| Previous changeset 9:98c37a5d67f4 (2018-02-07) Next changeset 11:15b23cdde685 (2018-04-20) |
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Commit message:
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac |
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modified:
AnnotationStatsFromVCF/annotationStatsFromVCF_wrapper.xml GetHaplotypesFromPhasedVCF/getHaplotypesFromPhasedVCF.xml MDSplot/mdsplot.xml PedToFasta/pedToFasta.xml README.txt Rooting/rooting.xml SNP_density/calculateSlidingWindowsSNPdensitiesFromVCF_wrapper.xml VCF2Hapmap/vcf2FastaAndHapmap.xml check_gwas_inputs/CheckGWASInputs.xml egglib/CalculateDiversityIndexes.xml hapmap2mlmm/HapmapToMLMMFiles.pl hapmap2mlmm/HapmapToMLMMFiles.xml hapmap2mlmm/transpose.awk ped2bed/ped2bed.xml test-data/MDSplot-output.mds_plot.txt test-data/ped2bed-result.bim |
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added:
test-data/MDSplot-output.mds_plot.txt_old test-data/annotationStatsFromVCF.effect test-data/annotationStatsFromVCF.location test-data/annotationStatsFromVCF.txt test-data/annotationStatsFromVCF.vcf test-data/ped2bed-result.bim_old |
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removed:
AnnotationStatsFromVCF/annotationStatsFromVCF AnnotationStatsFromVCF/annotationStatsFromVCF.effect AnnotationStatsFromVCF/annotationStatsFromVCF.location tool_dependencies.xml |
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| diff -r 98c37a5d67f4 -r c6640c49fd01 AnnotationStatsFromVCF/annotationStatsFromVCF --- a/AnnotationStatsFromVCF/annotationStatsFromVCF Wed Feb 07 22:08:47 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,10 +0,0 @@ -Chrom Bin dN/dS ratio -chr1 20000 0.606060606060606 -chr1 40000 0 -chr1 60000 5.5 -chr1 80000 0.363636363636364 -chr1 100000 0.764705882352941 -chr1 120000 1 -chr1 140000 1.11111111111111 -chr1 160000 7 -chr1 180000 2 |
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| diff -r 98c37a5d67f4 -r c6640c49fd01 AnnotationStatsFromVCF/annotationStatsFromVCF.effect --- a/AnnotationStatsFromVCF/annotationStatsFromVCF.effect Wed Feb 07 22:08:47 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,3 +0,0 @@ -Intron 960 Intron:960 -UTR 281 UTR:281 -Exon 3248 Synonym:124 Non-syn:120 |
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| diff -r 98c37a5d67f4 -r c6640c49fd01 AnnotationStatsFromVCF/annotationStatsFromVCF.location --- a/AnnotationStatsFromVCF/annotationStatsFromVCF.location Wed Feb 07 22:08:47 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,2 +0,0 @@ -Intergenic 466 Intergenic:466 -Genic 4489 Exon:3248 Intron:960 UTR:281 |
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| diff -r 98c37a5d67f4 -r c6640c49fd01 AnnotationStatsFromVCF/annotationStatsFromVCF_wrapper.xml --- a/AnnotationStatsFromVCF/annotationStatsFromVCF_wrapper.xml Wed Feb 07 22:08:47 2018 -0500 +++ b/AnnotationStatsFromVCF/annotationStatsFromVCF_wrapper.xml Mon Apr 16 09:00:24 2018 -0400 |
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| @@ -1,8 +1,9 @@ -<tool id="annotationStatsFromVCF" name="Get annotation statistics" version="1.0.0"> - <description> from VCF file </description> +<tool id="annotationStatsFromVCF" name="Get VCF annotation statistics" version="2.0.0"> + <description>Get annotation fromi a VCF file annotated by snpeff</description> <requirements> <requirement type="binary">perl</requirement> - <requirement type="package" version="0.1.12b">vcftools</requirement> + <requirement type="package" version="1.6.924">perl-bioperl</requirement> + <requirement type="package" version="0.1.14">vcftools</requirement> </requirements> <stdio> <exit_code range="1:" /> @@ -12,19 +13,21 @@ </command> <inputs> <param type="data" name="input" format="vcf" label="VCF file" /> - <param type="text" name="output_label" label="Output_label" value='VCF_stats' /> + <param name="step" type="integer" value="200000" label="Step" help="Step in bp"/> + <param type="text" name="output_label" label="Output_label" value='VCF_stats' optional='false' /> </inputs> <outputs> - <data name="output_count" format="txt" label="${output_label}."/> - <data name="output_stats_effect" format="txt" label="${output_label}."/> - <data name="output_stats_location" format="txt" label="${output_label}."/> + <data name="output_count" format="txt" label="${output_label}"/> + <data name="output_stats_effect" format="txt" label="${output_label}.effect"/> + <data name="output_stats_location" format="txt" label="${output_label}.location"/> </outputs> <tests> <test> - <param name="input" value="vcf2fastaAndHapmap-sample.vcf"/> - <output name="output_count" file="vcf2fastaAndHapmap-sample.vcf"/> - <output name="output_stats_effect" file="vcf2fastaAndHapmap-sample.vcf"/> - <output name="output_stats_location" file="vcf2fastaAndHapmap-sample.vcf"/> + <param name="input" value="annotationStatsFromVCF.vcf"/> + <param name="step" value="50000"/> + <output name="output_count" file="annotationStatsFromVCF.txt"/> + <output name="output_stats_effect" file="annotationStatsFromVCF.effect"/> + <output name="output_stats_location" file="annotationStatsFromVCF.location"/> </test> </tests> <help><![CDATA[ @@ -37,69 +40,61 @@ .. class:: infomark -**Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique. +**Galaxy integration** Provided by Southgreen & Andres Gwendoline (Institut Français de Bioinformatique) & Marcon Valentin (IFB & INRA) .. class:: infomark -**Support** For any questions, please send an e-mail to support.abims@sb-roscoff.fr +**Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr --------------------------------------------------- -============================== -Get Haplotypes From Phased VCF -============================== +========================= +Get annotation statistics +========================= ----------- Description ----------- - | Get Haplotype from phased VCF - ------------------ -Workflow position ------------------ - -**Upstream tool** + | Get annotation statistics from VCF -=============== ========================== ======= -Name output file(s) format -=============== ========================== ======= -Beagle Phased VCF file VCF -=============== ========================== ======= - +------------ +Dependencies +------------ +VCFtools + vcftools_ 0.1.14, Conda version +Bioperl + perl-bioperl_ 1.6.924, Conda version -**Downstream tool** - -=============== ========================== =========== -Name input file(s) format -=============== ========================== =========== -=============== ========================== =========== - +.. _vcftools: https://anaconda.org/bioconda/vcftools +.. _perl-bioperl: https://anaconda.org/bioconda/perl-bioperl ---------- Input file ---------- VCF file - Phased VCF file + VCF file ---------- Parameters ---------- -Output file basename - Prefix for the output VCF file +Step + Step in bp + +Output label + Prefix for the ouput files ------------ Output files ------------ +Output_name -Text file - File describing haplotypes +Output_name.effect file -Fasta file - Fasta file with haplotypes +Output_name.location file --------------------------------------------------- @@ -107,8 +102,8 @@ Working example --------------- -Input files -=========== +Input file +========== VCF file --------- @@ -126,33 +121,41 @@ Parameters ========== -Output name -> haplotypes +Step -> 50000 +Output label -> VCF_stats Output files ============ -haplotypes.distinct_haplotypes.txt +VCF_stats ---------------------------------- :: - ===Chr10=== - haplo1:2:CIRAD403_1,CIRAD403_2, - TTTAAGAAATTCCTATATAGGTCTTCTAAGCGTATCTATTAACAT - haplo2:2:MAHAE_1,MAHAE_2, - TAAATCTTGGTGCTGATCTGATATTTAATGCGT + Chrom Bin dN/dS ratio + chr1 50000 0.791666666666667 + chr1 100000 0.981132075471698 + chr1 150000 2.08333333333333 -haplotypes.haplo.fas +VCF_stats.effect -------------------- :: - >Chr10_AZUCENA_1 - TTTAAGAAATTCCTATATAGGTCTTCTAAGCGTATCTATTAACAT - >Chr10_AZUCENA_2 - TAAATCTTGGTGCTGATCTGATATTTAATGCGT + Intron 960 Intron:960 + UTR 281 UTR:281 + Exon 3248 Synonym:124 Non-syn:120 + +VCF_stats.location +-------------------- + +:: + + Intergenic 466 Intergenic:466 + Genic 4489 Exon:3248 Intron:960 UTR:281 + ]]></help> <citations> |
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| diff -r 98c37a5d67f4 -r c6640c49fd01 GetHaplotypesFromPhasedVCF/getHaplotypesFromPhasedVCF.xml --- a/GetHaplotypesFromPhasedVCF/getHaplotypesFromPhasedVCF.xml Wed Feb 07 22:08:47 2018 -0500 +++ b/GetHaplotypesFromPhasedVCF/getHaplotypesFromPhasedVCF.xml Mon Apr 16 09:00:24 2018 -0400 |
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| @@ -1,4 +1,6 @@ -<tool id="getHaplotypesFromPhasedVCF" name="Get Haplotypes From Phased VCF" version="1.0.0"> +<tool id="getHaplotypesFromPhasedVCF" name="Get Haplotypes From Phased VCF" version="2.0.0"> + <description>Get Haplotypes From Phased VCF</description> + <requirements> <requirement type="binary">perl</requirement> </requirements> @@ -19,8 +21,8 @@ <tests> <test> <param name="input" value="getHaplotypesFromPhasedVCF-input.vcf"/> - <output name="output_distinct" file="getHaplotypesFromPhasedVCF-result.distinct_haplotypes.txt"/> - <output name="output_haplo" file="getHaplotypesFromPhasedVCF-result.haplo.fas"/> + <output name="output_distinct" file="getHaplotypesFromPhasedVCF-result.distinct_haplotypes.txt" compare="sim_size" delta="0"/> + <output name="output_haplo" file="getHaplotypesFromPhasedVCF-result.haplo.fas" compare="sim_size" delta="0"/> </test> </tests> <help><![CDATA[ @@ -33,11 +35,11 @@ .. class:: infomark -**Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique. +**Galaxy integration** Provided by Southgreen & Andres Gwendoline (Institut Français de Bioinformatique) & Marcon Valentin (IFB & INRA) .. class:: infomark -**Support** For any questions, please send an e-mail to support.abims@sb-roscoff.fr +**Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr --------------------------------------------------- @@ -51,27 +53,6 @@ | Get Haplotype from phased VCF ------------------ -Workflow position ------------------ - -**Upstream tool** - -=============== ========================== ======= -Name output file(s) format -=============== ========================== ======= -Beagle Phased VCF file VCF -=============== ========================== ======= - - -**Downstream tool** - -=============== ========================== =========== -Name input file(s) format -=============== ========================== =========== -=============== ========================== =========== - - ---------- Input file ---------- @@ -79,9 +60,9 @@ VCF file Phased VCF file ----------- -Parameters ----------- +--------- +Parameter +--------- Output file basename Prefix for the output VCF file @@ -103,8 +84,8 @@ Working example --------------- -Input files -=========== +Input file +========== VCF file --------- @@ -119,8 +100,8 @@ Chr1 4299 . G A . PASS AR2=1;DR2=1;AF=0.168 GT:DS:GP 0|0:0:1,0,0 -Parameters -========== +Parameter +========= Output name -> haplotypes |
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| diff -r 98c37a5d67f4 -r c6640c49fd01 MDSplot/mdsplot.xml --- a/MDSplot/mdsplot.xml Wed Feb 07 22:08:47 2018 -0500 +++ b/MDSplot/mdsplot.xml Mon Apr 16 09:00:24 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="sniplay_mdsplot" name="MDS plot" version="1.2.0"> +<tool id="sniplay_mdsplot" name="PLINK: MDS plot" version="2.0.0"> <!-- [REQUIRED] Tool description displayed after the tool name --> <description> IBS matrix / multi-dimensional scaling</description> @@ -39,58 +39,44 @@ <!-- [REQUIRED] Output files --> <outputs> - <data name="fileout_matrix" type="data" format="txt" label="${fileout_label}.ibs_matrix.txt" /> - <data name="fileout_plot" type="data" format="txt" label="${fileout_label}.mds_plot.txt" /> - <data name="fileout_log" type="data" format="txt" label="${fileout_label}.log" /> + <data name="fileout_matrix" format="txt" label="${fileout_label}.ibs_matrix.txt" /> + <data name="fileout_plot" format="txt" label="${fileout_label}.mds_plot.txt" /> + <data name="fileout_log" format="txt" label="${fileout_label}.log" /> </outputs> <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> <tests> <!-- [HELP] Test files have to be in the ~/test-data directory --> - <test> <param name="fileped" value="MDSplot-input.ped" /> <param name="filemap" value="MDSplot-input.map" /> <output name="fileout_matrix" file="MDSplot-output.ibs_matrix.txt" /> <output name="fileout_plot" file="MDSplot-output.mds_plot.txt" /> </test> - - <!-- [HELP] Multiple tests can be defined with different parameters --> -<!-- - <test> - </test> ---> </tests> <!-- [OPTIONAL] Help displayed in Galaxy --> - <help> + <help><![CDATA[ .. class:: infomark -**Authors** plink_ +MDS plot is done with PLINK. +**Authors** PLINK: Shaun Purcell (https://www.cog-genomics.org/plink) -.. _plink: http://pngu.mgh.harvard.edu/purcell/plink/ - - | "PLINK: a toolset for whole-genome association and population-based linkage analysis.", **Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ, Sham PC.**, American Journal of Human Genetics, 81, 2007. - + | **Please cite** "PLINK: a toolset for whole-genome association and population-based linkage analysis.", **Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ, Sham PC.**, American Journal of Human Genetics, 81, 2007. + | **Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1). .. class:: infomark -**Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique. +**Galaxy integration** Provided by Southgreen & Andres Gwendoline (Institut Français de Bioinformatique) & Marcon Valentin (IFB & INRA) .. class:: infomark -**Support** For any questions about Galaxy integration, please send an e-mail to support.abims@sb-roscoff.fr - -.. class:: infomark - -**Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1). +**Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr --------------------------------------------------- - - ======== MDS plot ======== @@ -99,36 +85,41 @@ Description ----------- - Compute an IBS matrix and a multi-dimensional scaling. - - ------------------ -Workflow position ------------------ - -**Upstream tool** - -=============== ========================== =============== -Name output file(s) format -=============== ========================== =============== -VCFtools Filter PED and MAP file tabular and MAP -=============== ========================== =============== + | MDS plot compute an IBS matrix and a multi-dimensional scaling. + | + | MDS plot is done with PLINK + | PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. + | For further informations, please visit the PLINK website_. ----------- -Input file ----------- +.. _website: https://www.cog-genomics.org/plink + +------------ +Dependencies +------------ +PLINK + plink_ 1.90b4, Conda version +Bioperl + perl-bioperl_ 1.6.924, Conda version + +.. _plink: https://anaconda.org/bioconda/plink +.. _perl-bioperl: https://anaconda.org/bioconda/perl-bioperl + +----------- +Input files +----------- PED file + PED file usually from VCF tools MAP file 4 columns tabular file: chromosome, snp id, genetic distance, bp position ----------- -Parameters ----------- +--------- +Parameter +--------- Output name Output base name for the ouput files @@ -146,12 +137,6 @@ Output_name.log Log file - ------------- -Dependencies ------------- -plink - version 1.07 --------------------------------------------------- @@ -184,8 +169,8 @@ -Parameters -========== +Parameter +========= Output name -> densities @@ -213,7 +198,7 @@ - </help> + ]]></help> <citations> <!-- [HELP] As DOI or BibTex entry --> <citation type="bibtex">@article{Dereeper03062015, |
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| diff -r 98c37a5d67f4 -r c6640c49fd01 PedToFasta/pedToFasta.xml --- a/PedToFasta/pedToFasta.xml Wed Feb 07 22:08:47 2018 -0500 +++ b/PedToFasta/pedToFasta.xml Mon Apr 16 09:00:24 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="sniplay_pedToFasta" name="Ped2Fasta" version="1.0.0"> +<tool id="sniplay_pedToFasta" name="Ped2Fasta" version="2.0.0"> <!-- [REQUIRED] Tool description displayed after the tool name --> <description> Convert PED file to Fasta File </description> @@ -34,7 +34,7 @@ <!-- [REQUIRED] Output files --> <outputs> - <data name="fileout" type="data" format="fasta" label="${fileout_label}.fa" /> + <data name="fileout" format="fasta" label="${fileout_label}.fa" /> </outputs> <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> @@ -47,7 +47,7 @@ </tests> <!-- [OPTIONAL] Help displayed in Galaxy --> - <help> + <help><![CDATA[ .. class:: infomark @@ -57,11 +57,11 @@ .. class:: infomark -**Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique. +**Galaxy integration** Provided by Southgreen & Andres Gwendoline (Institut Français de Bioinformatique) & Marcon Valentin (IFB & INRA) .. class:: infomark -**Support** For any questions, please send an e-mail to support.abims@sb-roscoff.fr +**Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr --------------------------------------------------- @@ -73,29 +73,7 @@ Description ----------- - Convert PED file to Fasta File - ------------------ -Workflow position ------------------ - -**Upstream tool** - -=============== ========================== ======= -Name output file(s) format -=============== ========================== ======= -VCFtools Filter VCF file VCF -=============== ========================== ======= - - -**Downstream tool** - -=========== ========================== ======= -Name input file(s) format -=========== ========================== ======= -Readseq Fasta alignment fasta -=========== ========================== ======= - + | Convert PED file to Fasta File ---------- Input file @@ -104,16 +82,16 @@ PED file PED file usually from VCF tools ----------- -Parameters ----------- +--------- +Parameter +--------- Output file name Prefix for the output fasta file ------------- -Output files ------------- +----------- +Output file +----------- Fasta file PED file conversion @@ -124,8 +102,8 @@ Working example --------------- -Input files -=========== +Input file +========== PED file --------- @@ -134,13 +112,13 @@ CATB1 CATB1 0 0 0 0 C T T A C T A T A T A G G A -Parameters -========== +Parameter +========= Output name -> pedFile -Output files -============ +Output file +=========== pedFile.fa ---------- @@ -148,9 +126,7 @@ :: YWYWWRRSYYMKRRKMYRKSRKYRYRYKRKRSKKSYRWYSYRRYRRRWYWWYYWRRYRSRWSSRMYRRKSWMSKWRRYYWMYKYWRSYRWRYMWYYYMKYKYWRYRYRY - - - </help> + ]]></help> <citations> <!-- [HELP] As DOI or BibTex entry --> |
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| diff -r 98c37a5d67f4 -r c6640c49fd01 README.txt --- a/README.txt Wed Feb 07 22:08:47 2018 -0500 +++ b/README.txt Mon Apr 16 09:00:24 2018 -0400 |
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| @@ -1,6 +1,6 @@ ################################################################### In this repository you will find tools adapted for SNiPlay workflow. But not all required tools for running the workflow. -If you want to run the entire SNiPlay workflow, please search "sniplay2_complete_workflow". +If you want to run the entire SNiPlay workflow, please search for the complete_workflow. ################################################################### |
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| diff -r 98c37a5d67f4 -r c6640c49fd01 Rooting/rooting.xml --- a/Rooting/rooting.xml Wed Feb 07 22:08:47 2018 -0500 +++ b/Rooting/rooting.xml Mon Apr 16 09:00:24 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="sniplay_rooting" name="Rooting" version="1.0.3"> +<tool id="sniplay_rooting" name="Rooting" version="2.0.0"> <!-- [REQUIRED] Tool description displayed after the tool name --> <description> Midpoint rooting of newick tree </description> @@ -6,7 +6,7 @@ <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> <requirements> <requirement type="binary">perl</requirement> - <requirement type="package">Rootings_54.jar</requirement> + <requirement type="package" version="1.6.924">perl-bioperl</requirement> </requirements> <!-- [STRONGLY RECOMMANDED] Exit code rules --> @@ -30,58 +30,44 @@ <!-- [REQUIRED] Input files and tool parameters --> <inputs> - <param name="filein" type="data" format="nwk" optional="false" label="Fasta alignment input" /> + <param name="filein" type="data" format="nwk,nhx" optional="false" label="Newick tree input" /> <param name="fileout_label" type="text" value="out tree" label="Output name" help="Output name for files" /> </inputs> <!-- [REQUIRED] Output files --> <outputs> - <data name="fileout_log" type="data" format="txt" label="${fileout_label}.log" /> - <data name="fileout" type="data" format="nwk" label="${fileout_label}" /> + <data name="fileout_log" format="txt" label="${fileout_label}.log" /> + <data name="fileout" format="nwk,nhx" label="${fileout_label}" /> </outputs> <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> <tests> <!-- [HELP] Test files have to be in the ~/test-data directory --> - <test> <param name="filein" value="rooting-newick" /> <output name="fileout" file="rooting-out_tree" /> </test> - - <!-- [HELP] Multiple tests can be defined with different parameters --> -<!-- - <test> - </test> ---> </tests> <!-- [OPTIONAL] Help displayed in Galaxy --> - <help> - + <help><![CDATA[ .. class:: infomark **Authors** Jean-François Dufayard, CIRAD, South Green platform - -.. class:: infomark - -**Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique. + | **Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1). .. class:: infomark -**Support** For any questions about Galaxy integration, please send an e-mail to support.abims@sb-roscoff.fr +**Galaxy integration** Provided by Southgreen & Andres Gwendoline (Institut Français de Bioinformatique) & Marcon Valentin (IFB & INRA) .. class:: infomark -**Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1). +**Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr --------------------------------------------------- - - - ======= Rooting ======= @@ -92,27 +78,20 @@ Compute a midpoint newick rooted tree. - ------------------ -Workflow position ------------------ - -**Upstream tool** +------------ +Dependencies +------------ +Bioperl + perl-bioperl_ 1.6.924, Conda version -=========== ========================== ======= -Name output file(s) format -=========== ========================== ======= -fastme Newick tree Newick -=========== ========================== ======= - - +.. _perl-bioperl: https://anaconda.org/bioconda/perl-bioperl ---------- Input file ---------- Newick file - + Input tree file ---------- Parameters @@ -144,8 +123,8 @@ Working example --------------- -Input files -=========== +Input file +========== Newick file ----------- @@ -155,14 +134,14 @@ (((((((((((((((((((((((((GOGOLEMPUK:0.001198,GOGOLEMPAK:0.002128):0.030378,TREMBESE:0.013258):0.055246,(((JIMBRUKJOL:0.045219,KETANKONIR:0.035298):0.006267, ... -Parameters -========== +Parameter +========= Output name -> out tree -Output files -============ +Output file +=========== out tree -------- @@ -172,7 +151,7 @@ (ref:0.9384270000000001,(((((((((((((((((((((((((((((((((((IRAT257:0.044246,IRAT112:0.023421):0.009006,ARAGUAIA:0.093061):0.004662... - </help> + ]]></help> <citations> <!-- [HELP] As DOI or BibTex entry --> <citation type="bibtex">@article{Dereeper03062015, |
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| diff -r 98c37a5d67f4 -r c6640c49fd01 SNP_density/calculateSlidingWindowsSNPdensitiesFromVCF_wrapper.xml --- a/SNP_density/calculateSlidingWindowsSNPdensitiesFromVCF_wrapper.xml Wed Feb 07 22:08:47 2018 -0500 +++ b/SNP_density/calculateSlidingWindowsSNPdensitiesFromVCF_wrapper.xml Mon Apr 16 09:00:24 2018 -0400 |
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| @@ -3,7 +3,6 @@ <!-- [REQUIRED] Tool description displayed after the tool name --> <description> Calculate SNP densities along chromosome from a VCF input</description> - <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> <requirements> <requirement type="binary">perl</requirement> @@ -58,7 +57,7 @@ </tests> <!-- [OPTIONAL] Help displayed in Galaxy --> - <help> + <help><![CDATA[ .. class:: infomark @@ -66,19 +65,16 @@ | **Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1). +.. class:: infomark + +**Galaxy integration** Provided by Southgreen & Andres Gwendoline (Institut Français de Bioinformatique) & Marcon Valentin (IFB & INRA) .. class:: infomark -**Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique. - -.. class:: infomark - -**Support** For any questions about Galaxy integration, please send an e-mail to support.abims@sb-roscoff.fr +**Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr --------------------------------------------------- - - ============= SNP densities ============= @@ -89,18 +85,19 @@ Calculate SNP densities along chromosome from a VCF file - ------------------ -Workflow position ------------------ +------------ +Dependencies +------------ +VCFtools + vcftools_ 0.1.14, Conda version +VCFtools Perl libraries + perl-vcftools-vcf_ 0.1.14, Conda version +Bioperl + perl-bioperl_ 1.6.924, Conda version -**Upstream tool** - -=============== ====================== =========== -Name output file(s) format -=============== ====================== =========== -=============== ====================== =========== - +.. _vcftools: https://anaconda.org/bioconda/vcftools +.. _perl-vcftools-vcf: https://anaconda.org/bioconda/perl-vcftools-vcf +.. _perl-bioperl: https://anaconda.org/bioconda/perl-bioperl ---------- Input file @@ -109,7 +106,6 @@ VCF file File with SNPs - ---------- Parameters ---------- @@ -120,7 +116,6 @@ Output name Output base name for the two ouput files - ------------ Output files ------------ @@ -130,7 +125,6 @@ Output_name.by_sample Tabular file with SNP density for each sample - --------------------------------------------------- @@ -138,8 +132,8 @@ Working example --------------- -Input files -=========== +Input file +========== vcf file ----------- @@ -187,7 +181,7 @@ chr1 43 43 40 chr1 139 167 141 - </help> + ]]></help> <citations> <!-- [HELP] As DOI or BibTex entry --> <citation type="bibtex">@article{Dereeper03062015, |
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| diff -r 98c37a5d67f4 -r c6640c49fd01 VCF2Hapmap/vcf2FastaAndHapmap.xml --- a/VCF2Hapmap/vcf2FastaAndHapmap.xml Wed Feb 07 22:08:47 2018 -0500 +++ b/VCF2Hapmap/vcf2FastaAndHapmap.xml Mon Apr 16 09:00:24 2018 -0400 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="sniplay_vcf2fastaandhapmap" name="VCF to Hapmap" version="1.1.0"> +<tool id="sniplay_vcf2fastaandhapmap" name="VCF to Hapmap" version="2.0.0"> <!-- [REQUIRED] Tool description displayed after the tool name --> <description> Convert VCF to Hapmap </description> @@ -86,12 +86,12 @@ <param name="filegff" value="vcf2fastaAndHapmap-reference.gff" /> <output name="fileout" file="vcf2fastaAndHapmap-result3.hapmap" /> <output name="fileout_seq" file="vcf2fastaAndHapmap-result3.flanking.txt" /> - <output name="fileout_fa1" file="vcf2fastaAndHapmap-result3.gene_alignment.fas" /> + <output name="fileout_fa1" file="vcf2fastaAndHapmap-result3.gene_alignment.fas" compare="sim_size" delta="0"/> </test> </tests> <!-- [OPTIONAL] Help displayed in Galaxy --> - <help> + <help><![CDATA[ .. class:: infomark @@ -102,11 +102,11 @@ .. class:: infomark -**Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique. +**Galaxy integration** Provided by Southgreen & Andres Gwendoline (Institut Français de Bioinformatique) & Marcon Valentin (IFB & INRA) .. class:: infomark -**Support** For any questions, please send an e-mail to support.abims@sb-roscoff.fr +**Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr --------------------------------------------------- @@ -121,28 +121,6 @@ | Convert VCF to Hapmap. Additionnaly it creates flanking sequences of variants if fasta reference is provided. | Furthermore it also creates fasta alignment of genes if GFF annotation is provided ------------------ -Workflow position ------------------ - -**Upstream tool** - -=============== ========================== ======= -Name output file(s) format -=============== ========================== ======= -VCFtools Filter VCF file VCF -=============== ========================== ======= - - -**Downstream tool** - -=============== ========================== =========== -Name input file(s) format -=============== ========================== =========== -SNP density Hapmap file tabular -=============== ========================== =========== - - ---------- Input file ---------- @@ -237,7 +215,7 @@ TCCTCAAACTTTCTTCAGCGCCTATGAATACAGCGTGCTATAGTTACGTGGGGCGTTT - </help> + ]]></help> <citations> <!-- [HELP] As DOI or BibTex entry --> |
| b |
| diff -r 98c37a5d67f4 -r c6640c49fd01 check_gwas_inputs/CheckGWASInputs.xml --- a/check_gwas_inputs/CheckGWASInputs.xml Wed Feb 07 22:08:47 2018 -0500 +++ b/check_gwas_inputs/CheckGWASInputs.xml Mon Apr 16 09:00:24 2018 -0400 |
| [ |
| @@ -1,5 +1,5 @@ -<tool id="check_GWAS_inputs" name="Check GWAS Inputs" version="1.1"> - <description>checks concordance between input files for GWAS analysis</description> +<tool id="check_GWAS_inputs" name="Check GWAS Inputs" version="2.0.0"> + <description>Checks concordance between input files for GWAS analysis</description> <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> <requirements> @@ -32,15 +32,12 @@ <param name="hapmap" value="gwas-hapmap" /> <param name="trait" value="gwas-trait" /> <output name="out_hapmap" file="gwas-result.hapmap" /> - <output name="out_trait" file="gwas-result.trait" /> + <output name="out_trait" file="gwas-result.trait" compare="sim_size" delta="0"/> <output name="stats" file="gwas-result.stats" /> </test> </tests> - <help> + <help><![CDATA[ - <![CDATA[ - - .. class:: infomark **Authors** South Green @@ -49,11 +46,14 @@ .. class:: infomark -**Galaxy integration** South Green. +**Galaxy integration** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA) + +.. class:: infomark + +**Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr --------------------------------------------------- - =============== CheckGWASInputs =============== @@ -64,25 +64,9 @@ | CheckGWASInputs checks concordance between input files for GWAS analysis. - ------------------ -Workflow position ------------------ - -**Upstream tool** - -=============== ====================== =========== -Name output file(s) format -=============== ====================== =========== -VCF to Hapmap Hapmap file hapmap -=============== ====================== =========== - - - - ----------- -Input file ----------- +----------- +Input files +----------- Hapmap file Allelic file in Hapmap format @@ -171,10 +155,7 @@ Modified markers: Difference in variation: 0 - ]]> - - - </help> + ]]></help> <citations> <!-- [HELP] As DOI or BibTex entry --> <citation type="bibtex">@article{Dereeper03062015, |
| b |
| diff -r 98c37a5d67f4 -r c6640c49fd01 egglib/CalculateDiversityIndexes.xml --- a/egglib/CalculateDiversityIndexes.xml Wed Feb 07 22:08:47 2018 -0500 +++ b/egglib/CalculateDiversityIndexes.xml Mon Apr 16 09:00:24 2018 -0400 |
| [ |
| @@ -1,5 +1,11 @@ -<tool id="calculate_diversity" name="Diversity by gene" version="2.1.6"> - <description>calculates various diversity indexes with EggLib.</description> +<tool id="calculate_diversity" name="Diversity by gene" version="2.0.0"> + <description>Calculates various diversity indexes with EggLib</description> + <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> + <requirements> + <requirement type="binary">perl</requirement> + <requirement type="package" version="1.6.924">perl-bioperl</requirement> + <requirement type="package" version="1.90b4">plink</requirement> + </requirements> <!-- [STRONGLY RECOMMANDED] Exit code rules --> <stdio> <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> @@ -21,33 +27,28 @@ <!-- [HELP] Multiple tests can be defined with different parameters --> <test> <param name="input" value="egglib-alignment.fa" /> - <output name="output" file="egglib-result.txt" /> + <output name="output" file="egglib-result.txt" compare="sim_size" delta="0" /> </test> </tests> - <help> - - + <help><![CDATA[ .. class:: infomark -**Authors** EggLib_ +**Authors** EggLib : http://mycor.nancy.inra.fr/egglib/ -.. _EggLib: http://egglib.sourceforge.net/ - - | "EggLib: processing, analysis and simulation tools for population genetics and genomics.", **De Mita S. and M. Siol.**, BMC Genet. 2012. 13:27. + | **Please cite** "EggLib: processing, analysis and simulation tools for population genetics and genomics.", **De Mita S. and M. Siol.**, BMC Genet. 2012. 13:27. + | **Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1). .. class:: infomark -**Galaxy integration** South Green. +**Galaxy integration** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA) .. class:: infomark -**Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1). +**Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr --------------------------------------------------- - - ================== Diversity by genes ================== @@ -57,24 +58,23 @@ ----------- | Provides various diversity indexes using EggLib library. - | For further informations, please visite the EggLib website_. + | For further informations, please visit the EggLib website_. .. _website: http://egglib.sourceforge.net/ - ------------------ -Workflow position ------------------ - -**Upstream tool** +------------ +Dependencies +------------ +PLINK + plink_ 1.90b4, Conda version +Bioperl + perl-bioperl_ 1.6.924, Conda version +egglib + egglib_ 2.1.5, supplied with the wrapper -=============== ====================== =========== -Name output file(s) format -=============== ====================== =========== -VCF to Hapmap Fasta alignment fasta -=============== ====================== =========== - - +.. _plink: https://anaconda.org/bioconda/plink +.. _perl-bioperl: https://anaconda.org/bioconda/perl-bioperl +.. _egglib: https://anaconda.org/bioconda/egglib ---------- Input file @@ -83,22 +83,15 @@ Fasta file Fasta alignment - - ------------ Output files ------------ Diversity + Diversity indexes Log file - - ------------- -Dependencies ------------- -EggLib - version 2.1.5 + Log file --------------------------------------------------- @@ -106,8 +99,8 @@ Working example --------------- -Input files -=========== +Input file +========== Fasta file ---------- @@ -143,8 +136,8 @@ GCTGGTTTTGCTCAGAGAGCGGGCGCGTGTTCGCCGCGGGTCTCAACGACTTCGGGCAGCTCGGGATAGGCTCCTCCGTGACTCATTCCCTGGTACTGAGCTTCTTGTACATCATGCCTCCA TGTGAAATTTTCATCTACATTGTGAGCCAGCCTACTTTTACACAGTAAGCGAAAGCTGGCTGGACATATCAGAGTTGCAATGGGGATTGACCAAATCAATTCTGACTCCTGTTACATGTTGC -Output files -============ +Output file +=========== Diversity --------- @@ -155,7 +148,7 @@ LOCOs11g09160;8;6577;6577;2;0.00011728;0.000130324;0.414213;2;0.428571;0.857143;0;1; - </help> + ]]></help> <citations> <!-- [HELP] As DOI or BibTex entry --> <citation type="bibtex">@article{Dereeper03062015, |
| b |
| diff -r 98c37a5d67f4 -r c6640c49fd01 hapmap2mlmm/HapmapToMLMMFiles.pl --- a/hapmap2mlmm/HapmapToMLMMFiles.pl Wed Feb 07 22:08:47 2018 -0500 +++ b/hapmap2mlmm/HapmapToMLMMFiles.pl Mon Apr 16 09:00:24 2018 -0400 |
| b |
| @@ -98,7 +98,7 @@ } close($M); -system("$TRANSPOSE_EXE geno_transposed >geno_transposed2"); +system("gawk -E $TRANSPOSE_EXE geno_transposed >geno_transposed2"); open(my $F,">$geno"); open(my $G,"geno_transposed2"); |
| b |
| diff -r 98c37a5d67f4 -r c6640c49fd01 hapmap2mlmm/HapmapToMLMMFiles.xml --- a/hapmap2mlmm/HapmapToMLMMFiles.xml Wed Feb 07 22:08:47 2018 -0500 +++ b/hapmap2mlmm/HapmapToMLMMFiles.xml Mon Apr 16 09:00:24 2018 -0400 |
| [ |
| @@ -1,6 +1,9 @@ -<tool id="hapmap_to_mlmm_files" name="HapmapToMLMMFiles" version="1.1"> - <description>converts a hapmap file into MLMM input files</description> +<tool id="hapmap_to_mlmm_files" name="HapmapToMLMMFiles" version="2.0.0"> + <description>Converts a hapmap file into MLMM input files</description> <!-- [STRONGLY RECOMMANDED] Exit code rules --> + <requirements> + <requirement type="package" version="4.1.3">gawk</requirement> + </requirements> <stdio> <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> <exit_code range="1:" level="fatal" /> @@ -26,10 +29,7 @@ <output name="genot" file="hapmap2mlmm-result_genot" /> </test> </tests> - <help> - - - + <help><![CDATA[ .. class:: infomark @@ -39,11 +39,14 @@ .. class:: infomark -**Galaxy integration** South Green. +**Galaxy integration** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA) + +.. class:: infomark + +**Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr --------------------------------------------------- - ================= HapmapToMLMMFiles ================= @@ -54,29 +57,13 @@ | HapmapToMLMMFiles converts a hapmap file into input files compatible with the MLMM software. - ------------------ -Workflow position ------------------ - -**Upstream tool** +------------ +Dependencies +------------ +GAWK + gawk_ 4.1.3, Conda version -=============== ====================== =========== -Name output file(s) format -=============== ====================== =========== -VCF to Hapmap Fasta alignment fasta -=============== ====================== =========== - - -**Downstream tool** - -=========== ========================== ======= -Name input file(s) format -=========== ========================== ======= -MLMM -=========== ========================== ======= - - +.. _gawk: https://anaconda.org/bioconda/gawk ---------- Input file @@ -140,7 +127,7 @@ Ind2 0 0 0 0 0 2 2 0 0 0 0 0 0 0 - </help> + ]]></help> <citations> <!-- [HELP] As DOI or BibTex entry --> <citation type="bibtex">@article{Dereeper03062015, |
| b |
| diff -r 98c37a5d67f4 -r c6640c49fd01 hapmap2mlmm/transpose.awk --- a/hapmap2mlmm/transpose.awk Wed Feb 07 22:08:47 2018 -0500 +++ b/hapmap2mlmm/transpose.awk Mon Apr 16 09:00:24 2018 -0400 |
| b |
| @@ -1,5 +1,3 @@ -#!/usr/bin/gawk -f - BEGIN { max_x =0; max_y =0; |
| b |
| diff -r 98c37a5d67f4 -r c6640c49fd01 ped2bed/ped2bed.xml --- a/ped2bed/ped2bed.xml Wed Feb 07 22:08:47 2018 -0500 +++ b/ped2bed/ped2bed.xml Mon Apr 16 09:00:24 2018 -0400 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="ped2bed" name="plink: ped2bed" version="1.24"> +<tool id="ped2bed" name="PLINK: ped2bed" version="2.0.0"> <description>Convert ped to bed</description> <requirements> <requirement type="binary">perl</requirement> @@ -35,30 +35,27 @@ <output name="bim" file="ped2bed-result.bim" /> </test> </tests> - <help> + <help><![CDATA[ .. class:: infomark -**Authors** plink_ +Ped to Bed format conversion is done with PLINK. +**Authors** PLINK: Shaun Purcell (https://www.cog-genomics.org/plink) -.. _plink: http://pngu.mgh.harvard.edu/purcell/plink/ - - | "PLINK: a toolset for whole-genome association and population-based linkage analysis.", **Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ, Sham PC.**, American Journal of Human Genetics, 81, 2007. + | **Please cite** "PLINK: a toolset for whole-genome association and population-based linkage analysis.", **Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ, Sham PC.**, American Journal of Human Genetics, 81, 2007. + | **Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1). .. class:: infomark -**Galaxy integration** South Green. +**Galaxy integration** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA) .. class:: infomark -**Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1). - +**Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr --------------------------------------------------- - - ======= Ped2Bed ======= @@ -67,45 +64,31 @@ Description ----------- + | Ped to Bed format conversion is done with PLINK | PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. - | For further informations, please visite the plink website_. - -.. _website: http://pngu.mgh.harvard.edu/purcell/plink/ - + | For further informations, please visit the PLINK website_. ------------------ -Workflow position ------------------ - -**Upstream tool** +.. _website: https://www.cog-genomics.org/plink -=============== ========================== =========== -Name output file(s) format -=============== ========================== =========== -VCFtools filter PED and map files ped and map -=============== ========================== =========== - - -**Downstream tool** +------------ +Dependencies +------------ +PLINK + plink_ 1.90b4, Conda version +Bioperl + perl-bioperl_ 1.6.924, Conda version -=========== ========================== ======= -Name input file(s) format -=========== ========================== ======= -Admixture Bed, fam and bim file txt -=========== ========================== ======= +.. _plink: https://anaconda.org/bioconda/plink +.. _perl-bioperl: https://anaconda.org/bioconda/perl-bioperl - ----------- -Input file ----------- +----------- +Input files +----------- PED file - Allelic file in PED format MAP file - - ------------ Output files ------------ @@ -117,14 +100,6 @@ Bim file All logs - Log file - - ------------- -Dependencies ------------- -plink - version 1.07 --------------------------------------------------- @@ -181,7 +156,7 @@ 0 Chr8:18058 0 18058 C T - </help> + ]]></help> <citations> <!-- [HELP] As DOI or BibTex entry --> <citation type="bibtex">@article{Dereeper03062015, |
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| diff -r 98c37a5d67f4 -r c6640c49fd01 test-data/MDSplot-output.mds_plot.txt --- a/test-data/MDSplot-output.mds_plot.txt Wed Feb 07 22:08:47 2018 -0500 +++ b/test-data/MDSplot-output.mds_plot.txt Mon Apr 16 09:00:24 2018 -0400 |
| b |
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| b |
| diff -r 98c37a5d67f4 -r c6640c49fd01 test-data/MDSplot-output.mds_plot.txt_old --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MDSplot-output.mds_plot.txt_old Mon Apr 16 09:00:24 2018 -0400 |
| b |
| @@ -0,0 +1,93 @@ +Pop1 IRAT112 -0.0969382 0.0376036 +Pop1 IAC25 -0.0918126 0.0501177 +Pop1 IAC165 -0.104815 0.0453876 +Pop1 KARASUKARASURANKASU 0.107782 -0.0683546 +Pop1 DOURADOPRECOCE -0.0831697 0.0516412 +Pop1 CUIABANA 0.0327877 0.0497752 +Pop1 BICOBRANCO -0.0554177 0.0501857 +Pop1 CAAWA/FORTUNA6 -0.052355 0.0170584 +Pop1 CANELADEFERRO -0.0142283 0.0598394 +Pop1 CIRAD358 0.0497841 0.0645487 +Pop1 COLOMBIA1 -0.110347 -0.172742 +Pop1 CIRAD409 -0.113614 -0.105898 +Pop1 BAGANANASALAO 0.0247582 0.0186246 +Pop1 BAKUNGH 0.0199022 0.0613692 +Pop1 FOHISOMOTRA 0.0344309 0.0697592 +Pop1 KAKANI2 0.147713 -0.0780455 +Pop1 GUARANI -0.0892761 0.0387007 +Pop1 DOURADOAGULHA -0.0831373 0.0514523 +Pop1 IRAT13 -0.0757215 0.00312413 +Pop1 DAWASANRED 0.131309 -0.102364 +Pop1 GRAZI 0.0177091 0.0870472 +Pop1 IRAT144 0.0146443 0.0067734 +Pop1 IAC47 -0.0968934 0.0477667 +Pop1 MOROBEREKAN 0.0395544 0.0952695 +Pop1 IRAT362 -0.0921075 -0.00860852 +Pop1 GIZA171 0.14498 -0.0932001 +Pop1 IDSA77 -0.122827 -0.120219 +Pop1 IRAT216 -0.120205 -0.136803 +Pop1 IRAT177 -0.0762395 0.00230332 +Pop1 CHAPHUMA 0.149543 -0.0680637 +Pop1 CIRAD392 0.0187265 -0.047646 +Pop1 ARROZCEBADA 0.0110416 0.0787137 +Pop1 INDANE 0.108691 -0.0338065 +Pop1 DINORADO -0.00819237 0.0386578 +Pop1 63-104 -0.053974 -0.00204494 +Pop1 IR63380-16 -0.0968028 -0.0931822 +Pop1 CANAROXA -0.0756689 0.0253328 +Pop1 CICIHBETON 0.108857 0.142633 +Pop1 IR68704-145-1-1-B -0.103292 -0.071382 +Pop1 HAWMOM 0.129651 -0.0473323 +Pop1 IRAT364 -0.0118523 0.0472973 +Pop1 IRAT212 0.0231616 -0.00146178 +Pop1 KHAODAM 0.123936 -0.0654516 +Pop1 62667 -0.0752552 0.00278556 +Pop1 IRAT234 -0.0346607 0.0551203 +Pop1 NIPPONBARE_D 0.133199 -0.0963396 +Pop1 JUMULA2 0.104558 -0.0524994 +Pop1 CUBA65 -0.0124835 0.013679 +Pop1 BABER 0.090299 -0.0460696 +Pop1 CIRAD488 -0.0201481 -0.0262103 +Pop1 BENGALYVAKARINA 0.028631 0.0637662 +Pop1 ESPERANZA -0.108888 -0.00812147 +Pop1 BULUPANDAK 0.119762 0.143912 +Pop1 ARIAS 0.0327948 0.0827878 +Pop1 GOMPA2 0.133341 -0.0543414 +Pop1 CT13582-15-5-M -0.0922561 -0.0543988 +Pop1 IRAT335 -0.0886849 0.0522465 +Pop1 M202 0.13463 -0.106462 +Pop1 IR65907-188-1-B -0.0755893 -0.136821 +Pop1 IR71525-19-1-1 -0.0353444 0.0478985 +Pop1 CNA-7_BO_1_1_33-13-6-1 -0.0823478 -0.0435581 +Pop1 IRAT257 -0.0606191 0.0564989 +Pop1 IRAT109 -0.1006 -0.00959445 +Pop1 KANIRANGA 0.0705459 0.129888 +Pop1 IR66421-096-2-1-1 -0.00859728 -0.0570793 +Pop1 GOGO 0.0232414 0.0351889 +Pop1 GEMJYAJYANAM 0.170032 -0.0857315 +Pop1 DANGREY 0.175792 -0.113683 +Pop1 BINULAWAN -0.0208225 0.0611919 +Pop1 CAIAPO -0.0149329 -0.0122987 +Pop1 IGUAPECATETO -0.0740464 0.0552386 +Pop1 IRAT170 -0.0756928 0.00297643 +Pop1 IRAT380 -0.0210318 -0.00092536 +Pop1 ARAGUAIA -0.123443 0.0273298 +Pop1 GOGOLEMPAK 0.0598291 0.107462 +Pop1 JAOHAW 0.17563 -0.0587865 +Pop1 CHALOYOE 0.0904761 -0.0565325 +Pop1 GANIGI 0.0526286 0.0960475 +Pop1 GUNDILKUNING 0.116788 0.130234 +Pop1 IRAT2 -0.0762849 0.00262428 +Pop1 IRAT366 0.0273652 0.13551 +Pop1 IRAT104 -0.00310702 0.0636479 +Pop1 DAVAO -0.00538403 0.0564886 +Pop1 HD1-4 -0.0960109 0.0459137 +Pop1 CURINCA -0.128876 -0.121141 +Pop1 DAM 0.129029 -0.0660183 +Pop1 CIRAD403 -0.117849 -0.134651 +Pop1 JUMALI 0.123992 -0.0843623 +Pop1 JIMBRUKJOLOWORO 0.0549906 0.135017 +Pop1 GOGOLEMPUK 0.0597267 0.10733 +Pop1 CIRAD394 0.0040454 -0.0885135 +Pop1 IR63372-08 -0.0951857 -0.140804 +Pop1 IR60080-46A -0.0732581 0.0197832 |
| b |
| diff -r 98c37a5d67f4 -r c6640c49fd01 test-data/annotationStatsFromVCF.effect --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annotationStatsFromVCF.effect Mon Apr 16 09:00:24 2018 -0400 |
| b |
| @@ -0,0 +1,3 @@ +Intron 960 Intron:960 +UTR 281 UTR:281 +Exon 3248 Synonym:124 Non-syn:120 |
| b |
| diff -r 98c37a5d67f4 -r c6640c49fd01 test-data/annotationStatsFromVCF.location --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annotationStatsFromVCF.location Mon Apr 16 09:00:24 2018 -0400 |
| b |
| @@ -0,0 +1,2 @@ +Intergenic 466 Intergenic:466 +Genic 4489 Exon:3248 Intron:960 UTR:281 |
| b |
| diff -r 98c37a5d67f4 -r c6640c49fd01 test-data/annotationStatsFromVCF.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annotationStatsFromVCF.txt Mon Apr 16 09:00:24 2018 -0400 |
| b |
| @@ -0,0 +1,4 @@ +Chrom Bin dN/dS ratio +chr1 50000 0.791666666666667 +chr1 100000 0.981132075471698 +chr1 150000 2.08333333333333 |
| b |
| diff -r 98c37a5d67f4 -r c6640c49fd01 test-data/annotationStatsFromVCF.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annotationStatsFromVCF.vcf Mon Apr 16 09:00:24 2018 -0400 |
| [ |
| b'@@ -0,0 +1,5000 @@\n+##fileformat=VCFv4.1\n+##FILTER=<ID=LowQual,Description="Low quality">\n+##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">\n+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">\n+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">\n+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">\n+##GATKCommandLine=<ID=UnifiedGenotyper,Version=2.7-4-g6f46d11,Date="Fri Nov 01 16:17:42 CET 2013",Epoch=1383319062999,CommandLineOptions="analysis_type=UnifiedGenotyper input_file=[/scratch/hueber-35211/CATB1.RG.sorted.indelrealigned.bam] read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[BadCigar] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/data/projects/coffee_snp/donnees_genomiques/pseudomolecules.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=4 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=null help=false version=false genotype_likelihoods_model=SNP pcr_error_rate=1.0E-4 computeSLOD=false annotateNDA=false pair_hmm_implementation=LOGLESS_CACHING min_base_quality_score=17 max_deletion_fraction=0.05 allSitePLs=false min_indel_count_for_genotyping=5 min_indel_fraction_per_sample=0.25 indelGapContinuationPenalty=10 indelGapOpenPenalty=45 indelHaplotypeSize=80 indelDebug=false ignoreSNPAlleles=false allReadsSP=false ignoreLaneInfo=false reference_sample_calls=(RodBinding name= source=UNBOUND) reference_sample_name=null sample_ploidy=2 min_quality_score=1 max_quality_score=40 site_quality_prior=20 min_power_threshold_for_calling=0.95 min_reference_depth=100 exclude_filtered_reference_sites=false output_mode=EMIT_VARIANTS_ONLY heterozygosity=0.001 indel_heterozygosity=1.25E-4 genotyping_mode=DISCOVERY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=10.0 alleles=(RodBinding name= source=UNBOUND) max_alternate_alleles=6 input_prior=[] contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=EXACT_INDEPENDENT exactcallslog=null dbsnp=(RodBinding name= source=UNBOUND) comp=[] out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub onlyEmitSamples=[] debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">\n+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">\n+##INFO=<ID=AF,Number=A,Type'..b'm=1.599;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856)\tGT:AD:DP:GQ:PL\t0/1:20,22:42:99:726,0,669\n+chr1\t188266\t.\tA\tG\t878.77\t.\tAC=1;AF=0.500;AN=2;BaseQRankSum=0.261;DP=56;Dels=0.00;FS=2.268;HaplotypeScore=3.8663;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.827;QD=15.69;ReadPosRankSum=0.412;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856)\tGT:AD:DP:GQ:PL\t0/1:28,27:56:99:907,0,965\n+chr1\t188270\t.\tA\tG\t850.77\t.\tAC=1;AF=0.500;AN=2;BaseQRankSum=1.747;DP=54;Dels=0.00;FS=3.828;HaplotypeScore=4.8662;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.692;QD=15.75;ReadPosRankSum=0.709;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856)\tGT:AD:DP:GQ:PL\t0/1:27,27:54:99:879,0,898\n+chr1\t188311\t.\tT\tG\t901.77\t.\tAC=1;AF=0.500;AN=2;BaseQRankSum=-0.508;DP=53;Dels=0.00;FS=2.345;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.454;QD=17.01;ReadPosRankSum=0.223;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856)\tGT:AD:DP:GQ:PL\t0/1:25,28:53:99:930,0,831\n+chr1\t188357\t.\tC\tT\t1327.77\t.\tAC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=24.46;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856)\tGT:AD:DP:GQ:PL\t1/1:0,36:36:99:1356,105,0\n+chr1\t188364\t.\tG\tC\t578.77\t.\tAC=1;AF=0.500;AN=2;BaseQRankSum=0.285;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.585;QD=14.47;ReadPosRankSum=-0.612;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856)\tGT:AD:DP:GQ:PL\t0/1:22,18:40:99:607,0,770\n+chr1\t188393\t.\tT\tC\t515.77\t.\tAC=1;AF=0.500;AN=2;BaseQRankSum=-1.106;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=2.5781;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.191;QD=12.28;ReadPosRankSum=-1.385;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856)\tGT:AD:DP:GQ:PL\t0/1:24,18:42:99:544,0,828\n+chr1\t188395\t.\tC\tG\t543.77\t.\tAC=1;AF=0.500;AN=2;BaseQRankSum=-1.484;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=2.5781;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.775;QD=13.26;ReadPosRankSum=-1.773;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856)\tGT:AD:DP:GQ:PL\t0/1:23,18:41:99:572,0,791\n+chr1\t188416\t.\tT\tC\t397.77\t.\tAC=1;AF=0.500;AN=2;BaseQRankSum=-0.717;DP=39;Dels=0.00;FS=1.302;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.893;QD=10.20;ReadPosRankSum=0.571;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856)\tGT:AD:DP:GQ:PL\t0/1:25,14:39:99:426,0,821\n+chr1\t188438\t.\tC\tA\t930.77\t.\tAC=1;AF=0.500;AN=2;BaseQRankSum=2.123;DP=50;Dels=0.00;FS=5.900;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.41;MQ0=0;MQRankSum=0.020;QD=18.62;ReadPosRankSum=-0.472;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856)\tGT:AD:DP:GQ:PL\t0/1:21,29:50:99:959,0,659\n+chr1\t188621\t.\tG\tA\t704.77\t.\tAC=1;AF=0.500;AN=2;BaseQRankSum=0.090;DP=49;Dels=0.00;FS=5.986;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.090;QD=14.38;ReadPosRankSum=-0.774;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),SYNONYMOUS_CODING(LOW|SILENT|ttG/ttA|L4|Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856)\tGT:AD:DP:GQ:PL\t0/1:27,22:49:99:733,0,926\n' |
| b |
| diff -r 98c37a5d67f4 -r c6640c49fd01 test-data/ped2bed-result.bim --- a/test-data/ped2bed-result.bim Wed Feb 07 22:08:47 2018 -0500 +++ b/test-data/ped2bed-result.bim Mon Apr 16 09:00:24 2018 -0400 |
| b |
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|
| b |
| diff -r 98c37a5d67f4 -r c6640c49fd01 test-data/ped2bed-result.bim_old --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ped2bed-result.bim_old Mon Apr 16 09:00:24 2018 -0400 |
| b |
| b'@@ -0,0 +1,2013 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|
| b |
| diff -r 98c37a5d67f4 -r c6640c49fd01 tool_dependencies.xml --- a/tool_dependencies.xml Wed Feb 07 22:08:47 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,5 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="plink" version="1.90b4"/> - <package name="vcftools" version="0.1.14"/> -</tool_dependency> |