# HG changeset patch # User pitagora # Date 1427343514 -32400 # Node ID 0283d2d3f8d6e4a6854d03947fe85331468ef139 # Parent 05154d5ffbdbb4454addce4e540eb343b6d10c60 commit diff -r 05154d5ffbdb -r 0283d2d3f8d6 README.rst --- a/README.rst Thu Mar 26 13:15:17 2015 +0900 +++ b/README.rst Thu Mar 26 13:18:34 2015 +0900 @@ -1,53 +1,9 @@ -Galaxy wrappers for sailfish -===================================== - -These wrappers are copyright 2014 by Björn Grüning and additional contributors. -All rights reserved. See the licence text below. - -Currently tested with sailfish 0.6.3. - - -Automated Installation -====================== +This code is originated from the followings. Prease refer them for the licence information: -Galaxy should be able to automatically install the sailfish for you. - - -History -======= - -======== ====================================================================== -Version Changes --------- ---------------------------------------------------------------------- -v0.6.3.0 - First release - -======== ====================================================================== - +Mika Yoshimura's code: https://github.com/myoshimura080822/galaxy-mytools_sailfish -Bug Reports -=========== - -You can file an issue here https://github.com/bgruening/galaxytools/issues or ask -us on the Galaxy development list http://lists.bx.psu.edu/listinfo/galaxy-dev - - -Licence (MIT) -============= +Björn Grüning's code: https://github.com/bgruening/galaxytools/tree/master/tools/sailfish -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: +If you use this Galaxy tool in work leading to a scientific publication please cite the following: -The above copyright notice and this permission notice shall be included in -all copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN -THE SOFTWARE. +Sailfish: http://www.cs.cmu.edu/~ckingsf/software/sailfish/ diff -r 05154d5ffbdb -r 0283d2d3f8d6 sailfish.xml --- a/sailfish.xml Thu Mar 26 13:15:17 2015 +0900 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,81 +0,0 @@ - - transcript quantification from RNA-seq data - sailfish -version - - ->" - #elif $single_or_paired_opts.orientation == "away": - -l "TYPE=PE:O=<>" - #else: - -l "TYPE=PE:O=><" - #end if - #end if --o - -]]> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -> denotes that the mates are oriented in the same direction --- e.g. if the 5' end of mate 1 is -upstream from the 3' end, then the 5' end of mate 2 is upstream from its 3' end and vice-versa. - -The second option <> denotes that the mates are oriented away from each other. This implies that start -of mate1 is closer to start of mate 2 than the end of mate 2, etc. - -The third option >< is, perhaps, the most common relative orientation. It denotes that the mates are -oriented toward each other, so that the start of mate 1 is farther from the start of mate 2 than it is from the end of mate 2 and vice-versa. - -------- - -**References** - -If you use this Galaxy tool in work leading to a scientific publication please -cite the following: - - -]]> - - diff -r 05154d5ffbdb -r 0283d2d3f8d6 sailfish_linux.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sailfish_linux.xml Thu Mar 26 13:18:34 2015 +0900 @@ -0,0 +1,117 @@ + + + transcript quantification from RNA-seq data + sailfish -version + + + sailfish_linux + + +>:S=S" + #elif $single_or_paired.strandedness == "antisense": + -l "T=PE:O=>>:S=A" + #else: + -l "T=PE:O=>>:S=U" + #end if + #elif $single_or_paired.orientation == "away": + #if $single_or_paired.strandedness == "sense": + -l "T=PE:O=<>:S=S" + #elif $single_or_paired.strandedness == "antisense": + -l "T=PE:O=<>:S=A" + #else: + -l "T=PE:O=<>:S=U" + #end if + #else: + #if $single_or_paired.strandedness == "sense": + -l "T=PE:O=><:S=S" + #elif $single_or_paired.strandedness == "antisense": + -l "T=PE:O=><:S=A" + #else: + -l "T=PE:O=><:S=U" + #end if + #end if + -1 $single_or_paired.input_mate1 + -2 $single_or_paired.input_mate2 + #end if + -o ./ >> $log 2>&1 +]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +> denotes that the mates are oriented in the same direction --- e.g. if the 5' end of mate 1 is +upstream from the 3' end, then the 5' end of mate 2 is upstream from its 3' end and vice-versa. + +The second option <> denotes that the mates are oriented away from each other. This implies that start +of mate1 is closer to start of mate 2 than the end of mate 2, etc. + +The third option >< is, perhaps, the most common relative orientation. It denotes that the mates are +oriented toward each other, so that the start of mate 1 is farther from the start of mate 2 than it is from the end of mate 2 and vice-versa. + +------- + +**References** + +This code is originated from the followings. Prease refer them for the licence information: + +Mika Yoshimura's code: https://github.com/myoshimura080822/galaxy-mytools_sailfish + +Björn Grüning's code: https://github.com/bgruening/galaxytools/tree/master/tools/sailfish + +If you use this Galaxy tool in work leading to a scientific publication please cite the following: + +Sailfish: http://www.cs.cmu.edu/~ckingsf/software/sailfish/ + +]]> + + + diff -r 05154d5ffbdb -r 0283d2d3f8d6 tool_dependencies.xml --- a/tool_dependencies.xml Thu Mar 26 13:15:17 2015 +0900 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ - - - - - - diff -r 05154d5ffbdb -r 0283d2d3f8d6 tool_dependency.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependency.xml Thu Mar 26 13:18:34 2015 +0900 @@ -0,0 +1,7 @@ + + + + + + +