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1 <?xml version="1.0"?>
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2 <macros>
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3 <token name="@TOOL_VERSION@">2.10.0</token>
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4 <xml name = "edamInc">
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5 <edam_topics>
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6 <edam_topic>topic_3307</edam_topic>
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7 <edam_topic>topic_0092</edam_topic>
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8 </edam_topics>
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9 <edam_operations>
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10 <edam_operation>operation_0573</edam_operation>
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11 <edam_operation>operation_0564</edam_operation>
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12 </edam_operations>
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13 </xml>
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14 <xml name="requirements">
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15 <requirements>
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16 <requirement type="package" version="@TOOL_VERSION@">jbrowse2</requirement>
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17 <requirement type="package" version="1.82">biopython</requirement>
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18 <requirement type="package" version="0.7.0">bcbio-gff</requirement>
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19 <requirement type="package" version="1.19">samtools</requirement>
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20 <requirement type="package" version="6.0.1">pyyaml</requirement>
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21 <requirement type="package" version="1.11">tabix</requirement>
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22 <requirement type="package" version="4.6.0">findutils</requirement>
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23 <yield/>
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24 </requirements>
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25 </xml>
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26 <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token>
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27 <token name="@WRAPPER_VERSION@">galaxy0</token>
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28 <token name="@ATTRIBUTION@"><![CDATA[
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29 **Attribution**
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30 This Galaxy tool relies on the JBrowse, maintained by the GMOD Community. The Galaxy wrapper is developed by the IUC
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31 This xml currently fails silently when profile=22.05 is set.
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32 ]]>
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33 </token>
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34 <xml name="track_styling"
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35 token_classname="feature"
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36 token_label="product,name,id"
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37 token_description="note,description"
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38 token_height="10px"
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39 token_maxheight="600">
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40 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false">
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41 <param label="JBrowse style.className" type="text"
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42 name="style_classname"
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43 value="@CLASSNAME@"
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44 help="Set CSS style.className property"/>
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45 <param label="JBrowse style.label"
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46 type="text"
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47 name="style_label"
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48 value="@LABEL@"
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49 help="Comma-separated list of case-insensitive feature tags to use for showing the feature's label. The first one found will be used. Default 'name,id'" />
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50 <param label="JBrowse style.description"
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51 type="text"
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52 name="style_description"
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53 value="@DESCRIPTION@"
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54 help="Comma-separated list of case-insensitive feature tags to check for the feature's long description. The first one found will be used."/>
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55 <param label="JBrowse style.height"
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56 type="text"
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57 name="style_height"
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58 value="@HEIGHT@"
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59 help="Height in pixels of glyphs. Default value varies from glyph to glyph. Note that the 'compact' displayMode uses style->height * 0.35 so changing style height can adjust the compact visualization."/>
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60 <param label="JBrowse maxHeight"
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61 type="text"
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62 name="max_height"
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63 value="@MAXHEIGHT@"
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64 help="Maximum height that the track is permitted to reach in pixels."/>
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65 </section>
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66 </xml>
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67
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68 <xml name="input_conditional" token_label="Track Data" token_format="data">
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69 <param label="@LABEL@" format="@FORMAT@" name="annotation" type="data" multiple="True"/>
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70 </xml>
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71 <xml name="citations">
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72 <citations>
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73 <citation type="doi">10.1101/gr.094607.109</citation>
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74 </citations>
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75 </xml>
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76 </macros>
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