# HG changeset patch # User Vimalkumar Velayudhan # Date 1445948979 0 # Node ID 5a242f289347ba7c245b8f81712367b258dac7b3 # Parent 423ad61697c4cfac36d8aa0aee200ddfa85ba79b# Parent de357bab306db34fda42f7a073c19ae4d52eeadc Merge diff -r 423ad61697c4 -r 5a242f289347 .hgignore --- a/.hgignore Tue Oct 27 12:21:50 2015 +0000 +++ b/.hgignore Tue Oct 27 12:29:39 2015 +0000 @@ -1,3 +1,4 @@ syntax: glob +.git* *.pyc diff -r 423ad61697c4 -r 5a242f289347 Galaxy-Workflow-riboSeqR_chlamydomonas_test_data.ga --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Galaxy-Workflow-riboSeqR_chlamydomonas_test_data.ga Tue Oct 27 12:29:39 2015 +0000 @@ -0,0 +1,155 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "", + "format-version": "0.1", + "name": "riboSeqR chlamydomonas test data", + "steps": { + "0": { + "annotation": "", + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Input Dataset" + } + ], + "name": "Input dataset", + "outputs": [], + "position": { + "left": 10, + "top": 10 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"Input Dataset\"}", + "tool_version": null, + "type": "data_input", + "user_outputs": [] + }, + "1": { + "annotation": "", + "id": 1, + "input_connections": { + "rdata_load": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "name": "Triplet Periodicity", + "outputs": [ + { + "name": "rdata_save", + "type": "rda" + }, + { + "name": "html_file", + "type": "html" + } + ], + "position": { + "left": 230, + "top": 10 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/vimalkumarvelayudhan/riboseqr_wrapper/riboseqr_triplet_periodicity/0.4.0", + "tool_state": "{\"__page__\": 0, \"analyze_plot_lengths\": \"\\\"26:30\\\"\", \"include_lengths\": \"\\\"25:30\\\"\", \"fasta_file\": \"null\", \"stop_codons\": \"\\\"TAG, TAA, TGA\\\"\", \"start_codons\": \"\\\"ATG\\\"\", \"rdata_load\": \"null\", \"text_legend\": \"\\\"Frame 0, Frame 1, Frame 2\\\"\", \"chromInfo\": \"\\\"/mnt/workspace/DATA/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null}", + "tool_version": null, + "type": "tool", + "user_outputs": [] + }, + "2": { + "annotation": "", + "id": 2, + "input_connections": { + "rdata_load": { + "id": 1, + "output_name": "rdata_save" + } + }, + "inputs": [], + "name": "Metagene Analysis", + "outputs": [ + { + "name": "rdata_save", + "type": "rda" + }, + { + "name": "html_file", + "type": "html" + } + ], + "position": { + "left": 450, + "top": 10 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/vimalkumarvelayudhan/riboseqr_wrapper/riboseqr_metagene/0.4.0", + "tool_state": "{\"__page__\": 0, \"rdata_load\": \"null\", \"unique_hit_mean\": \"\\\"10\\\"\", \"min3p\": \"\\\"-200\\\"\", \"__rerun_remap_job_id__\": null, \"cap\": \"\\\"\\\"\", \"ratio_check\": \"\\\"True\\\"\", \"max3p\": \"\\\"20\\\"\", \"plot_lengths\": \"\\\"27,28\\\"\", \"max5p\": \"\\\"200\\\"\", \"selected_lengths\": \"\\\"27,28\\\"\", \"plot_title\": \"\\\"\\\"\", \"hit_mean\": \"\\\"50\\\"\", \"selected_frames\": \"\\\"1,0\\\"\", \"chromInfo\": \"\\\"/mnt/workspace/DATA/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"min5p\": \"\\\"-20\\\"\"}", + "tool_version": null, + "type": "tool", + "user_outputs": [] + }, + "3": { + "annotation": "", + "id": 3, + "input_connections": { + "rdata_load": { + "id": 2, + "output_name": "rdata_save" + } + }, + "inputs": [], + "name": "Plot Ribosome Profile", + "outputs": [ + { + "name": "html_file", + "type": "html" + } + ], + "position": { + "left": 670, + "top": 10 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/vimalkumarvelayudhan/riboseqr_wrapper/riboseqr_ribosome_profile/0.4.0", + "tool_state": "{\"__page__\": 0, \"transcript_cap\": \"\\\"200\\\"\", \"__rerun_remap_job_id__\": null, \"transcript_length\": \"\\\"27\\\"\", \"rdata_load\": \"null\", \"transcript_name\": \"\\\"CUFF.37930.1\\\"\", \"chromInfo\": \"\\\"/mnt/workspace/DATA/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", + "tool_version": null, + "type": "tool", + "user_outputs": [] + }, + "4": { + "annotation": "", + "id": 4, + "input_connections": { + "rdata_load": { + "id": 2, + "output_name": "rdata_save" + } + }, + "inputs": [], + "name": "Differential Translation Analysis", + "outputs": [ + { + "name": "html_file", + "type": "html" + } + ], + "position": { + "left": 670, + "top": 130 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/vimalkumarvelayudhan/riboseqr_wrapper/difftrans/0.1.0", + "tool_state": "{\"normalize\": \"\\\"True\\\"\", \"__page__\": 0, \"num_counts\": \"\\\"10\\\"\", \"__rerun_remap_job_id__\": null, \"rdata_load\": \"null\", \"group1\": \"\\\"1,1,1,1\\\"\", \"frames_type\": \"{\\\"select_frames\\\": \\\"each\\\", \\\"frames_each\\\": \\\"0,2\\\", \\\"__current_case__\\\": 1}\", \"group2\": \"\\\"WT,WT,M,M\\\"\", \"frames\": \"\\\"0,2\\\"\", \"slice_lengths\": \"\\\"27,28\\\"\", \"chromInfo\": \"\\\"/mnt/workspace/DATA/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", + "tool_version": null, + "type": "tool", + "user_outputs": [] + } + } +} diff -r 423ad61697c4 -r 5a242f289347 README.rst --- a/README.rst Tue Oct 27 12:21:50 2015 +0000 +++ b/README.rst Tue Oct 27 12:29:39 2015 +0000 @@ -1,22 +1,13 @@ -README ------- - +riboseqr_wrapper +================ `riboSeqR `_ -integration for `Galaxy `_ / -`RiboGalaxy `_. +integration for `RiboGalaxy `_ and `Galaxy `_. Included tools -.............. -In the order in which they are run - -#. Prepare riboSeqR Input +-------------- +In the order they are run - Prepare riboSeqR format input files from alignment files (SAM format, - Ribo-Seq or RNA-Seq alignments). - -#. Triplet Periodicity - - Plot triplet periodicity for different read lengths. +#. Plot triplet periodicity for different read lengths. #. Metagene Analysis @@ -33,12 +24,52 @@ Get Ribo and RNA-Seq counts with riboSeqR. Perform differential translation analysis with baySeq. -Tested with -........... -**R** ``3.1.2`` +Dependencies +------------ +Tested on Ubuntu Linux 14.04 LTS, 64-bit. Dependencies should install automatically on Linux 64-bit. + +R ``3.1.2``, riboSeqR ``1.0.5``, baySeq ``2.0.50``, rpy2 ``2.3.10``. + +How to test +----------- +1. Upload the following test data files from the test-data folder. + + Prepare riboSeqR input (R data file) + + rsem_chlamy236_deNovo.transcripts.fa + +2. A workflow with test data is included in this repository. All tools with the exception of "Prepare riboSeqR input" + can currently be tested using this workflow. Import this workflow into Galaxy. + +3. Run workflow + + In Step 1 of the workflow, select "Prepare riboSeqR input (R data file)" as input. + + In Step 2, select rsem_chlamy236_deNovo.transcripts.fa as input. + + Run workflow. -**riboSeqR** ``1.0.5`` + +About the test data files +......................... +The included "Prepare riboSeqR input (R data file)" is saved from an R session using sample data included with the +riboSeqR package. The commands used were :: + + library(riboSeqR) + + datadir <- system.file("extdata", package = "riboSeqR") + chlamyFasta <- paste(datadir, "/rsem_chlamy236_deNovo.transcripts.fa", sep = "") -**baySeq** ``2.0.50`` + fastaCDS <- findCDS(fastaFile = chlamyFasta, startCodon = c("ATG"), stopCodon = c("TAG", "TAA", "TGA")) + + ribofiles <- paste(datadir, "/chlamy236_plus_deNovo_plusOnly_Index", c(17,3,5,7), sep = "") + rnafiles <- paste(datadir, "/chlamy236_plus_deNovo_plusOnly_Index", c(10,12,14,16), sep = "") -**rpy2** ``2.3.10`` + riboDat <- readRibodata(ribofiles, rnafiles, replicates = c("WT", "WT", "M", "M")) + save(riboDat, file="Prepare riboSeqR input (R data file)") + +rsem_chlamy236_deNovo.transcripts.fa - sample data from the riboSeqR package. + +Bugs/Issues? +------------ +Please report here https://github.com/vimalkumarvelayudhan/riboseqr_wrapper/issues diff -r 423ad61697c4 -r 5a242f289347 difftrans.xml --- a/difftrans.xml Tue Oct 27 12:21:50 2015 +0000 +++ b/difftrans.xml Tue Oct 27 12:29:39 2015 +0000 @@ -25,7 +25,7 @@ --output_path "$html_file.files_path" - - + diff -r 423ad61697c4 -r 5a242f289347 metagene.xml --- a/metagene.xml Tue Oct 27 12:21:50 2015 +0000 +++ b/metagene.xml Tue Oct 27 12:29:39 2015 +0000 @@ -27,7 +27,7 @@ --output_path "$html_file.files_path" - @@ -103,14 +103,14 @@ - - + @@ -119,7 +119,7 @@ - + diff -r 423ad61697c4 -r 5a242f289347 ribosome_profile.xml --- a/ribosome_profile.xml Tue Oct 27 12:21:50 2015 +0000 +++ b/ribosome_profile.xml Tue Oct 27 12:29:39 2015 +0000 @@ -21,7 +21,7 @@ --output_path "$html_file.files_path" - - + diff -r 423ad61697c4 -r 5a242f289347 test-data/Prepare riboSeqR input (R data file) diff -r 423ad61697c4 -r 5a242f289347 triplet.xml --- a/triplet.xml Tue Oct 27 12:21:50 2015 +0000 +++ b/triplet.xml Tue Oct 27 12:29:39 2015 +0000 @@ -25,7 +25,7 @@ --output_path "$html_file.files_path" - - - - - - - - - - - - - - - + + + + + + + + + + + + + Triplet Periodicity -------------------