| Previous changeset 21:51b28ce6ef7e (2012-06-18) Next changeset 23:01d5d20eaadd (2012-06-19) |
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Commit message:
Fix a bug in GeneTrackToWig where +/- strands were not merged correctly. Add option to vary the chunk size of tools that process chromosomes in chunks. |
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modified:
dist/java-genomics-toolkit.jar galaxy-conf/._IntervalStats.xml galaxy-conf/IntervalStats.xml galaxy-conf/Scale.xml galaxy-conf/Shift.xml galaxy-conf/ZScore.xml |
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| diff -r 51b28ce6ef7e -r 727fbba02ef7 dist/java-genomics-toolkit.jar |
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| Binary file dist/java-genomics-toolkit.jar has changed |
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| diff -r 51b28ce6ef7e -r 727fbba02ef7 galaxy-conf/._IntervalStats.xml |
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| Binary file galaxy-conf/._IntervalStats.xml has changed |
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| diff -r 51b28ce6ef7e -r 727fbba02ef7 galaxy-conf/IntervalStats.xml --- a/galaxy-conf/IntervalStats.xml Mon Jun 18 14:50:31 2012 -0400 +++ b/galaxy-conf/IntervalStats.xml Tue Jun 19 22:09:23 2012 -0400 |
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| @@ -1,5 +1,5 @@ <tool id="IntervalStats" name="Compute mean/min/max of intervals" version="1.0.0"> - <description>of data in a Wiggle file</description> + <description>of data in a (Big)Wig file</description> <command interpreter="sh"> galaxyToolRunner.sh ngs.IntervalStats -l $windows -s $stat -o $output #for $input in $inputs @@ -7,7 +7,7 @@ #end for </command> <inputs> - <repeat name="inputs" title="BigWig file"> + <repeat name="inputs" title="(Big)Wig file"> <param name="file" type="data" format="bigwig,wig" /> </repeat> <param format="bed,bedgraph,gff" name="windows" type="data" label="List of intervals" /> |
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| diff -r 51b28ce6ef7e -r 727fbba02ef7 galaxy-conf/Scale.xml --- a/galaxy-conf/Scale.xml Mon Jun 18 14:50:31 2012 -0400 +++ b/galaxy-conf/Scale.xml Tue Jun 19 22:09:23 2012 -0400 |
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| @@ -4,7 +4,7 @@ <inputs> <param format="bigwig,wig" name="input" type="data" label="Scale the data in" /> <param name="M" type="float" value="0" label="Multiply by (leave 0 to scale by 1/mean)" /> - <param name="chr" type="boolean" checked="false" truevalue="-c" falsevalue="" label="Scale chromosomes to 1/mean individually (no effect if scale factor is specified)" /> + <param name="chr" type="boolean" checked="false" truevalue="--bychr" falsevalue="" label="Scale chromosomes to 1/mean individually (no effect if scale factor is specified)" /> </inputs> <outputs> <data format="wig" name="output" metadata_source="input" /> |
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| diff -r 51b28ce6ef7e -r 727fbba02ef7 galaxy-conf/Shift.xml --- a/galaxy-conf/Shift.xml Mon Jun 18 14:50:31 2012 -0400 +++ b/galaxy-conf/Shift.xml Tue Jun 19 22:09:23 2012 -0400 |
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| @@ -4,7 +4,7 @@ <inputs> <param format="bigwig,wig" name="input" type="data" label="Shift the data in" /> <param name="M" type="float" value="0" label="To have mean" /> - <param name="chr" type="boolean" checked="false" truevalue="-c" falsevalue="" label="Mean-shift chromosomes individually" /> + <param name="chr" type="boolean" checked="false" truevalue="--bychr" falsevalue="" label="Mean-shift chromosomes individually" /> </inputs> <outputs> <data format="wig" name="output" metadata_source="input" /> |
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| diff -r 51b28ce6ef7e -r 727fbba02ef7 galaxy-conf/ZScore.xml --- a/galaxy-conf/ZScore.xml Mon Jun 18 14:50:31 2012 -0400 +++ b/galaxy-conf/ZScore.xml Tue Jun 19 22:09:23 2012 -0400 |
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| @@ -3,7 +3,7 @@ <command interpreter="sh">galaxyToolRunner.sh wigmath.ZScore -i $input $chr -o $output</command> <inputs> <param format="bigwig,wig" name="input" type="data" label="Z-score the data in" /> - <param name="chr" type="boolean" checked="false" truevalue="-c" falsevalue="" label="Z-score chromosomes individually" /> + <param name="chr" type="boolean" checked="false" truevalue="--bychr" falsevalue="" label="Z-score chromosomes individually" /> </inputs> <outputs> <data format="wig" name="output" metadata_source="input" /> |