# HG changeset patch # User crs4 # Date 1381946078 14400 # Node ID 0a71a7d35d092d93566950d4bea610026f02f8d1 Uploaded diff -r 000000000000 -r 0a71a7d35d09 COPYING --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/COPYING Wed Oct 16 13:54:38 2013 -0400 @@ -0,0 +1,23 @@ +Copyright © 2013 CRS4 Srl. http://www.crs4.it/ +Created by: +Andrea Pinna +Nicola Soranzo + +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: + +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. diff -r 000000000000 -r 0a71a7d35d09 blat_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/blat_wrapper.xml Wed Oct 16 13:54:38 2013 -0400 @@ -0,0 +1,229 @@ + + + + blat + + + blat $database $query -t=$databaseType.databaseType_select -q=$databaseType.queryType + #if str($databaseType.tileSize) + -tileSize=$databaseType.tileSize + #end if + #if str($stepSize) + -stepSize=$stepSize + #end if + #if $oneOff + -oneOff=1 + #end if + #if str($databaseType.minMatch) + -minMatch=$databaseType.minMatch + #end if + #if str($minScore) + -minScore=$minScore + #end if + #if str($databaseType.minIdentity) + -minIdentity=$databaseType.minIdentity + #end if + #if str($maxGap) + -maxGap=$maxGap + #end if + #if str($repMatch) + -repMatch=$repMatch + #end if + #if $mask.mask_select + -mask=$mask.mask_select + #else if $mask.repeats + -repeats=$mask.repeats + #end if + #if $qMask + -qMask=$qMask + #end if + #if str($dots) + -dots=$dots + #end if + #if $trimT + -trimT + #end if + #if $noTrimA + -noTrimA + #end if + #if $trimHardA + -trimHardA + #end if + #if $fastMap + -fastMap + #end if + #if $fine + -fine + #end if + #if str($maxIntron) + -maxIntron=$maxIntron + #end if + #if $extendThroughN + -extendThroughN + #end if + -out=$out + $output > $logfile + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +BLAT produces two major classes of alignments: + +- at the DNA level between two sequences that are of 95% or greater identity, but which may include large inserts; +- at the protein or translated DNA level between sequences that are of 80% or greater identity and may also include large inserts. + +The output of BLAT is flexible. By default it is a simple tab-delimited file which describes the alignment, but which does not include the sequence of the alignment itself. Optionally it can produce BLAST and WU-BLAST compatible output as well as a number of other formats. + +**License and citation** + +This Galaxy tool is Copyright © 2013 `CRS4 Srl.`_ and is released under the `MIT license`_. + +.. _CRS4 Srl.: http://www.crs4.it/ +.. _MIT license: http://opensource.org/licenses/MIT + +If you use this tool in Galaxy, please cite |Cuccuru2013|_. + +.. |Cuccuru2013| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2013) Orione, a web-based framework for NGS analysis in microbiology. *Submitted* +.. _Cuccuru2013: http://orione.crs4.it/ + +This tool uses `BLAT`_, which is licensed separately. Please cite |Kent2002|_. + +.. _BLAT: http://genome.ucsc.edu/FAQ/FAQblat.html +.. |Kent2002| replace:: Kent, W. J. (2002) BLAT – The BLAST-Like Alignment Tool. *Genome Res.* 12(4), 656-664 +.. _Kent2002: http://genome.cshlp.org/content/12/4/656 + + diff -r 000000000000 -r 0a71a7d35d09 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Oct 16 13:54:38 2013 -0400 @@ -0,0 +1,15 @@ + + + + + + + http://hgwdev.cse.ucsc.edu/~kent/src/blatSrc35.zip + export MACHTYPE=`uname -m` && export HOME=$INSTALL_DIR && mkdir -p $HOME/bin/$MACHTYPE && make + + $INSTALL_DIR/bin/`uname -m` + + + + +