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Merge pull request #6683 from khaled196/cnvkit_export
Add Cnvkit export subcomand tools to convert the CNVkit output into suitable formats
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| <tool id="cnvkit_export_bed" name="CNVkit Export BED" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> | ||
| <description>Converts the Segmented copy ratio data file (*.cns) file into BED file</description> | ||
| <macros> | ||
| <import>macros.xml</import> | ||
| </macros> | ||
| <expand macro="xrefs"/> | ||
| <expand macro="creators"/> | ||
| <expand macro="requirements"/> | ||
| <command detect_errors="exit_code"><![CDATA[ | ||
| ln -s '$input_segmented_file' ./sample.cns && | ||
| cnvkit.py export bed | ||
| ./sample.cns | ||
| $advanced_settings.label_genes | ||
| #if $advanced_settings.sample_id | ||
| --sample-id '$advanced_settings.sample_id' | ||
| #end if | ||
| #if $advanced_settings.ploidy | ||
| --ploidy $advanced_settings.ploidy | ||
| #end if | ||
| #if str($advanced_settings.sample_sex) and $advanced_settings.sample_sex != "" | ||
| --sample-sex '$advanced_settings.sample_sex' | ||
| #end if | ||
| $advanced_settings.male_reference | ||
| --output sample.cnv.bed | ||
| #if $advanced_settings.diploid_parx_genome | ||
| --diploid-parx-genome '$advanced_settings.diploid_parx_genome' | ||
| #end if | ||
| ]]></command> | ||
| <inputs> | ||
| <param name="input_segmented_file" type="data" format="tabular" label="Segmented Copy Ratio Data File (cns file)" help="" /> | ||
| <section name="advanced_settings" title="Advanced settings" expanded="false"> | ||
| <param argument="--label-genes" type="boolean" checked="false" truevalue="--label-genes" falsevalue="" label="Label Genes" help="Show gene names in the 4th column of the BED file" /> | ||
| <param argument="--sample-id" optional="true" type="text" label="Sample ID" value="" help="Sample name to write in the genotype field of the output VCF file" /> | ||
| <param argument="--ploidy" optional="true" type="integer" label="Ploidy" min="1" value="2" help="Ploidy of the sample cells. [Default: 2]" /> | ||
| <expand macro="sample_sex"/> | ||
| <param argument="--male-reference" type="boolean" checked="false" truevalue="--male-reference" falsevalue="" label="Male Reference" help="Assume inputs were normalized to a male reference" /> | ||
| <param argument="--diploid-parx-genome" optional="true" type="text" label="Diploid Parx Genome" value="" help="Considers the given human genome's PAR of chromosome X as autosomal. Example: 'grch38'" /> | ||
| </section> | ||
| </inputs> | ||
| <outputs> | ||
| <data name="CNVs_BED" format="bed" label="${tool.name} on ${on_string}: CNVs BED file" from_work_dir="sample.cnv.bed" /> | ||
| </outputs> | ||
| <tests> | ||
| <test expect_num_outputs="1"> | ||
| <param name="input_segmented_file" ftype="tabular" value="sample.cns" /> | ||
| <param name="sample_id" value="SampleID" /> | ||
| <param name="sample_sex" value="Female" /> | ||
| <output name="CNVs_BED" file="sample.cnv.bed" /> | ||
| </test> | ||
| </tests> | ||
| <help><![CDATA[ | ||
| Export the segmented copy number data (from a .cns file) to BED format. | ||
| The resulting BED file describes copy number gains and losses across each segment. | ||
| ]]></help> | ||
| <expand macro="citations" /> | ||
| </tool> | ||
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| <tool id="cnvkit_export_cdt" name="CNVkit Export CDT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> | ||
| <description>Convert log2 ratios to Clustered Data Table (CDT)</description> | ||
| <macros> | ||
| <import>macros.xml</import> | ||
| </macros> | ||
| <expand macro="xrefs"/> | ||
| <expand macro="creators"/> | ||
| <expand macro="requirements"/> | ||
| <command detect_errors="exit_code"><![CDATA[ | ||
| ln -s '$input_segmented_file' ./sample.cnr && | ||
| cnvkit.py export cdt | ||
| ./sample.cnr | ||
| --output sample.cnv.cdt | ||
| ]]></command> | ||
| <inputs> | ||
| <param name="input_segmented_file" type="data" format="tabular" label="Log2 Copy Ratio Data File" help="The output of the CNVkit 'fix' sub-command" /> | ||
| </inputs> | ||
| <outputs> | ||
| <data name="CNVs_cdt" format="cdt" label="${tool.name} on ${on_string}: CNVs Nexus Basic File" from_work_dir="sample.cnv.cdt" /> | ||
| </outputs> | ||
| <tests> | ||
| <test expect_num_outputs="1"> | ||
| <param name="input_segmented_file" ftype="tabular" value="sample.cnr" /> | ||
| <output name="CNVs_cdt" file="sample.cnv.cdt" /> | ||
| </test> | ||
| </tests> | ||
| <help><![CDATA[ | ||
| This tool converts CNVkit log2 copy ratio data to the CDT format, which is compatible with Java TreeView for visualisation and hierarchical clustering. | ||
| The conversion enables efficient exploration and interpretation of genomic copy number variations. | ||
| ]]></help> | ||
| <expand macro="citations" /> | ||
| </tool> |
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| <tool id="cnvkit_export_jtv" name="CNVkit Export JTV" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> | ||
| <description>Convert log2 ratios to Java TreeView's native format</description> | ||
| <macros> | ||
| <import>macros.xml</import> | ||
| </macros> | ||
| <expand macro="xrefs"/> | ||
| <expand macro="creators"/> | ||
| <expand macro="requirements"/> | ||
| <command detect_errors="exit_code"><![CDATA[ | ||
| ln -s '$input_segmented_file' ./sample.cnr && | ||
| cnvkit.py export jtv | ||
| ./sample.cnr | ||
| --output sample.cnv.jtv | ||
| ]]></command> | ||
| <inputs> | ||
| <param name="input_segmented_file" type="data" format="tabular" label="Log2 Copy Ratio Data File" help="The output of the CNVkit 'fix' sub-command" /> | ||
| </inputs> | ||
| <outputs> | ||
| <data name="CNVs_cdt" format="jtv" label="${tool.name} on ${on_string}: CNVs Nexus Basic File" from_work_dir="sample.cnv.jtv" /> | ||
| </outputs> | ||
| <tests> | ||
| <test expect_num_outputs="1"> | ||
| <param name="input_segmented_file" ftype="tabular" value="sample.cnr" /> | ||
| <output name="CNVs_cdt" file="sample.cnv.jtv" /> | ||
| </test> | ||
| </tests> | ||
| <help><![CDATA[ | ||
| This tool converts CNVkit log2 copy ratio data to Java TreeView's native format (.jtv), | ||
| enabling easy visualisation and clustering analysis with preserved settings for seamless data exploration. | ||
| ]]></help> | ||
| <expand macro="citations" /> | ||
| </tool> |
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| <tool id="cnvkit_export_nexus_basic" name="CNVkit Export Nexus Basics" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> | ||
| <description>Convert bin-level log2 ratios to Nexus Copy Number "basic" format</description> | ||
| <macros> | ||
| <import>macros.xml</import> | ||
| </macros> | ||
| <expand macro="xrefs"/> | ||
| <expand macro="creators"/> | ||
| <expand macro="requirements"/> | ||
| <command detect_errors="exit_code"><![CDATA[ | ||
| ln -s '$input_segmented_file' ./sample.cnr && | ||
| cnvkit.py export nexus-basic | ||
| ./sample.cnr | ||
| --output sample.cnv.tsv | ||
| ]]></command> | ||
| <inputs> | ||
| <param name="input_segmented_file" type="data" format="tabular" label="Log2 Copy Ratio Data File" help="The output of the CNVkit 'fix' sub-command" /> | ||
| </inputs> | ||
| <outputs> | ||
| <data name="CNVs_NexusBasic" format="tabular" label="${tool.name} on ${on_string}: CNVs Nexus Basic File" from_work_dir="sample.cnv.tsv" /> | ||
| </outputs> | ||
| <tests> | ||
| <test expect_num_outputs="1"> | ||
| <param name="input_segmented_file" ftype="tabular" value="sample.cnr" /> | ||
| <output name="CNVs_NexusBasic" file="sample.cnv.tsv" /> | ||
| </test> | ||
| </tests> | ||
| <help><![CDATA[ | ||
| This tool converts CNVkit log2 copy ratio data to the Nexus Copy Number "basic" format, | ||
| enabling efficient visualisation and analysis of genomic alterations in Nexus software. | ||
| This conversion facilitates downstream interpretation and integration with other genomic data. | ||
| ]]></help> | ||
| <expand macro="citations" /> | ||
| </tool> |
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| <tool id="cnvkit_export_nexus_ogt" name="CNVkit Export Nexus OGT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> | ||
| <description>Convert log2 ratios and b-allele freqs to Nexus "Custom-OGT" format</description> | ||
| <macros> | ||
| <import>macros.xml</import> | ||
| </macros> | ||
| <expand macro="xrefs"/> | ||
| <expand macro="creators"/> | ||
| <expand macro="requirements"/> | ||
| <command detect_errors="exit_code"><![CDATA[ | ||
| ln -s '$input_segmented_file' ./sample.cnr && | ||
| ln -s '$input_vcf' ./sample.vcf && | ||
| cnvkit.py export nexus-ogt | ||
| ./sample.cnr | ||
| ./sample.vcf | ||
| #if $advanced_settings.sample_id | ||
| --sample-id '$advanced_settings.sample_id' | ||
| #end if | ||
| #if $advanced_settings.normal_id | ||
| --normal-id '$advanced_settings.normal_id' | ||
| #end if | ||
| #if $advanced_settings.min_variant_depth | ||
| --min-variant-depth $advanced_settings.min_variant_depth | ||
| #end if | ||
| #if $advanced_settings.zygosity_freq | ||
| --zygosity-freq $advanced_settings.zygosity_freq | ||
| #end if | ||
| #if $advanced_settings.min_weight | ||
| --min-weight $advanced_settings.min_weight | ||
| #end if | ||
| --output sample.cnv.txt | ||
| ]]></command> | ||
| <inputs> | ||
| <param name="input_segmented_file" type="data" format="tabular" label="Segmented Copy Ratio Data File (cns file)" help="The output of the CNVkit 'fix' sub-command" /> | ||
| <param name="input_vcf" type="data" format="vcf" label="VCF of SNVs for the Same Sample" help="Used to calculate b-allele frequencies" /> | ||
| <section name="advanced_settings" title="Advanced settings" expanded="false"> | ||
| <param argument="--sample-id" optional="true" type="text" label="Sample ID" value="" help="Sample name to write in the genotype field of the output VCF file" /> | ||
| <param argument="--normal-id" optional="true" type="text" label="Normal Id" value="" help="Corresponding normal sample ID in the input VCF" /> | ||
| <param argument="--min-variant-depth" optional="true" type="integer" label="Minimum Variant Depth" min="1" value="20" help="Minimum read depth for a SNP in the VCF to be counted. [Default: 20]" /> | ||
| <param argument="--zygosity-freq" optional="true" type="float" label="Zygosity Frequency" min="0" value="0.25" help="Ignore VCF's genotypes (GT field) and instead infer zygosity from allele frequencies. [Default if used without a number: 0.25]" /> | ||
| <param argument="--min-weight" optional="true" type="float" label="Minimum Weight" min="0" max="1" value="0.0" help="Minimum weight (between 0 and 1) for a bin to be included in the output. [Default: 0.0]" /> | ||
| </section> | ||
| </inputs> | ||
| <outputs> | ||
| <data name="CNVs_NexusOGT" format="txt" label="${tool.name} on ${on_string}: CNVs theta file" from_work_dir="sample.cnv.txt" /> | ||
| </outputs> | ||
| <tests> | ||
| <test expect_num_outputs="1"> | ||
| <param name="input_segmented_file" ftype="tabular" value="sample.cnr" /> | ||
| <param name="input_vcf" ftype="vcf" value="sample.cnv.vcf" /> | ||
| <output name="CNVs_NexusOGT" file="sample.cnv.txt" /> | ||
| </test> | ||
| </tests> | ||
| <help><![CDATA[ | ||
| This tool converts CNVkit log2 copy ratios and B-allele frequencies to the Nexus "Custom-OGT" format, | ||
| enabling comprehensive CNV analysis with allelic imbalance insights. The output is compatible with Nexus software, | ||
| facilitating advanced genomic interpretation and integration with other datasets. | ||
| ]]></help> | ||
| <expand macro="citations" /> | ||
| </tool> | ||
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| <tool id="cnvkit_export_seg" name="CNVkit Export SEG" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> | ||
| <description>Convert segments to Segment (SEG) format</description> | ||
| <macros> | ||
| <import>macros.xml</import> | ||
| </macros> | ||
| <expand macro="xrefs"/> | ||
| <expand macro="creators"/> | ||
| <expand macro="requirements"/> | ||
| <command detect_errors="exit_code"><![CDATA[ | ||
| ln -s '$input_segmented_file' ./sample.cns && | ||
| cnvkit.py export seg | ||
| ./sample.cns | ||
| $advanced_settings.enumerate_chroms | ||
| --output sample.cnv.seg | ||
| ]]></command> | ||
| <inputs> | ||
| <param name="input_segmented_file" type="data" format="tabular" label="Segmented copy ratio data file (cns file)" help="" /> | ||
| <section name="advanced_settings" title="Advanced settings" expanded="false"> | ||
| <param argument="--enumerate-chroms" type="boolean" checked="false" truevalue="--enumerate-chroms" falsevalue="" label="Enumerate Chroms" help="Replace chromosome names with sequential integer IDs" /> | ||
| </section> | ||
| </inputs> | ||
| <outputs> | ||
| <data name="CNVs_SEG" format="seg" label="${tool.name} on ${on_string}: CNVs SEG file" from_work_dir="sample.cnv.seg" /> | ||
| </outputs> | ||
| <tests> | ||
| <test expect_num_outputs="1"> | ||
| <param name="input_segmented_file" ftype="tabular" value="sample.cns" /> | ||
| <output name="CNVs_SEG" file="sample.cnv.seg" /> | ||
| </test> | ||
| </tests> | ||
| <help><![CDATA[ | ||
| Export the segmented copy number data (from a .cns file) to the standard SEG format. | ||
| ]]></help> | ||
| <expand macro="citations" /> | ||
| </tool> |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1 @@ | ||
| chrM 848 16023 SampleID 1 |
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| GID CLID NAME GWEIGHT sample | ||
| AID ARRY000X | ||
| EWEIGHT 1 | ||
| GENE0X IMAGE:0 chrM:848-1121:- 1 -0.545691 | ||
| GENE1X IMAGE:1 chrM:1394-1667:- 1 0.488494 | ||
| GENE2X IMAGE:2 chrM:1667-1940:- 1 0.0200539 | ||
| GENE3X IMAGE:3 chrM:2212-2485:- 1 -0.234816 | ||
| GENE4X IMAGE:4 chrM:2485-2758:- 1 0.153636 | ||
| GENE5X IMAGE:5 chrM:2758-3031:- 1 -1.35597 | ||
| GENE6X IMAGE:6 chrM:3031-3304:- 1 0.385198 | ||
| GENE7X IMAGE:7 chrM:3306-3579:- 1 -1.37983 | ||
| GENE8X IMAGE:8 chrM:3579-3853:- 1 0.471839 | ||
| GENE9X IMAGE:9 chrM:3853-4126:- 1 0.444955 | ||
| GENE10X IMAGE:10 chrM:4126-4400:- 1 0.465611 | ||
| GENE11X IMAGE:11 chrM:4401-4695:- 1 -0.583114 | ||
| GENE12X IMAGE:12 chrM:4695-4990:- 1 1.13235 | ||
| GENE13X IMAGE:13 chrM:4990-5284:- 1 0.209867 | ||
| GENE14X IMAGE:14 chrM:5284-5579:- 1 1.18493 | ||
| GENE15X IMAGE:15 chrM:5586-5655:- 1 -21.0389 | ||
| GENE16X IMAGE:16 chrM:5656-5729:- 1 -19.8096 | ||
| GENE17X IMAGE:17 chrM:5760-5891:- 1 0.0 | ||
| GENE18X IMAGE:18 chrM:5903-6171:- 1 -0.0283011 | ||
| GENE19X IMAGE:19 chrM:6171-6440:- 1 -0.212606 | ||
| GENE20X IMAGE:20 chrM:6440-6708:- 1 -0.38297 | ||
| GENE21X IMAGE:21 chrM:6708-6977:- 1 -0.317296 | ||
| GENE22X IMAGE:22 chrM:6977-7245:- 1 -0.127011 | ||
| GENE23X IMAGE:23 chrM:7245-7514:- 1 0.72831 | ||
| GENE24X IMAGE:24 chrM:7517-7767:- 1 0.680162 | ||
| GENE25X IMAGE:25 chrM:7767-8018:- 1 -0.510836 | ||
| GENE26X IMAGE:26 chrM:8018-8269:- 1 -0.663743 | ||
| GENE27X IMAGE:27 chrM:8365-8630:- 1 0.28099 | ||
| GENE28X IMAGE:28 chrM:8630-8896:- 1 -0.154606 | ||
| GENE29X IMAGE:29 chrM:8896-9162:- 1 0.147562 | ||
| GENE30X IMAGE:30 chrM:9162-9427:- 1 0.937798 | ||
| GENE31X IMAGE:31 chrM:9693-9959:- 1 0.459741 | ||
| GENE32X IMAGE:32 chrM:9959-10224:- 1 -8.75948 | ||
| GENE33X IMAGE:33 chrM:10224-10490:- 1 0.509209 | ||
| GENE34X IMAGE:34 chrM:10490-10756:- 1 0.0655732 | ||
| GENE35X IMAGE:35 chrM:10756-11022:- 1 0.238204 | ||
| GENE36X IMAGE:36 chrM:11022-11287:- 1 1.20043 | ||
| GENE37X IMAGE:37 chrM:11287-11553:- 1 0.224804 | ||
| GENE38X IMAGE:38 chrM:11553-11819:- 1 -1.50066 | ||
| GENE39X IMAGE:39 chrM:11819-12084:- 1 0.0920864 | ||
| GENE40X IMAGE:40 chrM:12084-12350:- 1 -1.15941 | ||
| GENE41X IMAGE:41 chrM:12350-12616:- 1 -1.25242 | ||
| GENE42X IMAGE:42 chrM:12616-12882:- 1 -0.187246 | ||
| GENE43X IMAGE:43 chrM:12882-13147:- 1 0.419127 | ||
| GENE44X IMAGE:44 chrM:13147-13413:- 1 -0.730007 | ||
| GENE45X IMAGE:45 chrM:13413-13679:- 1 -0.0213761 | ||
| GENE46X IMAGE:46 chrM:13944-14210:- 1 -0.337011 | ||
| GENE47X IMAGE:47 chrM:14210-14476:- 1 -0.0427224 | ||
| GENE48X IMAGE:48 chrM:14746-14987:- 1 0.722701 | ||
| GENE49X IMAGE:49 chrM:14987-15228:- 1 -0.105067 | ||
| GENE50X IMAGE:50 chrM:15228-15470:- 1 -0.96567 | ||
| GENE51X IMAGE:51 chrM:15470-15711:- 1 0.576278 | ||
| GENE52X IMAGE:52 chrM:15711-15953:- 1 -1.38778 | ||
| GENE53X IMAGE:53 chrM:15955-16023:- 1 -21.1972 |
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| @@ -0,0 +1,2 @@ | ||
| #ID chrm start end tumorCount normalCount | ||
| start_1_848:end_1_16023 1 848 16023 14716 39185 |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,55 @@ | ||
| CloneID Name sample | ||
| IMAGE: chrM:848-1121:- -0.545691 | ||
| IMAGE: chrM:1394-1667:- 0.488494 | ||
| IMAGE: chrM:1667-1940:- 0.0200539 | ||
| IMAGE: chrM:2212-2485:- -0.234816 | ||
| IMAGE: chrM:2485-2758:- 0.153636 | ||
| IMAGE: chrM:2758-3031:- -1.35597 | ||
| IMAGE: chrM:3031-3304:- 0.385198 | ||
| IMAGE: chrM:3306-3579:- -1.37983 | ||
| IMAGE: chrM:3579-3853:- 0.471839 | ||
| IMAGE: chrM:3853-4126:- 0.444955 | ||
| IMAGE: chrM:4126-4400:- 0.465611 | ||
| IMAGE: chrM:4401-4695:- -0.583114 | ||
| IMAGE: chrM:4695-4990:- 1.13235 | ||
| IMAGE: chrM:4990-5284:- 0.209867 | ||
| IMAGE: chrM:5284-5579:- 1.18493 | ||
| IMAGE: chrM:5586-5655:- -21.0389 | ||
| IMAGE: chrM:5656-5729:- -19.8096 | ||
| IMAGE: chrM:5760-5891:- 0.0 | ||
| IMAGE: chrM:5903-6171:- -0.0283011 | ||
| IMAGE: chrM:6171-6440:- -0.212606 | ||
| IMAGE: chrM:6440-6708:- -0.38297 | ||
| IMAGE: chrM:6708-6977:- -0.317296 | ||
| IMAGE: chrM:6977-7245:- -0.127011 | ||
| IMAGE: chrM:7245-7514:- 0.72831 | ||
| IMAGE: chrM:7517-7767:- 0.680162 | ||
| IMAGE: chrM:7767-8018:- -0.510836 | ||
| IMAGE: chrM:8018-8269:- -0.663743 | ||
| IMAGE: chrM:8365-8630:- 0.28099 | ||
| IMAGE: chrM:8630-8896:- -0.154606 | ||
| IMAGE: chrM:8896-9162:- 0.147562 | ||
| IMAGE: chrM:9162-9427:- 0.937798 | ||
| IMAGE: chrM:9693-9959:- 0.459741 | ||
| IMAGE: chrM:9959-10224:- -8.75948 | ||
| IMAGE: chrM:10224-10490:- 0.509209 | ||
| IMAGE: chrM:10490-10756:- 0.0655732 | ||
| IMAGE: chrM:10756-11022:- 0.238204 | ||
| IMAGE: chrM:11022-11287:- 1.20043 | ||
| IMAGE: chrM:11287-11553:- 0.224804 | ||
| IMAGE: chrM:11553-11819:- -1.50066 | ||
| IMAGE: chrM:11819-12084:- 0.0920864 | ||
| IMAGE: chrM:12084-12350:- -1.15941 | ||
| IMAGE: chrM:12350-12616:- -1.25242 | ||
| IMAGE: chrM:12616-12882:- -0.187246 | ||
| IMAGE: chrM:12882-13147:- 0.419127 | ||
| IMAGE: chrM:13147-13413:- -0.730007 | ||
| IMAGE: chrM:13413-13679:- -0.0213761 | ||
| IMAGE: chrM:13944-14210:- -0.337011 | ||
| IMAGE: chrM:14210-14476:- -0.0427224 | ||
| IMAGE: chrM:14746-14987:- 0.722701 | ||
| IMAGE: chrM:14987-15228:- -0.105067 | ||
| IMAGE: chrM:15228-15470:- -0.96567 | ||
| IMAGE: chrM:15470-15711:- 0.576278 | ||
| IMAGE: chrM:15711-15953:- -1.38778 | ||
| IMAGE: chrM:15955-16023:- -21.1972 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,2 @@ | ||
| ID chrom loc.start loc.end num.mark seg.mean | ||
| sample chrM 849 16023 54 -1.39012 |
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