Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/IntervalToWig.xml @ 25:b43c420a6135 draft default tip

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Incorporate fix: https://github.com/timpalpant/java-genomics-toolkit/commit/9a6c61b7c6b8d85a1cd3f595eed657a537b85dc9
author timpalpant
date Sat, 09 Feb 2019 14:02:24 -0500
parents 9d56b5b85740
children
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1 <tool id="BedToWig" name="Bed/BedGraph/GFF to Wig" version="1.1.0">
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2 <description>converter</description>
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b43c420a6135 Incorporate fix: https://github.com/timpalpant/java-genomics-toolkit/commit/9a6c61b7c6b8d85a1cd3f595eed657a537b85dc9
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3 <command interpreter="bash">galaxyToolRunner.sh converters.IntervalToWig -i $input $zero -a ${chromInfo} -o $output</command>
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4 <inputs>
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5 <param name="input" type="data" format="bed,bedgraph,gff" label="Input Bed/BedGraph/GFF file" />
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6 <param name="zero" type="boolean" checked="false" truevalue="-z" falsevalue="" label="Assume zero where there is no data (default is NaN)" />
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7 </inputs>
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8 <outputs>
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9 <data name="output" format="wig" metadata_source="input" />
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10 </outputs>
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11
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12 <help>
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13
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14 This tool converts data from an interval format, such as Bed, BedGraph or GFF, to Wig format. This can be used to convert data from microarrays to Wig format. The value of each interval is mapped into the Wig file. Intervals that overlap in the original file (multiple-valued base pairs) are averaged, and bases without data in the original interval file are set to NaN.
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16 .. class:: warningmark
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17
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18 This tool requires Bed, BedGraph, or GFF formatted data. If you have tabular data that was not correctly autodetected, change the metadata by clicking on the pencil icon for the dataset.
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19
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20 </help>
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21 </tool>