Mercurial > repos > timpalpant > java_genomics_toolkit
changeset 11:b1952a90d4bf
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--- a/galaxy-conf/Average.xml Sat Mar 17 08:11:55 2012 -0400 +++ b/galaxy-conf/Average.xml Mon Apr 09 11:50:23 2012 -0400 @@ -7,8 +7,8 @@ #end for </command> <inputs> - <param name="(Big)Wig file 1" type="data" format="bigwig,wig" /> - <param name="(Big)Wig file 2" type="data" format="bigwig,wig" /> + <param name="file1" label="(Big)Wig file 1" type="data" format="bigwig,wig" /> + <param name="file2" label="(Big)Wig file 2" type="data" format="bigwig,wig" /> <repeat name="inputs" title="Additional (Big)Wig file"> <param name="file" type="data" format="bigwig,wig" /> </repeat>
--- a/galaxy-conf/Divide.xml Sat Mar 17 08:11:55 2012 -0400 +++ b/galaxy-conf/Divide.xml Mon Apr 09 11:50:23 2012 -0400 @@ -36,8 +36,5 @@ </tests> <help> - .. class:: warningmark - - This tool was contributed by Timothy Palpant. </help> </tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy-conf/FilterOutlierRegions.xml Mon Apr 09 11:50:23 2012 -0400 @@ -0,0 +1,12 @@ +<tool id="WigFilterOutliers" name="Filter outlier regions" version="1.0.0"> + <description>in a (Big)Wig file</description> + <command interpreter="sh">galaxyToolRunner.sh wigmath.FilterOutlierRegions -i $input -w $window -t $threshold -o $output</command> + <inputs> + <param format="bigwig,wig" name="input" type="data" label="Filter outlier regions in" /> + <param name="window" type="integer" value="150" label="Window size" /> + <param name="threshold" type="float" value="3" label="Threshold (fold times the mean)" /> + </inputs> + <outputs> + <data format="wig" name="output" metadata_source="input" /> + </outputs> +</tool>
--- a/galaxy-conf/FindBoundaryNucleosomes.xml Sat Mar 17 08:11:55 2012 -0400 +++ b/galaxy-conf/FindBoundaryNucleosomes.xml Mon Apr 09 11:50:23 2012 -0400 @@ -12,6 +12,6 @@ <help> .. class:: warningmark - Use the Greedy Caller tool to create a file of called nucleosomes, then use this tool to identify the first nucleosome's dyad position from the 5' or 3' end. + Use the Call Nucleosomes tool to create a file of called nucleosomes, then use this tool to identify the first nucleosome's dyad position from the 5' or 3' end. </help> </tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy-conf/GeneTrackToBedGraph.xml Mon Apr 09 11:50:23 2012 -0400 @@ -0,0 +1,21 @@ +<tool id="GeneTrackToBedGraph" name="GeneTrack to BedGraph" version="1.0.0"> + <description>converter</description> + <command interpreter="sh">galaxyToolRunner.sh converters.GeneTrackToBedGraph -i $input -o $output</command> + <inputs> + <param name="input" type="data" format="genetrack" label="Input GeneTrack index" /> + </inputs> + <outputs> + <data name="output" format="bedgraph" metadata_source="input" /> + </outputs> + +<help> + +.. class:: warningmark + +This tool will sum the counts from the forward and reverse strands in a GeneTrack index to create a BedGraph file. + +.. class:: warningmark + +This tool requires GeneTrack formatted data. If you have tabular data that was not correctly autodetected, change the metadata by clicking on the pencil icon for the dataset. +</help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy-conf/GeneTrackToWig.xml Mon Apr 09 11:50:23 2012 -0400 @@ -0,0 +1,18 @@ +<tool id="GeneTrackToWig" name="GeneTrack to Wig" version="1.0.0"> + <description>converter</description> + <command interpreter="sh">galaxyToolRunner.sh converters.GeneTrackToWig -i $input $zero -a ${chromInfo} -o $output</command> + <inputs> + <param name="input" type="data" format="genetrack" label="Input GeneTrack index" /> + <param name="zero" type="boolean" checked="false" truevalue="-z" falsevalue="" label="Assume zero where there is no data (default is NaN)" /> + </inputs> + <outputs> + <data name="output" format="wig" metadata_source="input" /> + </outputs> + +<help> + +.. class:: warningmark + +This tool requires GeneTrack formatted data. If you have tabular data that was not correctly autodetected, change the metadata by clicking on the pencil icon for the dataset. +</help> +</tool>
--- a/galaxy-conf/GreedyCaller.xml Sat Mar 17 08:11:55 2012 -0400 +++ b/galaxy-conf/GreedyCaller.xml Mon Apr 09 11:50:23 2012 -0400 @@ -14,9 +14,5 @@ .. class:: warningmark This tool requires dyad counts and smoothed dyad counts. - -.. class:: warningmark - -This tool was contributed by Timothy Palpant. </help> </tool>
--- a/galaxy-conf/IntervalToWig.xml Sat Mar 17 08:11:55 2012 -0400 +++ b/galaxy-conf/IntervalToWig.xml Mon Apr 09 11:50:23 2012 -0400 @@ -1,8 +1,9 @@ <tool id="BedToWig" name="Interval to Wig" version="1.0.0"> <description>converter</description> - <command interpreter="sh">galaxyToolRunner.sh converters.IntervalToWig -i $input -a ${chromInfo} -o $output</command> + <command interpreter="sh">galaxyToolRunner.sh converters.IntervalToWig -i $input $zero -a ${chromInfo} -o $output</command> <inputs> <param name="input" type="data" format="bed,bedGraph,gff" label="Input Bed/BedGraph/GFF file" /> + <param name="zero" type="boolean" checked="false" truevalue="-z" falsevalue="" label="Assume zero where there is no data (default is NaN)" /> </inputs> <outputs> <data name="output" format="wig" metadata_source="input" />
--- a/galaxy-conf/KMeans.xml Sat Mar 17 08:11:55 2012 -0400 +++ b/galaxy-conf/KMeans.xml Mon Apr 09 11:50:23 2012 -0400 @@ -5,7 +5,7 @@ <param format="tabular" name="input" type="data" label="Aligned matrix" /> <param name="K" type="integer" value="10" label="Number of clusters" /> <param name="min" type="integer" value="1" label="Minimum column to use for clustering" /> - <param name="min" type="integer" value="-1" label="Maximum column to use for clustering (-1 to end)" /> + <param name="max" type="integer" value="-1" label="Maximum column to use for clustering (-1 to end)" /> </inputs> <outputs> <data format="tabular" name="output" metadata="input" />
--- a/galaxy-conf/MapDyads.xml Sat Mar 17 08:11:55 2012 -0400 +++ b/galaxy-conf/MapDyads.xml Mon Apr 09 11:50:23 2012 -0400 @@ -32,6 +32,6 @@ .. class:: warningmark -For paired-end MNase data, read centers are approximated by using the center of the read. For single-end data, the estimated mononucleosome fragment length must be specified, which will be used to offset reads from the + and - strands. +For paired-end MNase data, read centers are approximated using the center of the read. For single-end data, the estimated mononucleosome fragment length must be specified, which will be used to offset reads from the + and - strands. </help> </tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy-conf/PercusDecomposition.xml Mon Apr 09 11:50:23 2012 -0400 @@ -0,0 +1,17 @@ +<tool id="PercusDecomposition" name="Derive Percus energy landscape" version="1.0.0"> + <description>from occupancy data</description> + <command interpreter="sh">galaxyToolRunner.sh nucleosomes.PercusDecomposition -d $dyads -n $N -o $output</command> + <inputs> + <param name="dyads" type="data" format="bigwig,wig" label="Dyad counts (smoothed)" /> + <param name="N" type="integer" value="147" optional="true" label="Assumed nucleosome size" /> + </inputs> + <outputs> + <data name="output" format="wig" /> + </outputs> + +<help> +.. class:: warningmark + +See Locke G, Tolkunov D, Moqtaderi Z, Struhl K and Morozov AV (2010) High-throughput sequencing reveals a simple model of nucleosome energetics. Proceedings of the National Academy of Sciences 107: 20998–21003 and Percus JK (1976) Equilibrium state of a classical fluid of hard rods in an external field. J Stat Phys 15: 505–511 for derivation. +</help> +</tool>
--- a/galaxy-conf/RollingReadLength.xml Sat Mar 17 08:11:55 2012 -0400 +++ b/galaxy-conf/RollingReadLength.xml Mon Apr 09 11:50:23 2012 -0400 @@ -12,9 +12,5 @@ .. class:: warningmark This tool requires paired-end SAM, BAM, or Bed formatted data. Using single-end data will result in a constant read length. - -.. class:: warningmark - -This tool was contributed by Timothy Palpant. </help> </tool>
--- a/galaxy-conf/ValueDistribution.xml Sat Mar 17 08:11:55 2012 -0400 +++ b/galaxy-conf/ValueDistribution.xml Mon Apr 09 11:50:23 2012 -0400 @@ -1,8 +1,10 @@ <tool id="ValueDistribution" name="Compute the value distribution" version="1.0.0"> <description>of a (Big)Wig file</description> - <command interpreter="sh">galaxyToolRunner.sh wigmath.ValueDistribution -i $input -n $bins -o $output</command> + <command interpreter="sh">galaxyToolRunner.sh wigmath.ValueDistribution -i $input --max $max --min $min -n $bins -o $output</command> <inputs> <param format="bigwig,wig" name="input" type="data" label="(Big)Wig file" /> + <param name="min" type="float" optional="true" label="Minimum bin value (optional)" /> + <param name="max" type="float" optional="true" label="Maximum bin value (optional)" /> <param name="bins" type="integer" value="40" label="Number of bins" /> </inputs> <outputs>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy-conf/matrix2png.xml Mon Apr 09 11:50:23 2012 -0400 @@ -0,0 +1,110 @@ +<tool id="matrix2png" name="Make heatmap" version="1.0.0"> + <description>using matrix2png</description> + <requirement type='package'>matrix2png</requirement> + <command>matrix2png -data $input + #if str( $range ) != '' + -range $range + #end if + + -con $con + -size $size + -numcolors $numcolors + -minsize $minsize + -mincolor $mincolor + -maxcolor $maxcolor + -bkgcolor $bkgcolor + -missingcolor $missingcolor + + #if str( $map ) != '' + -map $map + #end if + + #if str( $discrete_color_maps.discrete ) != 'false' + -discrete + -dmap $dmap + #end if + + #if str( $numr ) != '' + -numr $numr + #end if + + #if str( $numc ) != '' + -numc $numc + #end if + + -startrow $startrow + -startcol $startcol + + #if str( $trim ) != '0' + -trim $trim + #end if + + #if str( $title ) != '' + -title '$title' + #end if + + $z $b $d $s $r $c $f $e $l $u + + > $output</command> + <inputs> + <param name="input" type="data" format="tabular" label="Input data" /> + <param name="title" type="text" optional="true" size="30" label="Add a title" /> + <param name="size" type="text" optional="true" value="1:1" label="Pixel dimensions per value as x:y" /> + <param name="minsize" type="text" optional="true" value="800:600" label="Minimum image size as x:y pixels" /> + <!-- Not sure what this is, so exclude for now + <param name="desctext" type="data" label="Description Text?" /> --> + <param name="range" type="text" optional="true" label="Values assigned to mincolor and maxcolor as min:max (default is data range)" /> + <param name="con" type="float" optional="true" value="1.0" label="Contrast (only applies when not using -range option)" /> + <param name="numcolors" type="integer" optional="true" value="64" label="Number of colors" /> + <param name="mincolor" type="text" optional="true" value="blue" label="Color used at lowest value (name or r:g:b triplet)" /> + <param name="maxcolor" type="text" optional="true" value="yellow" label="Color used at highest value (name or r:g:b triplet)" /> + <param name="bkgcolor" type="text" optional="true" value="white" label="Color used as background (name or r:g:b triplet)" /> + <param name="missingcolor" type="text" optional="true" value="grey" label="Color used for missing values (name or r:g:b triplet)" /> + <param name="map" type="text" optional="true" label="Color choices from preset maps: overrides min/max colors and -b (default = 0 (none))" /> + <conditional name="discrete_color_maps"> + <param name="discrete" type="select" label="Use discretized mapping of values to colors"> + <option value="true">Yes</option> + <option value="false" selected="true">No</option> + </param> + <when value="true"> + <param name="dmap" type="data" label="Discrete color mapping file to use for discrete mapping (default = preset)" /> + </when> + <when value="false"> + <!-- No values here --> + </when> + </conditional> + <param name="numr" type="text" optional="true" label="Number of rows to process (default = all)" /> + <param name="numc" type="text" optional="true" label="Number of columns to process (default = all)" /> + <param name="startrow" type="integer" optional="true" value="1" label="Index of the first row to be processed" /> + <param name="startcol" type="integer" optional="true" value="1" label="Index of the first column to be processed" /> + <param name="trim" type="integer" optional="true" value="0" label="Trim this percent of data extremes when determining data range (only without the -range option)" /> + <param name="z" type="boolean" checked="false" truevalue="-z" falsevalue="" label="Row-normalize the data to mean 0 and variance 1" /> + <param name="b" type="boolean" checked="true" truevalue="-b" falsevalue="" label="Middle of color range is black" /> + <param name="d" type="boolean" checked="false" truevalue="-d" falsevalue="" label="Add cell dividers" /> + <param name="s" type="boolean" checked="true" truevalue="-s" falsevalue="" label="Add scale bar" /> + <param name="r" type="boolean" checked="false" truevalue="-r" falsevalue="" label="Add row names" /> + <param name="c" type="boolean" checked="false" truevalue="-c" falsevalue="" label="Add column names" /> + <param name="f" type="boolean" checked="false" truevalue="-f" falsevalue="" label="Data file has a format line" /> + <param name="e" type="boolean" checked="false" truevalue="-e" falsevalue="" label="Draw ellipses instead of rectangles" /> + <param name="l" type="boolean" checked="false" truevalue="-l" falsevalue="" label="Log transform the data (base 2)" /> + <param name="u" type="boolean" checked="false" truevalue="-u" falsevalue="" label="Put the column labels under the picture instead of above (ignored unless column names)" /> + <param name="g" type="boolean" checked="false" truevalue="-g" falsevalue="" label="Put the row labels to the left instead of the right (ignored unless row names)" /> + </inputs> + <outputs> + <data name="output" format="png" /> + </outputs> + + <help> + .. class:: warningmark + + This tool requires that matrix2png be available in Galaxy's PATH. + + .. class:: warningmark + + This tool requires tabular data with column AND row headers. For more information about the required format and usage instructions, see http://bioinformatics.ubc.ca/matrix2png/dataformat.html + + .. class:: warningmark + + It is recommended to specify the colorspace range. + </help> +</tool>