Mercurial > repos > iuc > crossmap_wig

annotate crossmap_wig.xml @ 0:0d0d8d882315 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
author iuc
date Sat, 01 Jul 2017 17:46:16 -0400
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0d0d8d882315 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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1 <tool id="crossmap_wig" name="CrossMap Wig" version="@WRAPPER_VERSION@-0">
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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[
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10
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11 #set $input_file = str($seq_source.input)
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12
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13 CrossMap.py wig
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14 '${chain_source.input_chain}'
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15 '${input_file}'
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16 '${output}'
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17
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18 && mv '${output}.bw' '${output}'
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19 && mv '${output}.sorted.bgr' '${output2}'
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20 ]]></command>
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21
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22 <inputs>
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23 <conditional name="seq_source">
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24 <expand macro="source" />
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25 <when value="cached">
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26 <param format="wig" name="input" type="data" label="Wiggle file">
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27 <validator type="unspecified_build"/>
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28 <!-- Gives error in tests
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29 <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build."/>
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30 -->
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31 </param>
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32 </when>
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33 <when value="history">
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34 <param format="wig" name="input" type="data" label="Wiggle file"/>
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35 </when>
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36 </conditional>
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37 <expand macro="chain" />
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38 </inputs>
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39
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40 <outputs>
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41 <data format="wig" name="output" label="${tool.name} on ${on_string}" />
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42 <data format="wig" name="output2" label="${tool.name} (bedgraph) on ${on_string}" />
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43 </outputs>
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44
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45 <tests>
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46 <!-- WIG - Doesn't understand fixedStep -->
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47 <test>
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48 <param name="index_source" value="history"/>
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49 <param name="input" value="test_wig_01_input_a.wig" ftype="wig"/>
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50 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
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51
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52 <output name="output" file="test_wig_01_output_a.bw"/>
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53 <output name="output2" file="test_wig_01_output_a.sorted.bgr"/>
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54 </test>
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55 </tests>
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56 <help><![CDATA[
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57 @HELP_GENERAL@
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58
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59 Wig
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60 ---
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61
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62 Input wiggle data can be in variableStep (for data with irregular
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63 intervals) or fixedStep (for data with regular intervals). Regardless of
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64 the input, the output will always in bedGraph format. bedGraph format is
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65 similar to wiggle format and can be converted into BigWig format using UCSC
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66 wigToBigWig tool. We export files in bedGraph because it is usually much
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67 smaller than file in wiggle format, and more importantly, CrossMap
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68 internally transforms wiggle into bedGraph to increase running speed.
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69
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70 Please see `the manual <http://crossmap.sourceforge.net/#convert-wiggle-bigwig-format-files>`__ for more details
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71 ]]></help>
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72
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73 <citations>
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74 <citation type="doi">10.1093/bioinformatics/btt730</citation>
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75 </citations>
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76 </tool>