Mercurial > repos > iuc > crossmap_wig

annotate crossmap_wig.xml @ 10:754f70dd85ae draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 1b4c5b184b10336bca092cf347019c4368a7771c
author iuc
date Wed, 09 Jul 2025 11:13:03 +0000
parents f7229c8445da
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282a658c6569 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7"
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1 <tool id="crossmap_wig" name="CrossMap Wig" 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>
0e6f675cea09 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>
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5 </macros>
0e6f675cea09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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6 <expand macro="requirements"/>
0e6f675cea09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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7 <expand macro="stdio"/>
0e6f675cea09 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[
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10 CrossMap wig
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11 '${chain_source.input_chain}'
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12 '${input}'
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13 output
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14 ]]></command>
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15 <inputs>
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16 <param name="input" type="data" format="wig" label="Wiggle file"/>
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17 <expand macro="chain"/>
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18 </inputs>
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19 <outputs>
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20 <data name="output" format="bigwig" label="${tool.name} on ${on_string}" from_work_dir="output.bw"/>
f7229c8445da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit ad4d739b4837dd61abc85614568d22f271f14568
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21 <data name="output2" format="bedgraph" label="${tool.name} (bedgraph) on ${on_string}" from_work_dir="output.sorted.bgr"/>
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22 </outputs>
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23 <tests>
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24 <!-- WIG - Doesn't understand fixedStep -->
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25 <test>
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26 <param name="input" value="test_wig_01_input_a.wig" ftype="wig"/>
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27 <param name="index_source" value="history"/>
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0e6f675cea09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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28 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
0e6f675cea09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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29 <output name="output" file="test_wig_01_output_a.bw"/>
0e6f675cea09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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30 <output name="output2" file="test_wig_01_output_a.sorted.bgr"/>
0e6f675cea09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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31 </test>
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32 <test>
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33 <!-- cached reference genome -->
f7229c8445da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit ad4d739b4837dd61abc85614568d22f271f14568
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34 <param name="input" value="test_wig_01_input_a.wig" ftype="wig" dbkey="hg18"/>
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35 <param name="index_source" value="cached"/>
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36 <output name="output" file="test_wig_01_output_a.bw"/>
81986a56b281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
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37 <output name="output2" file="test_wig_01_output_a.sorted.bgr"/>
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38 </test>
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39 </tests>
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40 <help><![CDATA[
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41 @HELP_GENERAL@
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42
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43 Wig
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44 ---
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45
1
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46 Input wiggle data can be in variableStep (for data with irregular
81986a56b281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
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47 intervals) or fixedStep (for data with regular intervals). Regardless of
81986a56b281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
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48 the input, the output will always in bedGraph format. bedGraph format is
81986a56b281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
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49 similar to wiggle format and can be converted into BigWig format using UCSC
81986a56b281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
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50 wigToBigWig tool. We export files in bedGraph because it is usually much
81986a56b281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
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51 smaller than file in wiggle format, and more importantly, CrossMap
81986a56b281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
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52 internally transforms wiggle into bedGraph to increase running speed.
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53 ]]></help>
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54 <citations>
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55 <citation type="doi">10.1093/bioinformatics/btt730</citation>
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56 </citations>
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57 </tool>