| Previous changeset 2:ace9f5a2b40f (2016-02-05) Next changeset 4:d681e989ac95 (2017-06-09) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 |
|
modified:
README.rst rg_rnaStar.xml test-data/rnastar_test.log test-data/rnastar_test2.log test-data/rnastar_test2_mapped_reads.bam test-data/rnastar_test_mapped_reads.bam tool_data_table_conf.xml.sample |
|
added:
macros.xml test-data/test1.gtf test-data/test3.fastqsanger.gz test-data/tophat_test_reads_per_gene.txt tool-data/rnastar_index2.loc.sample |
|
removed:
tool-data/rnastar_index.loc.sample tool_dependencies.xml |
| b |
| diff -r ace9f5a2b40f -r 318b2a9d54dd README.rst --- a/README.rst Fri Feb 05 11:56:20 2016 -0500 +++ b/README.rst Fri Apr 21 07:58:59 2017 -0400 |
| b |
| @@ -3,5 +3,7 @@ =================== - **Memory**: To run efficiently, RNA-STAR requires enough free memory to - hold the SA-indexed reference genome in RAM. For Human Genome hg19 this is - index about 27GB and running RNA-STAR requires approximately ~30GB of RAM. + hold the SA-indexed reference genome in RAM. For Human Genome hg19 this + index is about 27GB and running RNA-STAR requires approximately ~30GB of RAM. + For custom genomes, the rule of thub is to multiply the size of the + reference FASTA file by 9 to estimated required amount of RAM. |
| b |
| diff -r ace9f5a2b40f -r 318b2a9d54dd macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Apr 21 07:58:59 2017 -0400 |
| b |
| @@ -0,0 +1,20 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="2.5.2b">star</requirement> + <requirement type="package" version="0.1.19">samtools</requirement> + </requirements> + </xml> + <token name="@FASTQ_GZ_OPTION@"> + --readFilesCommand zcat + </token> + <xml name="citations"> + <citations> + <citation type="doi">10.1093/bioinformatics/bts635</citation> + </citations> + </xml> + <xml name="@SJDBOPTIONS@"> + <param argument="--sjdbGTFfile" type="data" format="gff3,gtf" label="Gene model (gff3,gtf) file for splice junctions" optional="true" help="Exon junction information for mapping splices"/> + <param argument="--sjdbOverhang" type="integer" min="1" value="100" label="Length of the genomic sequence around annotated junctions" help="Used in constructing the splice junctions database. Ideal value is ReadLength-1"/> + </xml> +</macros> |
| b |
| diff -r ace9f5a2b40f -r 318b2a9d54dd rg_rnaStar.xml --- a/rg_rnaStar.xml Fri Feb 05 11:56:20 2016 -0500 +++ b/rg_rnaStar.xml Fri Apr 21 07:58:59 2017 -0400 |
| [ |
| b'@@ -1,143 +1,175 @@\n-<tool id="rna_star" name="RNA STAR" version="2.4.0d-2">\n+<tool id="rna_star" name="RNA STAR" version="2.5.2b-0" profile="17.01">\n <description>Gapped-read mapper for RNA-seq data</description>\n- <requirements>\n- <requirement type="package" version="2.4.0d">rnastar</requirement>\n- <requirement type="package" version="0.1.19">samtools</requirement>\n- </requirements>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements"/>\n+ \n <stdio>\n+ <regex match="FATAL error" source="both" level="fatal"/>\n <regex match="EXITING: FATAL INPUT ERROR:" source="both" level="fatal"/>\n <regex match="EXITING: fatal error trying to allocate genome arrays, exception thrown: std::bad_alloc" source="both" level="fatal"/>\n <regex match="\\[sam_read1\\] missing header\\? Abort!" source="both" level="fatal"/>\n- <regex match=".*" source="both" level="warning" description="Some stderr/stdout text"/>\n </stdio>\n \n+<!--\n+ important quote (https://groups.google.com/forum/#!topic/rna-star/q4zGzlPgwXY):\n+ Hi Gary,\n+\n+ if you generate the genome with GTF file, and do not specify the value for - -sjdbOverhang, it will be set to the default 100.\n+ If you want to be able to set arbitrary value of - -sjdbOverhang on the fly, you have to generate the genome without annotations (GTF) - then you supply both the - -sjdbOverhang and GTF file at the mapping step.\n+\n+ Cheers\n+ Alex\n+-->\n <command><![CDATA[\n ## Create temporary index for custom reference\n- #if str($refGenomeSource.genomeSource) == \'history\':\n+ #if str($refGenomeSource.geneSource) == \'history\':\n mkdir -p tempstargenomedir &&\n STAR\n --runMode genomeGenerate\n- --genomeDir "tempstargenomedir"\n- --genomeFastaFiles "$refGenomeSource.ownFile"\n- --runThreadN \\${GALAXY_SLOTS:-4}\n- \n- #if str($refGenomeSource.geneModel) != \'None\':\n- --sjdbOverhang "$refGenomeSource.overhang"\n- --sjdbGTFfile "$refGenomeSource.geneModel"\n- \n- #if str($refGenomeSource.geneModel.ext) == \'gff3\':\n- --sjdbGTFtagExonParentTranscript Parent\n+ --genomeDir \'tempstargenomedir\'\n+ --genomeFastaFiles \'$refGenomeSource.genomeFastaFiles\'\n+ #if $refGenomeSource.sjdbGTFfile:\n+ --sjdbGTFfile \'$refGenomeSource.sjdbGTFfile\'\n+ --sjdbOverhang \'$refGenomeSource.sjdbOverhang\'\n #end if\n- #end if\n- ;\n- #end if\n- \n- \n- ## Actual alignment\n- STAR\n- --runThreadN \\${GALAXY_SLOTS:-4}\n- --genomeLoad NoSharedMemory \n- #if str($refGenomeSource.genomeSource) == \'history\':\n- --genomeDir "tempstargenomedir"\n- #else\n- --genomeDir "$refGenomeSource.index.fields.path"\n- #end if\n- \n- --readFilesIn\n- #if str($singlePaired.sPaired) == "paired_collection"\n- "$singlePaired.input.forward" "$singlePaired.input.reverse"\n- #else\n- "$singlePaired.input1"\n- #if str($singlePaired.sPaired) == "paired"\n- "$singlePaired.input2"\n- #end if\n- #end if\n-\n- ## Output parameters\n- #if str( $output_params.output_select ) == "yes":\n- --outSAMattributes $output_params.outSAMattributes\n- --outSAMstrandField $output_params.outSAMstrandField\n- --outFilterIntronMotifs $output_params.outFilterIntronMotifs\n- #if str( $output_params.output_params2.output_select2 ) == "yes":\n- --outSAMunmapped $output_params.output_params2.unmapped_opt\n- --outSAMprimaryFlag $output_params.output_params2.primary_opt\n- --outSAMmapqUnique "$output_params.output_params2.unique"\n- --outFilterType $output_params.output_params2.sjfilter_opt\n- --outFilterMultimapScoreRange "$output_params.output_params2.multiScoreRange"\n- --outFilterMultimapNmax "$out'..b'e="mapped_reads" file="rnastar_test2_mapped_reads.bam" compare="sim_size" delta="200" />\n </test>\n-\n <test>\n <param name="input1" value="test3.fastqsanger" ftype="fastqsanger" />\n- <param name="genomeSource" value="history" />\n- <param name="ownFile" value="test3.ref.fa" />\n+ <param name="geneSource" value="history" />\n+ <param name="genomeFastaFiles" value="test3.ref.fa" />\n <param name="sPaired" value="single" />\n \n <param name="output_select" value="yes" />\n <param name="outSAMattributes" value="All" />\n <param name="outSAMstrandField" value="intronMotif" />\n <param name="settingsType" value="star_fusion" />\n- \n+\n <output name="chimeric_junctions" file="test3.chimjunc.tabular"/>\n </test>\n- \n+ <test><!-- tests fastqsanger.gz -->\n+ <param name="input1" value="test3.fastqsanger.gz" ftype="fastqsanger.gz" />\n+ <param name="geneSource" value="history" />\n+ <param name="genomeFastaFiles" value="test3.ref.fa" />\n+ <param name="sPaired" value="single" />\n+\n+ <param name="output_select" value="yes" />\n+ <param name="outSAMattributes" value="All" />\n+ <param name="outSAMstrandField" value="intronMotif" />\n+ <param name="settingsType" value="star_fusion" />\n+\n+ <output name="chimeric_junctions" file="test3.chimjunc.tabular"/>\n+ </test>\n <test>\n <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />\n- <param name="genomeSource" value="history" />\n- <param name="ownFile" value="tophat_test.fa" />\n+ <param name="geneSource" value="history" />\n+ <param name="genomeFastaFiles" value="tophat_test.fa" />\n <param name="sPaired" value="single" />\n- \n+\n <param name="output_select" value="yes" />\n <param name="outSAMattributes" value="All" />\n <param name="outSAMstrandField" value="intronMotif" />\n <param name="outFilterIntronMotifs" value="RemoveNoncanonical" />\n- \n+\n <param name="output_select2" value="yes" />\n <param name="settingsType" value="full" />\n- <param name="seed_select" value="yes" />\n- <param name="align_select" value="yes" />\n- <param name="chim_select" value="yes" />\n+ <param name="chim_select" value="false" />\n \n- <!-- Uses default settings, should be similar to test1, but tests the parameters -->\n- <output name="output_log" file="rnastar_test.log" compare="diff" lines_diff="10"/>\n+ <output name="output_log" file="rnastar_test.log" compare="diff" lines_diff="12"/>\n <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/>\n- <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" /><!-- header is 434 bytes larger -->\n+ <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" />\n </test>\n-\n </tests>\n <help>\n **What it does**\n \n-This tool runs STAR, an ultrafast universal RNA-seq aligner.\n+STAR is an ultrafast universal RNA-seq aligner.\n \n **Extra SAM attributes**\n \n@@ -500,10 +563,6 @@\n \n **Attributions**\n \n-Note that each component has its own license:\n- - RNA STAR: GPLv3\n- - samtools: MIT/Expat License\n-\n rna_star - see the web site at rna_star_\n \n For details, please see the rna_starMS_\n@@ -525,8 +584,6 @@\n .. _rna_star: https://github.com/alexdobin/STAR\n .. _rna_starMS: http://bioinformatics.oxfordjournals.org/content/29/1/15.full\n .. _Galaxy: http://getgalaxy.org\n-</help>\n- <citations>\n- <citation type="doi">10.1093/bioinformatics/bts635</citation>\n- </citations>\n+ </help>\n+ <expand macro="citations"/>\n </tool>\n' |
| b |
| diff -r ace9f5a2b40f -r 318b2a9d54dd test-data/rnastar_test.log --- a/test-data/rnastar_test.log Fri Feb 05 11:56:20 2016 -0500 +++ b/test-data/rnastar_test.log Fri Apr 21 07:58:59 2017 -0400 |
| b |
| @@ -1,7 +1,7 @@ - Started job on | Feb 18 14:00:29 - Started mapping on | Feb 18 14:00:32 - Finished on | Feb 18 14:00:33 - Mapping speed, Million of reads per hour | 0.36 + Started job on | Mar 01 15:54:22 + Started mapping on | Mar 01 15:54:25 + Finished on | Mar 01 15:54:25 + Mapping speed, Million of reads per hour | inf Number of input reads | 100 Average input read length | 75 @@ -29,3 +29,6 @@ % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 0.00% % of reads unmapped: other | 0.00% + CHIMERIC READS: + Number of chimeric reads | 0 + % of chimeric reads | 0.00% |
| b |
| diff -r ace9f5a2b40f -r 318b2a9d54dd test-data/rnastar_test2.log --- a/test-data/rnastar_test2.log Fri Feb 05 11:56:20 2016 -0500 +++ b/test-data/rnastar_test2.log Fri Apr 21 07:58:59 2017 -0400 |
| b |
| @@ -1,7 +1,7 @@ - Started job on | Jul 23 12:00:42 - Started mapping on | Jul 23 12:00:42 - Finished on | Jul 23 12:00:43 - Mapping speed, Million of reads per hour | 0.36 + Started job on | Mar 01 15:53:05 + Started mapping on | Mar 01 15:53:08 + Finished on | Mar 01 15:53:08 + Mapping speed, Million of reads per hour | inf Number of input reads | 100 Average input read length | 75 @@ -29,3 +29,6 @@ % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 10.00% % of reads unmapped: other | 0.00% + CHIMERIC READS: + Number of chimeric reads | 0 + % of chimeric reads | 0.00% |
| b |
| diff -r ace9f5a2b40f -r 318b2a9d54dd test-data/rnastar_test2_mapped_reads.bam |
| b |
| Binary file test-data/rnastar_test2_mapped_reads.bam has changed |
| b |
| diff -r ace9f5a2b40f -r 318b2a9d54dd test-data/rnastar_test_mapped_reads.bam |
| b |
| Binary file test-data/rnastar_test_mapped_reads.bam has changed |
| b |
| diff -r ace9f5a2b40f -r 318b2a9d54dd test-data/test1.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1.gtf Fri Apr 21 07:58:59 2017 -0400 |
| b |
| @@ -0,0 +1,4 @@ +test_chromosome test gene 1 650 . + . gene_id "GENE1"; gene_name "GENE1"; transcript_id "GENE1_t1"; +test_chromosome test transcript 1 650 . + . gene_id "GENE1"; gene_name "GENE1"; transcript_id "GENE1_t1"; +test_chromosome test exon 1 650 . + . gene_id "GENE1"; transcript_id "GENE1_t1"; exon_number "1"; gene_name "GENE1"; +test_chromosome test CDS 100 550 . + . gene_id "GENE1"; transcript_id "GENE1_t1"; exon_number "1"; gene_name "GENE1"; |
| b |
| diff -r ace9f5a2b40f -r 318b2a9d54dd test-data/test3.fastqsanger.gz |
| b |
| Binary file test-data/test3.fastqsanger.gz has changed |
| b |
| diff -r ace9f5a2b40f -r 318b2a9d54dd test-data/tophat_test_reads_per_gene.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tophat_test_reads_per_gene.txt Fri Apr 21 07:58:59 2017 -0400 |
| b |
| @@ -0,0 +1,5 @@ +N_unmapped 0 0 0 +N_multimapping 1 1 1 +N_noFeature 0 51 48 +N_ambiguous 0 0 0 +GENE1 99 48 51 |
| b |
| diff -r ace9f5a2b40f -r 318b2a9d54dd tool-data/rnastar_index.loc.sample --- a/tool-data/rnastar_index.loc.sample Fri Feb 05 11:56:20 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,11 +0,0 @@ -#This is a sample file distributed with Galaxy that enables tools -#to use a directory of rna-star indexed sequences data files. You will -#need to create these data files and then create a bowtie_indices.loc -#file similar to this one (store it in this directory) that points to -#the directories in which those files are stored. The bowtie2_indices.loc -#file has this format (longer white space characters are TAB characters): -# -#<unique_build_id> <dbkey> <display_name> <file_base_path> -# -#hg19 hg19 hg19 full /mnt/galaxyIndices/genomes/hg19/rnastar - |
| b |
| diff -r ace9f5a2b40f -r 318b2a9d54dd tool-data/rnastar_index2.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/rnastar_index2.loc.sample Fri Apr 21 07:58:59 2017 -0400 |
| b |
| @@ -0,0 +1,23 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of rna-star indexed sequences data files. You will +#need to create these data files and then create a rnastar_index2.loc +#file similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The rnastar_index2.loc +#file has this format (longer white space characters are TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_base_path> <withGTF> +# +#The <with_gtf> column should be 1 or 0, indicating whether the index was made +#with an annotation (i.e., --sjdbGTFfile and --sjdbOverhang were used) or not, +#respecively. +# +#Note that STAR indices can become quite large. Consequently, it is only +#advisable to create indices with annotations if it's known ahead of time that +#(A) the annotations won't be frequently updated and (B) the read lengths used +#will also rarely vary. If either of these is not the case, it's advisable to +#create indices without annotations and then specify an annotation file and +#maximum read length (minus 1) when running STAR. +# +#hg19 hg19 hg19 full /mnt/galaxyIndices/genomes/hg19/rnastar 0 +#hg19Ensembl hg19Ensembl hg19 full with Ensembl annotation /mnt/galaxyIndices/genomes/hg19Ensembl/rnastar 1 + |
| b |
| diff -r ace9f5a2b40f -r 318b2a9d54dd tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Fri Feb 05 11:56:20 2016 -0500 +++ b/tool_data_table_conf.xml.sample Fri Apr 21 07:58:59 2017 -0400 |
| b |
| @@ -1,7 +1,7 @@ <!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> <tables> - <table name="rnastar_index" comment_char="#"> - <columns>value, dbkey, name, path</columns> - <file path="tool-data/rnastar_index.loc" /> + <table name="rnastar_index2" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path, with-gtf</columns> + <file path="tool-data/rnastar_index2.loc" /> </table> </tables> |
| b |
| diff -r ace9f5a2b40f -r 318b2a9d54dd tool_dependencies.xml --- a/tool_dependencies.xml Fri Feb 05 11:56:20 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,13 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="rnastar" version="2.4.0d"> - <repository changeset_revision="54c96a529c59" name="package_rnastar_2_4_0d" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - <readme> - Installs the STAR wrapper and dependency packages samtools and star - see https://code.google.com/p/rna-star/ - STAR is a very fast mapper for rna-seq giving junctions if the indexes are constructed with a junction library - </readme> - </package> - <package name="samtools" version="0.1.19"> - <repository changeset_revision="96aab723499f" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |