| Previous changeset 0:2ca1baabdae0 (2016-11-17) Next changeset 2:e3ba567abdf5 (2022-03-11) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content commit 0a56599c36b4968095ec5a3cb589f94fb139466c |
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modified:
get_length_and_gc_content.r get_length_and_gc_content.xml tool_data_table_conf.xml.sample |
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added:
test-data/cached_locally/all_fasta.loc test-data/cached_locally/gene_sets.loc test-data/cached_locally/ref.fasta test-data/cached_locally/ref.gtf tool-data/all_fasta.loc.sample tool-data/gene_sets.loc.sample tool_data_table_conf.xml.test |
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removed:
all_fasta.loc.sample test-data/gene_length.tab |
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| diff -r 2ca1baabdae0 -r f088370d2a3c all_fasta.loc.sample --- a/all_fasta.loc.sample Thu Nov 17 16:41:06 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,18 +0,0 @@ -#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 2ca1baabdae0 -r f088370d2a3c get_length_and_gc_content.r --- a/get_length_and_gc_content.r Thu Nov 17 16:41:06 2016 -0500 +++ b/get_length_and_gc_content.r Sun Jan 28 04:04:58 2018 -0500 |
| [ |
| @@ -15,9 +15,9 @@ 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.") + 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 ID and length."), + make_option(c("-gc","--gc_content"), type="character", default=FALSE, help="Output file with Gene ID and GC content.") ) parser <- OptionParser(usage = "%prog [options] file", option_list=option_list) |
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| diff -r 2ca1baabdae0 -r f088370d2a3c get_length_and_gc_content.xml --- a/get_length_and_gc_content.xml Thu Nov 17 16:41:06 2016 -0500 +++ b/get_length_and_gc_content.xml Sun Jan 28 04:04:58 2018 -0500 |
| [ |
| b'@@ -1,10 +1,10 @@\n-<tool id="length_and_gc_content" name="Gene length and gc content" version="0.1.0">\n- <description>from GTF file</description>\n+<tool id="length_and_gc_content" name="Gene length and GC content" version="0.1.1">\n+ <description>from GTF and FASTA file</description>\n <requirements>\n <requirement type="package" version="1.3.2">r-optparse</requirement>\n- <requirement type="package" version="1.4.1">r-reshape2</requirement>\n- <requirement type="package" version="1.9.6">r-data.table</requirement>\n- <requirement type="package" version="1.34.1">bioconductor-rtracklayer</requirement>\n+ <requirement type="package" version="1.4.2">r-reshape2</requirement>\n+ <requirement type="package" version="1.10.4">r-data.table</requirement>\n+ <requirement type="package" version="1.34.2">bioconductor-rtracklayer</requirement>\n </requirements>\n <stdio>\n <regex match="Execution halted"\n@@ -20,70 +20,165 @@\n level="fatal"\n description="An undefined error occured, please check your input carefully and contact your administrator." />\n </stdio>\n+ <version_command><![CDATA[\n+ echo $(R --version | grep version | grep -v GNU)", optparse version" $(R --vanilla --slave -e "library(optparse); cat(sessionInfo()\\$otherPkgs\\$optparse\\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", reshape2 version" $(R --vanilla --slave -e "library(reshape2); cat(sessionInfo()\\$otherPkgs\\$reshape2\\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rtracklayer version" $(R --vanilla --slave -e "library(rtracklayer); cat(sessionInfo()\\$otherPkgs\\$rtracklayer\\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", data.table version" $(R --vanilla --slave -e "library(data.table); cat(sessionInfo()\\$otherPkgs\\$data.table\\$Version)" 2> /dev/null | grep -v -i "WARNING: ")\n+ ]]></version_command>\n <command><![CDATA[\n- Rscript \'$__tool_directory__\'/get_length_and_gc_content.r --gtf \'$gtf\'\n- #if $fastaSource.genomeSource == \'indexed\':\n- --fasta \'$fastaSource.fasta_pre_installed.fields.path\'\n- #else:\n- --fasta \'$fastaSource.fasta_history\'\n- #end if\n- --length \'$length\'\n- --gc_content \'$gc_content\'\n+\n+## Get GTF\n+\n+#if $gtf_file.gtfSource == \'cached\':\n+ ln -s \'$gtf_file.gtf_pre_installed.fields.path\' gtf\n+#else:\n+ ln -s \'$gtf_file.gtf_history\' gtf\n+#end if\n+\n+&&\n+\n+## Get FASTA\n+\n+#if $fasta_file.fastaSource == \'indexed\':\n+ ln -s \'$fasta_file.fasta_pre_installed.fields.path\' fasta\n+#else:\n+ ln -s \'$fasta_file.fasta_history\' fasta\n+#end if\n+\n+&&\n+\n+Rscript \'$__tool_directory__/get_length_and_gc_content.r\'\n+\n+--gtf gtf\n+--fasta fasta\n+\n+#if $length_out:\n+ --length \'$length\'\n+#end if\n+\n+#if $gc_out:\n+ --gc_content \'$gc_content\'\n+#end if\n+\n ]]></command>\n+\n <inputs>\n- <param name="gtf" type="data" format="gtf" help="The GTF must match the FASTA file" label="GTF file for length and GC calculation"/>\n- <conditional name="fastaSource">\n- <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">\n- <option value="indexed">Use a built-in fasta</option>\n- <option value="history">Use fasta from history</option>\n+ <conditional name="gtf_file">\n+ <param name="gtfSource" type="select" label="Select a built-in GTF file or one from your history" help="Choose history if you don\'t see the correct GTF" >\n+ <option value="cached" selected="true">Use a built-in GTF</option>\n+ <option value="history">Use a GTF from history</option>\n+ </param>\n+ <when value="cached">\n+ <param name="gtf_pre_installed" type="select" label="Select a GTF file" help="Select the GTF from a list of pre-installed files">\n+ <option'..b'that matches the supplied GTF file" />\n+ </when>\n </conditional>\n+\n+\n+ <param name="length_out" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Output length file?" help="Default: Yes" />\n+ <param name="gc_out" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Output GC content file?" help="Default: Yes" />\n+\n </inputs>\n+\n <outputs>\n- <data name="length" format="tabular" label="gene length">\n+ <data name="length" format="tabular" label="Gene length">\n+ <filter>length_out is True</filter>\n <actions>\n- <action name="column_names" type="metadata" default="gene,length" />\n+ <action name="column_names" type="metadata" default="GeneID,Length" />\n </actions>\n </data>\n- <data name="gc_content" format="tabular" label="gene gc content">\n+ <data name="gc_content" format="tabular" label="Gene GC content">\n+ <filter>gc_out is True</filter>\n <actions>\n- <action name="column_names" type="metadata" default="gene,gc_content" />\n+ <action name="column_names" type="metadata" default="GeneID,GC_content" />\n </actions>\n </data>\n </outputs>\n+\n <tests>\n- <test>\n- <param name="gtf" value="in.gtf" ftype="gtf"></param>\n- <param name="fastaSource|genomeSource" value="history"></param>\n- <param name="fastaSource|fasta_history" value="in.fasta" ftype="fasta"></param>\n- <output name="length" file="length.tab"></output>\n- <output name="gc_content" file="gc.tab"></output>\n+ <!-- Ensure length and GC files are output -->\n+ <test expect_num_outputs="2">\n+ <param name="gtfSource" value="history" />\n+ <param name="gtf_history" ftype="gtf" value="in.gtf" />\n+ <param name="fastaSource" value="history" />\n+ <param name="fasta_history" ftype="fasta" value="in.fasta" />\n+ <output name="length" file="length.tab" />\n+ <output name="gc_content" file="gc.tab" />\n+ </test>\n+ <!-- Ensure built-in fasta and gtf work -->\n+ <test expect_num_outputs="2">\n+ <param name="gtfSource" value="cached" />\n+ <param name="fastaSource" value="indexed" />\n+ <output name="length" file="length.tab" />\n+ <output name="gc_content" file="gc.tab" />\n+ </test>\n+ <!-- Ensure optional gc content works -->\n+ <test expect_num_outputs="1">\n+ <param name="gtfSource" value="cached" />\n+ <param name="fastaSource" value="indexed" />\n+ <param name="gc_out" value="False" />\n+ <output name="length" file="length.tab" />\n+ </test>\n+ <!-- Ensure optional length works -->\n+ <test expect_num_outputs="1">\n+ <param name="gtfSource" value="cached" />\n+ <param name="fastaSource" value="indexed" />\n+ <param name="length_out" value="False" />\n+ <output name="gc_content" file="gc.tab" />\n </test>\n </tests>\n- <help>\n+ <help><![CDATA[\n+\n+**What it does**\n+\n+.. class:: infomark\n \n- **What it does**\n+This tool calculates the length and GC content for the genes in a GTF file. It requires a FASTA file that is the same genome version as the GTF.\n+\n+-----\n+\n+**Inputs**\n+\n+- a GTF file\n+- a FASTA file\n \n- 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.\n+-----\n+\n+**Outputs**\n+\n+- a tabular file with Gene ID and length\n+- a tabular file with Gene ID and GC content\n \n+-----\n \n- </help>\n+**More Information**\n+\n+To calculate gene length, this tool counts the number of bases in all exons of a gene, after merging any overlapping exons from different transcripts.\n+\n+ ]]></help>\n <citations>\n </citations>\n </tool>\n' |
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| diff -r 2ca1baabdae0 -r f088370d2a3c test-data/cached_locally/all_fasta.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/all_fasta.loc Sun Jan 28 04:04:58 2018 -0500 |
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| @@ -0,0 +1,1 @@ +hg38 hg38 Human (hg38) ${__HERE__}/ref.fasta |
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| diff -r 2ca1baabdae0 -r f088370d2a3c test-data/cached_locally/gene_sets.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/gene_sets.loc Sun Jan 28 04:04:58 2018 -0500 |
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| @@ -0,0 +1,1 @@ +hg38 hg38 hg38GTF ${__HERE__}/ref.gtf |
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| diff -r 2ca1baabdae0 -r f088370d2a3c test-data/cached_locally/ref.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/ref.fasta Sun Jan 28 04:04:58 2018 -0500 |
| b |
| @@ -0,0 +1,2 @@ +>1 +AAAAAAAAAATTTTTTTTTTCCCCCCCCCCGGGGGGGGGGAAAAAAAAAAAAAAAAAAAATTTTTTTTTTCCCCCCCCCCGGGGGGGGGGAAAAAAAAAATTTTT \ No newline at end of file |
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| diff -r 2ca1baabdae0 -r f088370d2a3c test-data/cached_locally/ref.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/ref.gtf Sun Jan 28 04:04:58 2018 -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"; |
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| diff -r 2ca1baabdae0 -r f088370d2a3c test-data/gene_length.tab --- a/test-data/gene_length.tab Thu Nov 17 16:41:06 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,948 +0,0 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|
| b |
| diff -r 2ca1baabdae0 -r f088370d2a3c tool-data/all_fasta.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/all_fasta.loc.sample Sun Jan 28 04:04:58 2018 -0500 |
| b |
| @@ -0,0 +1,18 @@ +#This file lists the locations and dbkeys of all the genome and transcriptome fasta files +#under the "genome" directory (a directory that contains a directory +#for each build. 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: +# +#apiMel4.5 apiMel4.5 Honeybee (Apis mellifera): apiMel4.5 /path/to/genome/apiMel4.5/apiMel4.5.fa +#hg38canon hg38 Human (Homo sapiens): hg38 Canonical /path/to/genome/hg38/hg38canon.fa +#hg38full hg38 Human (Homo sapiens): hg38 Full /path/to/genome/hg38/hg38full.fa +#hg38full.90 hg38 Human (Homo sapiens): hg38 Full Trans v90 /path/to/genome/hg38/hg38fulltrans.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 hg38 above. + |
| b |
| diff -r 2ca1baabdae0 -r f088370d2a3c tool-data/gene_sets.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/gene_sets.loc.sample Sun Jan 28 04:04:58 2018 -0500 |
| b |
| @@ -0,0 +1,15 @@ +# This is a sample file distributed with featureCounts that enables it and other# tools to use gene/exon annotations in the GFF/GTF format. +# +# The gene_sets.loc file syntax is: +#<unique_build_id> <dbkey> <display_name> <path> +# +# Please ensure that the above fields are tab separated. +# +# In case you have TWO or MORE providers PER dbkey, the one mentioned +# first in the file, should have the "default" priority. +# +#Example: +# +#Homo_sapiens.GRCh38.90 hg38 GRCh38 (hg38) annotation from Ensembl, release 90 /depot/data2/galaxy/hg38/gene_sets/Homo_sapiens.GRCh38.90.gtf +#Homo_sapiens.GRCh37.87 hg19 GRCh37 (hg19) annotation from Ensembl, release 87 /depot/data2/galaxy/hg19/gene_sets/Homo_sapiens.GRCh37.87.gtf + |
| b |
| diff -r 2ca1baabdae0 -r f088370d2a3c tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Thu Nov 17 16:41:06 2016 -0500 +++ b/tool_data_table_conf.xml.sample Sun Jan 28 04:04:58 2018 -0500 |
| b |
| @@ -1,7 +1,12 @@ <tables> <!-- Locations of all fasta files under genome directory --> - <table name="all_fasta" comment_char="#"> + <table name="all_fasta" comment_char="#" allow_duplicate_entries="False"> <columns>value, dbkey, name, path</columns> <file path="tool-data/all_fasta.loc" /> </table> + <!-- Locations of all gtf files with annotations of genome builds --> + <table name="gene_sets" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/gene_sets.loc" /> + </table> </tables> |
| b |
| diff -r 2ca1baabdae0 -r f088370d2a3c tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Sun Jan 28 04:04:58 2018 -0500 |
| b |
| @@ -0,0 +1,10 @@ +<tables> + <table name="all_fasta" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/cached_locally/all_fasta.loc" /> + </table> + <table name="gene_sets" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/cached_locally/gene_sets.loc" /> + </table> +</tables> \ No newline at end of file |