| Next changeset 1:f088370d2a3c (2018-01-28) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4 |
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added:
all_fasta.loc.sample get_length_and_gc_content.r get_length_and_gc_content.xml test-data/gc.tab test-data/gene_length.tab test-data/in.fasta test-data/in.gtf test-data/length.tab tool_data_table_conf.xml.sample |
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| diff -r 000000000000 -r 2ca1baabdae0 all_fasta.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/all_fasta.loc.sample Thu Nov 17 16:41:06 2016 -0500 |
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| @@ -0,0 +1,18 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the "genome" directory (a directory that contains a directory +#for each build). The script extract_fasta.py will generate the file +#all_fasta.loc. This file has the format (white space characters are +#TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#So, all_fasta.loc could look something like this: +# +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +# +#Your all_fasta.loc file should contain an entry for each individual +#fasta file. So there will be multiple fasta files for each build, +#such as with hg19 above. +# |
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| diff -r 000000000000 -r 2ca1baabdae0 get_length_and_gc_content.r --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_length_and_gc_content.r Thu Nov 17 16:41:06 2016 -0500 |
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| @@ -0,0 +1,59 @@ +# originally by Devon Ryan, https://www.biostars.org/p/84467/ + +options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) + +# we need that to not crash galaxy with an UTF8 error on German LC settings. +loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") + +suppressPackageStartupMessages({ + library("GenomicRanges") + library("rtracklayer") + library("Rsamtools") + library("optparse") + library("data.table") +}) + +option_list <- list( + make_option(c("-g","--gtf"), type="character", help="Input GTF file with gene / exon information."), + make_option(c("-f","--fasta"), type="character", default=FALSE, help="Fasta file that corresponds to the supplied GTF."), + make_option(c("-l","--length"), type="character", default=FALSE, help="Output file with gene name and length."), + make_option(c("-gc","--gc_content"), type="character", default=FALSE, help="Output file with gene name and GC content.") + ) + +parser <- OptionParser(usage = "%prog [options] file", option_list=option_list) +args = parse_args(parser) + +GTFfile = args$gtf +FASTAfile = args$fasta +length = args$length +gc_content = args$gc_content + +#Load the annotation and reduce it +GTF <- import.gff(GTFfile, format="gtf", genome=NA, feature.type="exon") +grl <- reduce(split(GTF, elementMetadata(GTF)$gene_id)) +reducedGTF <- unlist(grl, use.names=T) +elementMetadata(reducedGTF)$gene_id <- rep(names(grl), elementNROWS(grl)) + +#Open the fasta file +FASTA <- FaFile(FASTAfile) +open(FASTA) + +#Add the GC numbers +elementMetadata(reducedGTF)$nGCs <- letterFrequency(getSeq(FASTA, reducedGTF), "GC")[,1] +elementMetadata(reducedGTF)$widths <- width(reducedGTF) + +#Create a list of the ensembl_id/GC/length +calc_GC_length <- function(x) { + nGCs = sum(elementMetadata(x)$nGCs) + width = sum(elementMetadata(x)$widths) + c(width, nGCs/width) +} +output <- t(sapply(split(reducedGTF, elementMetadata(reducedGTF)$gene_id), calc_GC_length)) +output <- data.frame(setDT(data.frame(output), keep.rownames = TRUE)[]) + + +write.table(output[,c(1,2)], file=length, col.names=FALSE, row.names=FALSE, quote=FALSE, sep="\t") +write.table(output[,c(1,3)], file=gc_content, col.names=FALSE, row.names=FALSE, quote=FALSE, sep="\t") + + +sessionInfo() |
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| diff -r 000000000000 -r 2ca1baabdae0 get_length_and_gc_content.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_length_and_gc_content.xml Thu Nov 17 16:41:06 2016 -0500 |
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| @@ -0,0 +1,89 @@ +<tool id="length_and_gc_content" name="Gene length and gc content" version="0.1.0"> + <description>from GTF file</description> + <requirements> + <requirement type="package" version="1.3.2">r-optparse</requirement> + <requirement type="package" version="1.4.1">r-reshape2</requirement> + <requirement type="package" version="1.9.6">r-data.table</requirement> + <requirement type="package" version="1.34.1">bioconductor-rtracklayer</requirement> + </requirements> + <stdio> + <regex match="Execution halted" + source="both" + level="fatal" + description="Execution halted." /> + <regex match="Error in" + source="both" + level="fatal" + description="An undefined error occured, please check your input carefully and contact your administrator." /> + <regex match="Fatal error" + source="both" + level="fatal" + description="An undefined error occured, please check your input carefully and contact your administrator." /> + </stdio> + <command><![CDATA[ + Rscript '$__tool_directory__'/get_length_and_gc_content.r --gtf '$gtf' + #if $fastaSource.genomeSource == 'indexed': + --fasta '$fastaSource.fasta_pre_installed.fields.path' + #else: + --fasta '$fastaSource.fasta_history' + #end if + --length '$length' + --gc_content '$gc_content' + ]]></command> + <inputs> + <param name="gtf" type="data" format="gtf" help="The GTF must match the FASTA file" label="GTF file for length and GC calculation"/> + <conditional name="fastaSource"> + <param help="choose history if you don't see the correct genome fasta" label="Select a reference fasta from your history or use a built-in fasta?" name="genomeSource" type="select"> + <option value="indexed">Use a built-in fasta</option> + <option value="history">Use fasta from history</option> + </param> + <when value="indexed"> + <param name="fasta_pre_installed" type="select" help="Select the fasta file from a list of pre-installed genomes" label="Select a fasta sequence"> + <options from_data_table="all_fasta"> + <filter type="data_meta" key="dbkey" ref="gtf" column="0"/> + </options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> + </param> + </when> + <when value="history"> + <param name="fasta_history" type="data" format="fasta" label="Select a fasta file that matches the supplied GTF file"> + <options> + <filter type="data_meta" key="dbkey" ref="gtf"/> + </options> + <validator type="no_options" message="The current history does not include a fasta dataset with the build associated with the selected input file"/> + </param> + </when> + </conditional> + </inputs> + <outputs> + <data name="length" format="tabular" label="gene length"> + <actions> + <action name="column_names" type="metadata" default="gene,length" /> + </actions> + </data> + <data name="gc_content" format="tabular" label="gene gc content"> + <actions> + <action name="column_names" type="metadata" default="gene,gc_content" /> + </actions> + </data> + </outputs> + <tests> + <test> + <param name="gtf" value="in.gtf" ftype="gtf"></param> + <param name="fastaSource|genomeSource" value="history"></param> + <param name="fastaSource|fasta_history" value="in.fasta" ftype="fasta"></param> + <output name="length" file="length.tab"></output> + <output name="gc_content" file="gc.tab"></output> + </test> + </tests> + <help> + + **What it does** + + Returns a tabular file with gene id and length and a tabular file with gene id and GC content, based on a supplied GTF and a FASTA file. + + + </help> + <citations> + </citations> +</tool> |
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| diff -r 000000000000 -r 2ca1baabdae0 test-data/gc.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gc.tab Thu Nov 17 16:41:06 2016 -0500 |
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| @@ -0,0 +1,1 @@ +ENSG00000162526 0.388349514563107 |
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| diff -r 000000000000 -r 2ca1baabdae0 test-data/gene_length.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gene_length.tab Thu Nov 17 16:41:06 2016 -0500 |
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| diff -r 000000000000 -r 2ca1baabdae0 test-data/in.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/in.fasta Thu Nov 17 16:41:06 2016 -0500 |
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| @@ -0,0 +1,2 @@ +>1 +AAAAAAAAAATTTTTTTTTTCCCCCCCCCCGGGGGGGGGGAAAAAAAAAAAAAAAAAAAATTTTTTTTTTCCCCCCCCCCGGGGGGGGGGAAAAAAAAAATTTTT \ No newline at end of file |
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| diff -r 000000000000 -r 2ca1baabdae0 test-data/in.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/in.gtf Thu Nov 17 16:41:06 2016 -0500 |
| b |
| @@ -0,0 +1,6 @@ +1 ensembl_havana gene 1 103 . + . gene_id "ENSG00000162526"; gene_version "4"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000001094"; havana_gene_version "1"; +1 ensembl_havana transcript 1 103 . + . gene_id "ENSG00000162526"; gene_version "4"; transcript_id "ENST00000335137"; transcript_version "3"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000001094"; havana_gene_version "1"; transcript_name "OR4F5-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS30547"; havana_transcript "OTTHUMT00000003223"; havana_transcript_version "1"; tag "basic"; transcript_support_level "NA"; +1 ensembl_havana exon 1 103 . + . gene_id "ENSG00000162526"; gene_version "4"; transcript_id "ENST00000335137"; transcript_version "3"; exon_number "1"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000001094"; havana_gene_version "1"; transcript_name "OR4F5-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS30547"; havana_transcript "OTTHUMT00000003223"; havana_transcript_version "1"; exon_id "ENSE00002319515"; exon_version "1"; tag "basic"; transcript_support_level "NA"; +1 ensembl_havana CDS 1 100 . + 0 gene_id "ENSG00000162526"; gene_version "4"; transcript_id "ENST00000335137"; transcript_version "3"; exon_number "1"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000001094"; havana_gene_version "1"; transcript_name "OR4F5-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS30547"; havana_transcript "OTTHUMT00000003223"; havana_transcript_version "1"; protein_id "ENSP00000334393"; protein_version "3"; tag "basic"; transcript_support_level "NA"; +1 ensembl_havana start_codon 1 3 . + 0 gene_id "ENSG00000162526"; gene_version "4"; transcript_id "ENST00000335137"; transcript_version "3"; exon_number "1"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000001094"; havana_gene_version "1"; transcript_name "OR4F5-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS30547"; havana_transcript "OTTHUMT00000003223"; havana_transcript_version "1"; tag "basic"; transcript_support_level "NA"; +1 ensembl_havana stop_codon 101 103 . + 0 gene_id "ENSG00000162526"; gene_version "4"; transcript_id "ENST00000335137"; transcript_version "3"; exon_number "1"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000001094"; havana_gene_version "1"; transcript_name "OR4F5-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS30547"; havana_transcript "OTTHUMT00000003223"; havana_transcript_version "1"; tag "basic"; transcript_support_level "NA"; |
| b |
| diff -r 000000000000 -r 2ca1baabdae0 test-data/length.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/length.tab Thu Nov 17 16:41:06 2016 -0500 |
| b |
| @@ -0,0 +1,1 @@ +ENSG00000162526 103 |
| b |
| diff -r 000000000000 -r 2ca1baabdae0 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Thu Nov 17 16:41:06 2016 -0500 |
| b |
| @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/all_fasta.loc" /> + </table> +</tables> |