Mercurial > repos > iuc > crossmap_bw

annotate crossmap_bigwig.xml @ 9:964835f32a94 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit ad4d739b4837dd61abc85614568d22f271f14568
author iuc
date Mon, 02 Sep 2024 12:00:58 +0000
parents a6d677dbf019
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a6d677dbf019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7"
iuc
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1 <tool id="crossmap_bw" name="CrossMap BigWig" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
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2 <description>Convert genome coordinates or annotation files between genome assemblies</description>
143ec4d1c8f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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3 <macros>
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4 <import>macros.xml</import>
143ec4d1c8f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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5 </macros>
143ec4d1c8f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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6 <expand macro="requirements"/>
143ec4d1c8f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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7 <expand macro="stdio"/>
143ec4d1c8f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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8 <expand macro="version_command"/>
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9 <command><![CDATA[
9
964835f32a94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit ad4d739b4837dd61abc85614568d22f271f14568
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10 CrossMap bigwig
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11 '${chain_source.input_chain}'
3b82b6febfd3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
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12 '${input}'
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13 output
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143ec4d1c8f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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14 ]]></command>
143ec4d1c8f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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15 <inputs>
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16 <param name="input" type="data" format="bigwig" label="BigWig file"/>
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964835f32a94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit ad4d739b4837dd61abc85614568d22f271f14568
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17 <expand macro="chain"/>
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18 </inputs>
143ec4d1c8f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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19 <outputs>
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20 <data name="output" format="bigwig" label="${tool.name} on ${on_string}" from_work_dir="output.bw"/>
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143ec4d1c8f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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21 </outputs>
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22 <tests>
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23 <test>
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24 <param name="input" value="test_bigwig_01_input_a.bw" ftype="bigwig"/>
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143ec4d1c8f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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25 <param name="index_source" value="history"/>
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26 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
3b82b6febfd3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
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27 <output name="output" file="test_bigwig_01_output_a.bw"/>
3b82b6febfd3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
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28 </test>
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29 <test>
964835f32a94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit ad4d739b4837dd61abc85614568d22f271f14568
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30 <!-- cached chain file -->
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31 <param name="input" value="test_bigwig_01_input_a.bw" ftype="bigwig" dbkey="hg18"/>
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32 <param name="index_source" value="cached"/>
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33 <output name="output" file="test_bigwig_01_output_a.bw"/>
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34 </test>
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35 </tests>
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36 <help><![CDATA[
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37 @HELP_GENERAL@
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38
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39 BigWig
143ec4d1c8f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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40 ------
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41
1
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42 Input wiggle data can be in variableStep (for data with irregular
3b82b6febfd3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
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43 intervals) or fixedStep (for data with regular intervals). Regardless of
3b82b6febfd3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
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44 the input, the output will always in bedGraph format. bedGraph format is
3b82b6febfd3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
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45 similar to wiggle format and can be converted into BigWig format using UCSC
3b82b6febfd3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
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46 wigToBigWig tool. We export files in bedGraph because it is usually much
3b82b6febfd3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
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47 smaller than file in wiggle format, and more importantly, CrossMap
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48 internally transforms wiggle into bedGraph to increase running speed.
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49 ]]></help>
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50 <citations>
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51 <citation type="doi">10.1093/bioinformatics/btt730</citation>
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52 </citations>
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53 </tool>