Mercurial > repos > timpalpant > java_genomics_toolkit
changeset 7:4fc118372ae7
Uploaded new version with fixes and broader support for interval files
| author | timpalpant |
|---|---|
| date | Sun, 19 Feb 2012 01:54:28 -0500 |
| parents | 422ac2bbb274 |
| children | 5a3f8b0b80f9 |
| files | dist/java-genomics-toolkit.jar galaxy-conf/._BaseAlignCounts.xml galaxy-conf/._Phasogram.xml 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/.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 lib/java-genomics-io.jar lib/mg4j-2.0.1.jar |
| diffstat | 23 files changed, 8 insertions(+), 349 deletions(-) [+] |
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--- 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 @@ -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" />
--- 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 @@ -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>
--- 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 @@ -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>
--- 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 @@ -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" />
--- 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 @@ -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>
--- 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 @@ -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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