| Previous changeset 6:422ac2bbb274 (2012-02-14) Next changeset 8:5a3f8b0b80f9 (2012-02-28) |
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Commit message:
Uploaded new version with fixes and broader support for interval files |
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modified:
dist/java-genomics-toolkit.jar galaxy-conf/BaseAlignCounts.xml galaxy-conf/MapDyads.xml galaxy-conf/Phasogram.xml galaxy-conf/RollingReadLength.xml galaxy-conf/WigSummary.xml galaxy-conf/log4j.properties lib/java-genomics-io.jar |
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added:
galaxy-conf/._Phasogram.xml lib/mg4j-2.0.1.jar |
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removed:
galaxy-conf/._BaseAlignCounts.xml lib/.DS_Store lib/._.DS_Store lib/._bin lib/._macify-1.4.jar lib/bin/._COPYING lib/bin/._ld lib/bin/._readme.txt lib/bin/._windres lib/bin/COPYING lib/bin/ld lib/bin/readme.txt lib/bin/windres |
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| diff -r 422ac2bbb274 -r 4fc118372ae7 dist/java-genomics-toolkit.jar |
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| Binary file dist/java-genomics-toolkit.jar has changed |
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| diff -r 422ac2bbb274 -r 4fc118372ae7 galaxy-conf/._BaseAlignCounts.xml |
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| Binary file galaxy-conf/._BaseAlignCounts.xml has changed |
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| diff -r 422ac2bbb274 -r 4fc118372ae7 galaxy-conf/._Phasogram.xml |
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| Binary file galaxy-conf/._Phasogram.xml has changed |
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| diff -r 422ac2bbb274 -r 4fc118372ae7 galaxy-conf/BaseAlignCounts.xml --- a/galaxy-conf/BaseAlignCounts.xml Tue Feb 14 18:40:50 2012 -0500 +++ b/galaxy-conf/BaseAlignCounts.xml Sun Feb 19 01:54:28 2012 -0500 |
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| @@ -2,8 +2,8 @@ <description>of sequencing reads</description> <command interpreter="sh">galaxyToolRunner.sh ngs.BaseAlignCounts -i $input -a ${chromInfo} -x $X -o $output</command> <inputs> - <param name="input" type="data" format="bam" label="Sequencing reads" /> - <param name="X" type="integer" value="0" label="In silico extension (leave 0 for read length)" /> + <param name="input" type="data" format="sam,bam,bed,bedgraph" label="Sequencing reads" /> + <param name="X" type="integer" value="-1" label="In silico extension (-1 for read length)" /> </inputs> <outputs> <data name="output" format="wig" /> |
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| diff -r 422ac2bbb274 -r 4fc118372ae7 galaxy-conf/MapDyads.xml --- a/galaxy-conf/MapDyads.xml Tue Feb 14 18:40:50 2012 -0500 +++ b/galaxy-conf/MapDyads.xml Sun Feb 19 01:54:28 2012 -0500 |
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| @@ -7,7 +7,7 @@ #end if </command> <inputs> - <param name="input" type="data" format="bam" label="Sequencing reads" /> + <param name="input" type="data" format="sam,bam,bed,bedGraph" label="Sequencing reads" /> <conditional name="type"> <param name="read" type="select" label="Type of reads"> <option value="paired" selected="true">Paired-End</option> |
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| diff -r 422ac2bbb274 -r 4fc118372ae7 galaxy-conf/Phasogram.xml --- a/galaxy-conf/Phasogram.xml Tue Feb 14 18:40:50 2012 -0500 +++ b/galaxy-conf/Phasogram.xml Sun Feb 19 01:54:28 2012 -0500 |
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| @@ -2,7 +2,7 @@ <description>of dyads</description> <command interpreter="sh">galaxyToolRunner.sh nucleosomes.Phasogram -i $input -m $max -o $output</command> <inputs> - <param name="input" type="data" format="bigwig,wig" label="Dyads BigWig file" /> + <param name="input" type="data" format="bigwig,wig" label="Dyads (Big)Wig file" /> <param name="max" type="integer" value="1000" label="Maximum phase shift (bp)" /> </inputs> <outputs> |
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| diff -r 422ac2bbb274 -r 4fc118372ae7 galaxy-conf/RollingReadLength.xml --- a/galaxy-conf/RollingReadLength.xml Tue Feb 14 18:40:50 2012 -0500 +++ b/galaxy-conf/RollingReadLength.xml Sun Feb 19 01:54:28 2012 -0500 |
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| @@ -2,7 +2,7 @@ <description>from paired-end sequencing reads</description> <command interpreter="sh">galaxyToolRunner.sh ngs.RollingReadLength -i $input -a ${chromInfo} -o $output</command> <inputs> - <param format="bam" name="input" type="data" label="Mapped reads" /> + <param format="sam,bam,bed,bedgraph" name="input" type="data" label="Mapped reads" /> </inputs> <outputs> <data format="wig" name="output" /> |
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| diff -r 422ac2bbb274 -r 4fc118372ae7 galaxy-conf/WigSummary.xml --- a/galaxy-conf/WigSummary.xml Tue Feb 14 18:40:50 2012 -0500 +++ b/galaxy-conf/WigSummary.xml Sun Feb 19 01:54:28 2012 -0500 |
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| @@ -5,7 +5,7 @@ <param format="bigwig,wig" name="input" type="data" label="(Big)Wig file" /> </inputs> <outputs> - <data format="text" name="output" /> + <data format="txt" name="output" /> </outputs> <help> |
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| diff -r 422ac2bbb274 -r 4fc118372ae7 galaxy-conf/log4j.properties --- a/galaxy-conf/log4j.properties Tue Feb 14 18:40:50 2012 -0500 +++ b/galaxy-conf/log4j.properties Sun Feb 19 01:54:28 2012 -0500 |
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| @@ -1,10 +1,10 @@ -log4j.rootLogger=warn, stdout +log4j.rootLogger=info, stdout log4j.appender.stdout=org.apache.log4j.ConsoleAppender log4j.appender.stdout.layout=org.apache.log4j.PatternLayout # Pattern to output the caller's file name and line number. -log4j.appender.stdout.layout.ConversionPattern=%5p - %m%n +log4j.appender.stdout.layout.ConversionPattern=%m%n # Only output errors from the BigWig library log4j.logger.org.broad.igv.bbfile=ERROR \ No newline at end of file |
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| diff -r 422ac2bbb274 -r 4fc118372ae7 lib/.DS_Store |
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| diff -r 422ac2bbb274 -r 4fc118372ae7 lib/._.DS_Store |
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| diff -r 422ac2bbb274 -r 4fc118372ae7 lib/._bin |
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| diff -r 422ac2bbb274 -r 4fc118372ae7 lib/._macify-1.4.jar |
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| diff -r 422ac2bbb274 -r 4fc118372ae7 lib/bin/._COPYING |
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| diff -r 422ac2bbb274 -r 4fc118372ae7 lib/bin/._ld |
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| diff -r 422ac2bbb274 -r 4fc118372ae7 lib/bin/._readme.txt |
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| diff -r 422ac2bbb274 -r 4fc118372ae7 lib/bin/._windres |
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| diff -r 422ac2bbb274 -r 4fc118372ae7 lib/bin/COPYING --- a/lib/bin/COPYING Tue Feb 14 18:40:50 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,340 +0,0 @@\n-\t\t GNU GENERAL PUBLIC LICENSE\n-\t\t Version 2, June 1991\n-\n- Copyright (C) 1989, 1991 Free Software Foundation, Inc.\n- 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA\n- Everyone is permitted to copy and distribute verbatim copies\n- of this license document, but changing it is not allowed.\n-\n-\t\t\t Preamble\n-\n- The licenses for most software are designed to take away your\n-freedom to share and change it. By contrast, the GNU General Public\n-License is intended to guarantee your freedom to share and change free\n-software--to make sure the software is free for all its users. This\n-General Public License applies to most of the Free Software\n-Foundation\'s software and to any other program whose authors commit to\n-using it. (Some other Free Software Foundation software is covered by\n-the GNU Library General Public License instead.) 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| diff -r 422ac2bbb274 -r 4fc118372ae7 lib/bin/readme.txt --- a/lib/bin/readme.txt Tue Feb 14 18:40:50 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,1 +0,0 @@ -The MinGW binutils were built on Mac OS X 10.4 by Peter Centgraf |
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| diff -r 422ac2bbb274 -r 4fc118372ae7 lib/java-genomics-io.jar |
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