# HG changeset patch # User brasset_jensen # Date 1548847592 18000 # Node ID ff36e76d696a2af8edaaabae3312b738db0a9a97 # Parent 0e9adbd82bb4f3b8efcbaa43c5ff4c495fd567e7 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 42877e3bba93278af4319cee455e189712cc85c3 diff -r 0e9adbd82bb4 -r ff36e76d696a LICENSE --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/LICENSE Wed Jan 30 06:26:32 2019 -0500 @@ -0,0 +1,186 @@ +Academic Free License (AFL) v. 3.0 + +This Academic Free License (the "License") applies to any original +work of authorship (the "Original Work") whose owner (the "Licensor") +has placed the following licensing notice adjacent to the copyright +notice for the Original Work: + +Licensed under the Academic Free License version 3.0 + +1) Grant of Copyright License. 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However, You may modify the text of this License +and copy, distribute or communicate your modified version (the +"Modified License") and apply it to other original works of authorship +subject to the following conditions: (i) You may not indicate in any +way that your Modified License is the "Academic Free License" or "AFL" +and you may not use those names in the name of your Modified License; +(ii) You must replace the notice specified in the first paragraph +above with the notice "Licensed under " +or with a notice of your own that is not confusingly similar to the +notice in this License; and (iii) You may not claim that your original +works are open source software unless your Modified License has been +approved by Open Source Initiative (OSI) and You comply with its +license review and certification process. diff -r 0e9adbd82bb4 -r ff36e76d696a bin/sRNAPipe.pl --- a/bin/sRNAPipe.pl Wed Jan 30 02:41:24 2019 -0500 +++ b/bin/sRNAPipe.pl Wed Jan 30 06:26:32 2019 -0500 @@ -278,7 +278,7 @@ Usage: -sRNAPipe --fastq --fastq_n [--fastq --fastq_n --fastq -- fastq_n ...] --ref [--build_index] --transcripts [--build_transcripts] --TE [--build_TE] --miRNAs [--build_miRNAs] --snRNAs [--build_snRNAs] --rRNAs [--build_rRNAs] --tRNAs [--buid_tRNAs] [options] +sRNAPipe.pl --fastq --fastq_n [--fastq --fastq_n --fastq -- fastq_n ...] --ref [--build_index] --transcripts [--build_transcripts] --TE [--build_TE] --miRNAs [--build_miRNAs] --snRNAs [--build_snRNAs] --rRNAs [--build_rRNAs] --tRNAs [--buid_tRNAs] [options] Arguments: --fastq \t\tFastq file to process diff -r 0e9adbd82bb4 -r ff36e76d696a sRNAPipe.xml --- a/sRNAPipe.xml Wed Jan 30 02:41:24 2019 -0500 +++ b/sRNAPipe.xml Wed Jan 30 06:26:32 2019 -0500 @@ -252,20 +252,6 @@ "https://github.com/brassetjensen/sRNAPipe/blob/master/sRNAPipe_User_Manual.pdf" - 10.1038/nature12962 - 10.1038/nature11233 - 10.1186/gb4172 - 10.1038/nature04916 - 10.1016/j.cell.2007.01.043 - 10.1016/j.celrep.2015.02.062 - 10.1093/bioinformatics/btp324 - 10.1093/bioinformatics/btp352 - 10.1002/0471250953.bi1112s47 - 10.1093/bioinformatics/btu379 - 10.1002/embr.201337898 - 10.1038/ncomms13739 - 10.1093/nar/gkt310 - 10.1186/s13072-015-0041-5 - 10.1093/bioinformatics/btu647 + 10.1186/s13100-018-0130-7