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annotate stack-histogram.xml @ 13:c4bde687c846 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 0cfd88d16b0b20a66d4b21b037ddee6a8c440d88
author iuc
date Wed, 12 Apr 2023 15:09:05 +0000
parents 31a35811dda6
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
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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" />
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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'
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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.)"/>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
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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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c4bde687c846 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 0cfd88d16b0b20a66d4b21b037ddee6a8c440d88
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32 <output name="output" file="scatter/1.multi.out" ftype="tabular" sort="true"/>
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33 </test>
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
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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
740057a5126d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
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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>