annotate stack-histogram.xml @ 12:290a11559985 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit e3d1aad2204a3385aa66f3b0625747151e9f94e8"
author iuc
date Mon, 22 Nov 2021 12:23:12 +0000
parents 31a35811dda6
children c4bde687c846
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1 <?xml version="1.0"?>
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2 <tool id="circos_wiggle_to_stacked" name="Circos: Stack bigWigs as Histogram" version="@WRAPPER_VERSION@">
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3 <description>reformats for use in Circos stacked histogram plots</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <edam_topics>
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8 <edam_topic>topic_0797</edam_topic>
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9 <edam_topic>topic_0092</edam_topic>
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10 </edam_topics>
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11 <edam_operations>
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12 <edam_operation>operation_0335</edam_operation>
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13 </edam_operations>
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14 <expand macro="requirements" />
6
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15 <command detect_errors="exit_code"><![CDATA[
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16 python
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17 '$__tool_directory__/stack-histogram.py'
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18 #for i in $input
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19 '$i'
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20 #end for
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21 > '$output'
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
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22 ]]></command>
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23 <inputs>
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24 <param name="input" type="data" format="bigwig" label="BigWig files" multiple="True" help="These MUST have identical chromosomes and intervals, within their datasets. This tool is incredibly, intentionally naïve, and will crash if there are missing ranges in some bigwig files. This feels like a reasonable assumption to make (simplifies processing) at the expense of theoretical correctness, given that when you are stacking histograms they're probably coming from the same upstream pipeline with the same settings (i.e. step/width/etc.)"/>
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25 </inputs>
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26 <outputs>
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27 <data name="output" format="tabular" />
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28 </outputs>
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29 <tests>
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30 <test>
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31 <param name="input" value="scatter/1.bw,scatter/1.bw,scatter/1.bw" ftype="bigwig" />
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32 <output name="output" file="scatter/1.multi.out" ftype="tabular" />
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33 </test>
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34 </tests>
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35 <help><![CDATA[
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36 Converts standard bigWig files into a format appropriate for Circos stacked histogram plots
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37
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38 If you need to process bedgraph, please convert those to bigwig first.
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
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39 ]]></help>
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40 <expand macro="citations" />
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41 </tool>