{"push_id":1422540550,"size":1,"distinct_size":1,"ref":"refs/heads/master","head":"5937e8d61ae1203ebf2a536c669ba701b485cd1a","before":"b9d202134c3c6d0e5c398c3ae75e410067fcfc52","commits":[{"sha":"5937e8d61ae1203ebf2a536c669ba701b485cd1a","author":{"name":"Dilmurat Yusuf","email":"d85cd94da502a6a886cd66141ca9980d5f25f018@gmail.com"},"message":"Pipmir (#437)\n\n* add ribotaper\r\n\r\n* add newline at end of file\r\n\r\n* initialize create_annotation_files.xml\r\n\r\n* initialize ribotaper.xml\r\n\r\n* initialize create_metaplots.xml\r\n\r\n* galaxy ribotaper: add script folder\r\n\r\n* Ribotaper.sh: run R files with Rscript in commandline\r\n\r\n* create_annotation_files.xml: use a file to record annotation_path\r\n\r\n* ribotaper.xml: add input param for annotation_path\r\n\r\n* create_annotation_files.xml: use tar ball to output dir\r\n\r\n* create_metaplots.xml: modify command, input, output\r\nthe major change is to use gs to merge pdfs from create_metaplots.bash, then output the merged pdf.\r\n\r\n* ribotaper.xml: modify command, input and output.\r\nThe major change is to use tarball as one input to pass annotation directory. For the outputs, the number is increased from 2 to 8 files.\r\n\r\n* CCDS_orf_finder.R: prepend 'Rscript' so that include_multi_nomerge.R does not only rely on /usr/bin/Rscript\r\n\r\n* NONCCDS_orf_finder.R: prepend 'Rscript'\r\nThe reason is to avoid include_multi_nomerge.R only relying on /usr/bin/Rscript\r\n\r\n* Ribotaper_ORF_find.sh: prepend 'Rscript'\r\nThe reason is to avoid R files only relying on /usr/bin/Rscript\r\n\r\n* create_annotations_files.bash: prepend 'Rscript'\r\nThe reason is to avoid R files only relying on /usr/bin/Rscript\r\n\r\n* create_annotations_files.bash: prepend 'Rscript and add '/''\r\nThe reason is to avoid R files only relying on /usr/bin/Rscript. Some paths in the R file are missing '/'\r\n\r\n* create_metaplots.xml: modify inputs for the command, find.\r\nThe previous one failed with *.pdf. It now succeeds with *.pdf.\r\n\r\n* ribotaper.xml: add temporary tags in the help sections to guide the edition by Lorenzo.\r\n\r\n* create_annotation_files.xml: define test output\r\n\r\n* create_annotation_files.xml: provide help message.\r\n\r\n* create_metaplots.xml: define test parameters and output\r\n\r\n* ribotaper.xml: modify outputs and tests\r\nIn outputs, provide correct file names for ORFs_max and ORFs_max_filt. In tests, provide an additional parameter for .\r\n\r\n* create_metaplots.bash: provide tag to pdf files while moving them to metaplots\r\nThe reason is to restrict file movement to the pdf files only generated by metagene analysis.\r\n\r\n* add additional files to test-data folder for automatic test of the tools\r\n\r\n* rename galaxy tools of ribotaper\r\n\r\n* ribotaper conda package\r\nbuilt recipes for  r-multitaper,  r-xnomial, ribotaper\r\n\r\n* galaxy ribotaper: latest status\r\n\r\n* add the version of ribotaper\r\n\r\n* add addtional output for the table\r\n\r\n* ribotaper_part1_create_annotation_files.xml: update the help section.\r\n\r\n* ribotaper_part2_create_metaplots.xml: updated the help section\r\n\r\n* ribotaper_part3_main.xml: update the help section\r\n\r\n* delete the obsolete files\r\n\r\n* add metagene to test-data\r\n\r\n* create pipmir/.shed.yml\r\n\r\n* add pipmir/test-data/Aligned.out.sam\r\n\r\n* add pipmir/test-data/test_seq.2bit\r\n\r\n* add pipmir/test-data/test_predicted_miRNAs.txt\r\n\r\n* build pipmir/pipmir.xml\r\n\r\n* add bit_genome.loc.sample\r\n\r\n* add tool_data_table_conf.xml.sample\r\n\r\n* pipmir/pipmir.xml: polish help info\r\n\r\n* pipmir/pipmir.xml: add space\r\nThe extra space removes the extra blank line in the Galaxy display\r\n\r\n* pipmir/pipmir.xml: differentiate param name and option keyword\r\n\r\n* pipmir/pipmir.xml: unify the usage of single/double quotes in command\r\n\r\n* pipmir/pipmir.xml: use twobit\r\nto conform with the exsiting data table and loc file in the galaxy community\r\n\r\n* pipmir/pipmir.xml: use fasta instead of 2bit as input\r\n\r\n* add test-data/test_seq.fa\r\n\r\n* delete test-data/test_seq.2bit\r\n\r\n* pipmir/pipmir.xml: set minimum values for integer\r\n\r\n* pipmir/pipmir.xml: use twobit_update\r\nthe existing one seems to be outdated\r\n\r\n* delete tool-data/2bit_genome.loc.sample\r\n\r\n* pipmir/tool_data_table_conf.xml.sample: use twobit_update\r\n\r\n* add tool-data/twobit_update.loc.sample\r\n\r\n* pipmir/pipmir.xml: add two more outputs for testing\r\n\r\n* add test-data/test_predictedPrecursors.txt test-data/test_putativeMatures.bed\r\n\r\n* tool-data/twobit_update.loc.sample: update comment\r\n\r\n* pipmir/pipmir.xml: use lastz_seqs for 2bit location\r\n\r\n* pipmir/tool_data_table_conf.xml.sample: use lastz_seqs\r\n\r\n* add lastz_seqs.loc.sample\r\n\r\n* delete tool-data/twobit_update.loc.sample","distinct":true,"url":"https://api.github.com/repos/bgruening/galaxytools/commits/5937e8d61ae1203ebf2a536c669ba701b485cd1a"}]}
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