Mercurial > repos > iuc > crossmap_wig

annotate crossmap_wig.xml @ 6:eece97776a7a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 95fe80d08fb14c4c344da4979290e72261e31ae5"
author iuc
date Thu, 10 Oct 2019 04:01:46 -0400
parents 454886ffaa41
children b81b5d67bd3b
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454886ffaa41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 23fab16cd40acbd5b0e9d640ed3858040db7a622
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1 <tool id="crossmap_wig" name="CrossMap Wig" version="@WRAPPER_VERSION@">
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2 <description>Convert genome coordinates or annotation files between genome assemblies</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
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9 <command><![CDATA[
2
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10 CrossMap.py 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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16 <inputs>
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17 <param name="input" type="data" format="wig" label="Wiggle file"/>
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18
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19 <expand macro="chain" />
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20 </inputs>
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22 <outputs>
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23 <data name="output" format="bigwig" label="${tool.name} on ${on_string}" from_work_dir="output.bw" />
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24 <data name="output2" format="bedgraph" label="${tool.name} (bedgraph) on ${on_string}" from_work_dir="output.sorted.bgr" />
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25 </outputs>
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27 <tests>
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28 <!-- WIG - Doesn't understand fixedStep -->
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29 <test>
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30 <param name="input" value="test_wig_01_input_a.wig" ftype="wig"/>
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31 <param name="index_source" value="history"/>
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32 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
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34 <output name="output" file="test_wig_01_output_a.bw"/>
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35 <output name="output2" file="test_wig_01_output_a.sorted.bgr"/>
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36 </test>
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37
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38 <test><!-- cached reference genome -->
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39 <param name="input" value="test_wig_01_input_a.wig" ftype="wig" dbkey="hg18" />
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40 <param name="index_source" value="cached"/>
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42 <output name="output" file="test_wig_01_output_a.bw"/>
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43 <output name="output2" file="test_wig_01_output_a.sorted.bgr"/>
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44 </test>
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45 </tests>
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46 <help><![CDATA[
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47 @HELP_GENERAL@
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49 Wig
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50 ---
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51
2
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52 Input wiggle data can be in variableStep (for data with irregular
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53 intervals) or fixedStep (for data with regular intervals). Regardless of
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54 the input, the output will always in bedGraph format. bedGraph format is
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55 similar to wiggle format and can be converted into BigWig format using UCSC
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56 wigToBigWig tool. We export files in bedGraph because it is usually much
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57 smaller than file in wiggle format, and more importantly, CrossMap
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58 internally transforms wiggle into bedGraph to increase running speed.
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59 ]]></help>
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61 <citations>
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62 <citation type="doi">10.1093/bioinformatics/btt730</citation>
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63 </citations>
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64 </tool>