| Previous changeset 4:4b32ed5d4a1b (2012-02-14) Next changeset 6:422ac2bbb274 (2012-02-14) |
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Commit message:
Uploaded |
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modified:
dist/java-genomics-toolkit.jar galaxy-conf/BaseAlignCounts.xml galaxy-conf/MapDyads.xml galaxy-conf/NRLCalculator.xml galaxy-conf/Phasogram.xml |
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added:
galaxy-conf/._BaseAlignCounts.xml |
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| diff -r 4b32ed5d4a1b -r 604c98e58034 dist/java-genomics-toolkit.jar |
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| Binary file dist/java-genomics-toolkit.jar has changed |
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| diff -r 4b32ed5d4a1b -r 604c98e58034 galaxy-conf/._BaseAlignCounts.xml |
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| Binary file galaxy-conf/._BaseAlignCounts.xml has changed |
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| diff -r 4b32ed5d4a1b -r 604c98e58034 galaxy-conf/BaseAlignCounts.xml --- a/galaxy-conf/BaseAlignCounts.xml Tue Feb 14 00:59:33 2012 -0500 +++ b/galaxy-conf/BaseAlignCounts.xml Tue Feb 14 13:04:54 2012 -0500 |
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| @@ -1,6 +1,6 @@ <tool id="BaseAlignCounts" name="Map coverage" version="1.0.0"> <description>of sequencing reads</description> - <command interpreter="sh">galaxyToolRunner.sh ngs.BaseAlignCounts -i $input -g ${chromInfo} -x $X -o $output</command> + <command interpreter="sh">galaxyToolRunner.sh ngs.BaseAlignCounts -i $input -a ${chromInfo} -x $X -o $output</command> <inputs> <param name="input" type="data" format="bam,sam,bed,bedgraph" label="Sequencing reads" /> <param name="X" type="integer" value="0" label="In silico extension (leave 0 for read length)" /> |
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| diff -r 4b32ed5d4a1b -r 604c98e58034 galaxy-conf/MapDyads.xml --- a/galaxy-conf/MapDyads.xml Tue Feb 14 00:59:33 2012 -0500 +++ b/galaxy-conf/MapDyads.xml Tue Feb 14 13:04:54 2012 -0500 |
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| @@ -1,7 +1,7 @@ <tool id="MapDyads" name="Map dyads" version="1.0.0"> <description>from sequencing reads</description> <command interpreter="sh"> - galaxyToolRunner.sh nucleosome.MapDyads -i $input -a ${chromInfo} -o $output + galaxyToolRunner.sh nucleosomes.MapDyads -i $input -a ${chromInfo} -o $output #if $type.read == 'single' -s $type.size #end if |
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| diff -r 4b32ed5d4a1b -r 604c98e58034 galaxy-conf/NRLCalculator.xml --- a/galaxy-conf/NRLCalculator.xml Tue Feb 14 00:59:33 2012 -0500 +++ b/galaxy-conf/NRLCalculator.xml Tue Feb 14 13:04:54 2012 -0500 |
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| @@ -1,6 +1,6 @@ <tool id="NRLCalculator" name="Compute the NRL" version="1.0.0"> <description>from nucleosome calls</description> - <command interpreter="sh">galaxyToolRunner.sh nucleosome.NRLCalculator -i $input -l $windows -o $output</command> + <command interpreter="sh">galaxyToolRunner.sh nucleosomes.NRLCalculator -i $input -l $windows -o $output</command> <inputs> <param format="tabular" name="input" type="data" label="Nucleosome calls" /> <param format="bed,bedgraph,gff" name="windows" type="data" label="List of intervals/genes" /> |
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| diff -r 4b32ed5d4a1b -r 604c98e58034 galaxy-conf/Phasogram.xml --- a/galaxy-conf/Phasogram.xml Tue Feb 14 00:59:33 2012 -0500 +++ b/galaxy-conf/Phasogram.xml Tue Feb 14 13:04:54 2012 -0500 |
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| @@ -1,6 +1,6 @@ <tool id="Phasogram" name="Make phasogram" version="1.0.0"> <description>of dyads</description> - <command interpreter="ruby">phasogram.rb -i $input -m $max -o $output</command> + <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="max" type="integer" value="1000" label="Maximum phase shift (bp)" /> |