <param name="reference_sequence" ftype="fasta" value="reference.fa" />\n <param name="gzipped_output" value="false" />\n@@ -616,26 +612,25 @@\n <output name="output_vcf" file="Mutect2-out1.vcf" lines_diff="2" />\n <output name="output_vcf_stats" file="Mutect2-out1.vcf.stats" />\n </test>\n- <test>\n+ <test expect_num_outputs="2">\n+ <param name="tumor" ftype="bam" value="Mutect2-in2.bam" />\n <conditional name="mode">\n <param name="mode_parameters" value="tumor_only"/>\n- <param name="tumor" ftype="bam" value="Mutect2-in2.bam" />\n </conditional>\n <param name="reference_sequence" ftype="fasta" value="reference.fa" />\n <param name="gzipped_output" value="false" />\n <param name="reference_source_selector" value="history" />\n <param name="read_filter" value="AmbiguousBaseReadFilter,FirstOfPairReadF'..b'expect_num_outputs="2">\n+ <param name="tumor" ftype="bam" value="Mutect2-in3.bam" />\n <conditional name="mode">\n <param name="mode_parameters" value="tumor_only"/>\n- <param name="tumor" ftype="bam" value="Mutect2-in3.bam" />\n </conditional>\n <param name="reference_sequence" ftype="fasta" value="reference.fa" />\n <param name="gzipped_output" value="false" />\n@@ -647,10 +642,10 @@\n <param name="output_parameters" value="no" />\n <output name="output_vcf" file="Mutect2-out3.vcf" lines_diff="4" />\n </test>\n- <test>\n+ <test expect_num_outputs="2">\n+ <param name="tumor" ftype="bam" value="Mutect2-in4.bam" />\n <conditional name="mode">\n <param name="mode_parameters" value="tumor_only"/>\n- <param name="tumor" ftype="bam" value="Mutect2-in4.bam" />\n </conditional>\n <param name="reference_sequence" value="hg38"/>\n <param name="gzipped_output" value="false" />\n@@ -661,10 +656,10 @@\n <param name="output_parameters" value="no" />\n <output name="output_vcf" file="Mutect2-out4.vcf" lines_diff="2" />\n </test>\n- <test>\n+ <test expect_num_outputs="4">\n+ <param name="tumor" ftype="bam" value="Mutect2-in5.bam" />\n <conditional name="mode">\n <param name="mode_parameters" value="tumor_only"/>\n- <param name="tumor" ftype="bam" value="Mutect2-in5.bam" />\n </conditional>\n <param name="reference_sequence" ftype="fasta" value="reference.fa" />\n <param name="gzipped_output" value="false" />\n@@ -679,10 +674,10 @@\n <output name="assembly_region_out" file="Mutect2-out5-1.tabular" />\n <output name="bam_output" file="Mutect2-out5.bam" />\n </test>\n- <test>\n+ <test expect_num_outputs="2">\n+ <param name="tumor" ftype="bam" value="tumor.bam" />\n <conditional name="mode">\n <param name="mode_parameters" value="somatic"/>\n- <param name="tumor" ftype="bam" value="tumor.bam" />\n <param name="normal" ftype="bam" value="normal.bam" />\n </conditional>\n <param name="reference_sequence" ftype="fasta" value="chr20.fa" />\n@@ -697,16 +692,17 @@\n <help><![CDATA[Call somatic short variants via local assembly of haplotypes. Short\n variants include single nucleotide (SNV) and insertion and deletion\n (indel) variants. The caller combines the DREAM challenge-winning\n-somatic genotyping engine of the original MuTect (`Cibulskis et al.,\n-2013 <http://www.nature.com/nbt/journal/v31/n3/full/nbt.2514.html>`__)\n-with the assembly-based machinery of\n-`HaplotypeCaller <https://gatk.broadinstitute.org/hc/en-us/articles/360035531412-HaplotypeCaller-in-a-nutshell>`__.\n+somatic genotyping engine of the original MuTect_ (Cibulskis et al. 2013)\n+with the assembly-based machinery of HaplotypeCaller (see\n+gatk.broadinstitute.org/hc/en-us/articles/360035531412-HaplotypeCaller-in-a-nutshell).\n+\n+.. _MuTect: http://www.nature.com/nbt/journal/v31/n3/full/nbt.2514.html\n \n This tool is featured in the *Somatic Short Mutation calling Best\n-Practice Workflow*. See `this article <https://gatk.broadinstitute.org/hc/en-us/articles/360035531132>`__\n+Practice Workflow*. See gatk.broadinstitute.org/hc/en-us/articles/360035531132 \n for an overview of what traditional somatic calling entails, with usage examples. For the\n-latest pipeline scripts, see the `Mutect2 WDL scripts\n-directory <https://github.com/broadinstitute/gatk/tree/master/scripts/mutect2_wdl>`__.\n+latest pipeline scripts, see the Mutect2 WDL scripts directory (see\n+github.com/broadinstitute/gatk/tree/master/scripts/mutect2_wdl).\n Although we present the tool for somatic calling, it may apply to other\n contexts, such as mitochondrial variant calling.\n \n' |
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| diff -r b040adcfeefd -r 646e6943bcd2 macros.xml --- a/macros.xml Tue Jan 04 15:10:59 2022 +0000 +++ b/macros.xml Sun Oct 15 12:06:24 2023 +0000 |
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| @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> <token name="@VERSION@">4.1.7.0</token> - <token name="@WRAPPER_VERSION@">@VERSION@+galaxy2</token> + <token name="@WRAPPER_VERSION@">@VERSION@+galaxy3</token> <xml name="requirements"> <requirements> @@ -603,7 +603,7 @@ <data format="vcf_bgzip" name="output_vcf_bgzip" label="${tool.name} on ${on_string}: vcf_bgzip" from_work_dir="output.vcf.gz" > <filter>gzipped_output</filter> </data> - <data format="tabular" name="output_vcf_bgzip_stats" label="gatk vcf stats" from_work_dir="output.vcf.gz.stats" > + <data format="tabular" name="output_vcf_bgzip_stats" label="gatk vcf.gz stats" from_work_dir="output.vcf.gz.stats" > <filter>gzipped_output</filter> </data> </xml> |
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| diff -r b040adcfeefd -r 646e6943bcd2 macros_filtermutectcalls.xml --- a/macros_filtermutectcalls.xml Tue Jan 04 15:10:59 2022 +0000 +++ b/macros_filtermutectcalls.xml Sun Oct 15 12:06:24 2023 +0000 |
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| @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> <token name="@VERSION@">4.1.7.0</token> - <token name="@WRAPPER_VERSION@">@VERSION@+galaxy1</token> + <token name="@WRAPPER_VERSION@">@VERSION@+galaxy2</token> <xml name="requirements"> <requirements> |