Mercurial > repos > iuc > jbrowse2
annotate macros.xml @ 0:61add3f58f26 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
| author | iuc |
|---|---|
| date | Thu, 02 Oct 2025 10:19:44 +0000 |
| parents | |
| children |
| rev | line source |
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0
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
changeset
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1 <?xml version="1.0"?> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
changeset
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2 <macros> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
changeset
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3 <token name="@TOOL_VERSION@">3.6.5</token> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
changeset
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4 <xml name="requirements"> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
changeset
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5 <requirements> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
changeset
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6 <requirement type="package" version="@TOOL_VERSION@">jbrowse2</requirement> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
changeset
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7 <requirement type="package" version="1.22.1">samtools</requirement> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
changeset
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8 <requirement type="package" version="1.11">tabix</requirement> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
changeset
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9 <requirement type="package" version="3.13.7">python</requirement> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
changeset
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10 <requirement type="package" version="2.32.5">requests</requirement> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
changeset
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11 <yield/> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
changeset
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12 </requirements> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
changeset
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13 </xml> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
changeset
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14 <token name="@VERSION_SUFFIX@">0</token> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
changeset
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15 |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
changeset
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16 <xml name="general_options"> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
changeset
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17 <section name="jbgen" title="Advanced: general JBrowse options" expanded="false"> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
changeset
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18 <param label="Enable analytics" help="Will send usage data to Google Analytics, see https://github.com/GMOD/jbrowse-components/issues/1166" name="enableAnalytics" type="boolean" checked="false" truevalue="true" falsevalue="false" /> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
changeset
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19 |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
changeset
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20 <param name="primary_color" type="color" label="Primary color" value="#0d233f"/> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
changeset
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21 <param name="secondary_color" type="color" label="Secondary color" value="#721e63"/> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
changeset
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22 <param name="tertiary_color" type="color" label="Tertiary color" value="#135560"/> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
changeset
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23 <param name="quaternary_color" type="color" label="Quaternary color" value="#ffb11d"/> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
changeset
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24 |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
changeset
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25 <param label="Font size" name="font_size" type="integer" value="10" min="6" max="50" /> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
changeset
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26 </section> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
changeset
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27 </xml> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
changeset
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28 |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
changeset
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29 <xml name="track_metadata"> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
changeset
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30 <section name="metadata" title="Advanced: track metadata" expanded="false"> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
changeset
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31 <param name="galaxy_metadata" label="Show Galaxy track metadata" type="boolean" checked="true" truevalue="true" falsevalue="false" help="Make Galaxy metadata available in 'About track' window and faceted track selector" /> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
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32 <param name="metadata_bonus" type="data" format="tsv,tabular" label="Additional track metadata" optional="true" help="Display additional track metadata from a TSV file" /> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
changeset
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33 </section> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
changeset
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34 </xml> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
changeset
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35 |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
changeset
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36 <xml name="track_visibility"> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
changeset
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37 <param type="select" label="Track Visibility" name="track_visibility"> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
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38 <option value="default_off">Off when browser opens</option> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
changeset
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39 <option value="default_on" selected="true">On when browser opens</option> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
changeset
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40 </param> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
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41 </xml> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
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42 |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
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43 <xml name="track_styling_linear"> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
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44 |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
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changeset
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45 <param name="display_mode" type="select" label="Display mode"> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
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46 <option value="normal" selected="true">normal</option> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
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47 <option value="compact">compact</option> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
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48 <option value="reducedRepresentation">reducedRepresentation</option> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
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49 <option value="collapse">collapse</option> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
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50 </param> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
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51 |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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52 <param label="Show labels" name="show_labels" type="boolean" checked="true" truevalue="true" falsevalue="false" /> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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53 |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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54 <param label="Features label" |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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55 type="text" |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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56 name="labels_name" |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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57 value="jexl:get(feature,'name') || get(feature,'id')" |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
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58 help="See https://jbrowse.org/jb2/docs/config_guide/#configuration-callbacks for syntax"> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
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59 <expand macro="jexl_sanitize" /> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
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60 </param> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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61 |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
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62 <param label="Show descriptions" name="show_descriptions" type="boolean" checked="true" truevalue="true" falsevalue="false" /> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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63 |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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64 <param label="Features description" |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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65 type="text" |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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66 name="descriptions_name" |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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67 value="jexl:get(feature,'note') || get(feature,'description')" |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
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68 help="See https://jbrowse.org/jb2/docs/config_guide/#configuration-callbacks for syntax"> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
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69 <expand macro="jexl_sanitize" /> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
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70 </param> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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71 |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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72 <param label="Max height" name="max_height" type="integer" value="600" min="20" help="Maximum height that the track is permitted to reach in pixels."/> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
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73 </xml> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
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74 |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
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75 <xml name="track_styling_arc"> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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76 |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
changeset
|
77 <param name="display_mode" type="select" label="Display mode"> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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changeset
|
78 <option value="arcs" selected="true">arcs</option> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
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changeset
|
79 <option value="semicircles">semicircles</option> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
changeset
|
80 </param> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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changeset
|
81 |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
changeset
|
82 <param label="Arcs label" |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
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83 type="text" |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
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84 name="labels_name" |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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85 value="jexl:get(feature,'score')" |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
changeset
|
86 help="See https://jbrowse.org/jb2/docs/config_guide/#configuration-callbacks for syntax"> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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changeset
|
87 <expand macro="jexl_sanitize" /> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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diff
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|
88 </param> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
changeset
|
89 </xml> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
changeset
|
90 |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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changeset
|
91 <xml name="track_styling_feature"> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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diff
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92 <section name="jbstyle" title="Advanced: styling options" expanded="false"> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
changeset
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93 <conditional name="track_style"> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
changeset
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94 <param name="display" type="select" label="Display style" help="How the track will be displayed by default"> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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diff
changeset
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95 <option value="LinearBasicDisplay" selected="true">LinearBasicDisplay</option> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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96 <option value="LinearArcDisplay">LinearArcDisplay</option> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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97 </param> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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diff
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98 <when value="LinearBasicDisplay"> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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99 <expand macro="track_styling_linear"/> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
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100 </when> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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101 <when value="LinearArcDisplay"> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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102 <expand macro="track_styling_arc"/> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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103 </when> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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104 </conditional> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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|
105 </section> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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|
106 </xml> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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107 |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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108 <xml name="track_styling_xam"> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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109 <section name="jbstyle" title="Advanced: styling options" expanded="false"> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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110 <conditional name="track_style"> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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111 <param name="display" type="select" label="Display style" help="How the track will be displayed by default"> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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112 <option value="LinearAlignmentsDisplay" selected="true">Alignments (Pileup + SNP Coverage)</option> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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113 <option value="LinearPileupDisplay">Pileup</option> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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114 <option value="LinearSNPCoverageDisplay">SNP Coverage</option> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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115 <option value="LinearReadArcsDisplay">Arc</option> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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116 <option value="LinearReadCloudDisplay">Read Cloud</option> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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117 </param> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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118 <when value="LinearAlignmentsDisplay"/> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
changeset
|
119 <!-- TODO add options from both LinearPileupDisplay and LinearSNPCoverageDisplay (doesn't work currently) --> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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120 <when value="LinearPileupDisplay"/> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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changeset
|
121 <!-- TODO add more options (doesn't work currently) --> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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122 <when value="LinearSNPCoverageDisplay"> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
diff
changeset
|
123 <!-- TODO add more options (doesn't work currently) --> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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124 <param name="scale_type" type="select" label="Scale type"> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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125 <option value="linear" selected="true">Linear</option> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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126 <option value="log">Log</option> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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127 </param> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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128 <param name="min_score" label="Min score" type="integer" value="" optional="true"/> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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129 <param name="max_score" label="Max score" type="integer" value="" optional="true"/> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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130 </when> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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131 <when value="LinearReadArcsDisplay"/> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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132 <!-- TODO add more options --> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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133 <when value="LinearReadCloudDisplay"/> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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134 <!-- TODO add more options --> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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135 </conditional> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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|
136 </section> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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|
137 </xml> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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138 |
|
61add3f58f26
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139 <xml name="track_styling_vcf"> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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140 <section name="jbstyle" title="Advanced: styling options" expanded="false"> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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141 <conditional name="track_style"> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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142 <param name="display" type="select" label="Display style" help="How the track will be displayed by default"> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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143 <option value="LinearVariantDisplay" selected="true">Variant</option> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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144 <option value="MultiLinearVariantDisplay">Multi-sample variant display (matrix)</option> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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145 <option value="LinearVariantMatrixDisplay">Multi-sample variant display (regular)</option> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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146 <option value="LinearPairedArcDisplay">Arc</option> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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147 </param> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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148 <when value="LinearVariantDisplay"> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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149 <!-- TODO does not work (jbrowse side) --> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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150 <!--expand macro="track_styling_linear"/--> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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151 </when> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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152 <when value="MultiLinearVariantDisplay"/> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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153 <when value="LinearVariantMatrixDisplay"/> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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154 <when value="LinearPairedArcDisplay"/> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents:
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155 </conditional> |
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156 </section> |
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157 </xml> |
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158 |
|
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159 <xml name="track_styling_bigwig"> |
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160 <section name="jbstyle" title="Advanced: styling options" expanded="false"> |
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161 <conditional name="track_style"> |
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162 <param name="display" type="select" label="Display style" help="How the track will be displayed by default"> |
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163 <option value="LinearWiggleDisplay" selected="true">Wiggle</option> |
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164 <option value="MultiLinearWiggleDisplay" selected="true">Multiple Wiggle</option> |
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165 </param> |
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166 <when value="LinearWiggleDisplay"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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167 <param name="wig_renderer" type="select" label="Renderer type"> |
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168 <option value="xyplot" selected="true">XY Plot</option> |
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169 <option value="density">Density</option> |
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170 <option value="line">Line</option> |
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171 </param> |
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172 |
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173 <!-- TODO not working --> |
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174 <!--param name="autoscale" type="select" label="Autoscale type"> |
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175 <option value="local" selected="true">Local</option> |
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176 <option value="global">Global</option> |
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177 <option value="globalsd">Global ± 3σ</option> |
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178 <option value="localsd">Local ± 3σ</option> |
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179 </param> |
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180 <param name="resolution" label="Resolution" type="integer" value="1"/> |
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181 <param name="summaryScoreMode" type="select" label="Autoscale type"> |
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182 <option value="max">Max</option> |
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183 <option value="min">Min</option> |
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184 <option value="avg">Avg</option> |
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185 <option value="whiskers" selected="true">Whiskers (combines all three)</option> |
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186 </param> |
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187 <param name="filled" label="Fill in histogram" type="boolean" checked="true" truevalue="true" falsevalue="false" /> |
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188 <param name="scaleType" type="select" label="Scale type"> |
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189 <option value="linear" selected="true">Linear</option> |
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190 <option value="log">Log</option> |
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191 </param> |
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192 <param name="displayCrossHatches" label="Draw cross hatches" type="boolean" checked="true" truevalue="true" falsevalue="false" /> |
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193 <param name="minScore" label="Min score" type="integer" value="" optional="true"/> |
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194 <param name="maxScore" label="Max score" type="integer" value="" optional="true"/--> |
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195 </when> |
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196 <when value="MultiLinearWiggleDisplay"> |
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197 <param name="wig_renderer" type="select" label="Renderer type"> |
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198 <option value="multirowxy" selected="true">Multi row XY Plot</option> |
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199 <option value="xyplot">Multi XY Plot</option> |
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200 <option value="multirowdensity">Density</option> |
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201 <option value="multiline">Line</option> |
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202 <option value="multirowline">Row line</option> |
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203 </param> |
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204 </when> |
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205 </conditional> |
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206 </section> |
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207 </xml> |
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208 |
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209 <xml name="track_styling_maf"> |
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210 <param name="track_display" type="hidden" value="LinearMafDisplay" /> |
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211 </xml> |
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212 |
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213 <xml name="track_styling_hic"> |
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214 <param name="track_display" type="hidden" value="LinearHicDisplay" /> |
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215 </xml> |
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216 |
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217 <xml name="track_styling_gc"> |
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218 <param name="track_display" type="hidden" value="LinearGCContentDisplay" /> |
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219 </xml> |
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220 |
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221 <xml name="track_styling_synteny"> |
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222 <section name="jbstyle" title="Advanced: styling options" expanded="false"> |
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223 <conditional name="track_style"> |
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224 <param name="display" type="select" label="Display style" help="How the track will be displayed by default"> |
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225 <option value="LinearBasicDisplay" selected="true">Basic track display</option> |
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226 <option value="LinearSyntenyDisplay" selected="true">Synteny viewer</option> |
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227 </param> |
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228 <when value="LinearBasicDisplay"/> |
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229 <when value="LinearSyntenyDisplay"/> |
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230 </conditional> |
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231 </section> |
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232 </xml> |
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233 |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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234 <xml name="details_panel"> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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235 <section name="formatdetails" title="Advanced: feature details panel customization" expanded="false"> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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236 <param label="JEXL code to customize the top-level feature" |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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237 type="text" |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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238 name="formatdetails_feature" |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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239 optional="true" |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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240 help="e.g. jexl:{newfield:'Custom contents here: '+feature.name} (see https://jbrowse.org/jb2/docs/config_guides/customizing_feature_details/ for more details)"> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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241 <expand macro="jexl_sanitize" /> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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242 </param> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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243 <param label="JEXL code to customize the subfeatures" |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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244 type="text" |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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245 name="formatdetails_subfeature" |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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246 optional="true" |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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247 help="e.g. jexl:{newfield:'Custom contents here: '+feature.name} (see https://jbrowse.org/jb2/docs/config_guides/customizing_feature_details/ for more details)"> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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248 <expand macro="jexl_sanitize" /> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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249 </param> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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250 <param name="formatdetails_depth" label="Depth to customize the subfeatures to" type="integer" value="1"/> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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251 </section> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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252 </xml> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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253 |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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254 <xml name="jexl_sanitize"> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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255 <sanitizer> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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256 <mapping initial="galaxy.util.mapped_chars"> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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257 <add source=" " target=" " /> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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258 <add source=">" target="__gt__" /> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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259 <add source="<" target="__lt__" /> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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260 </mapping> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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261 <valid initial="default"> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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262 <add value="|" /> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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263 <add value="{"/> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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264 <add value="}"/> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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265 <add value="!"/> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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266 <add value="?"/> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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267 <add value="&"/> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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268 <add value="+"/> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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269 <add value="="/> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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270 <add value="'"/> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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271 <add value='"'/> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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272 </valid> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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273 </sanitizer> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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274 </xml> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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275 |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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276 <xml name="input_conditional" token_label="Track Data" token_format="data" token_help="" token_multiple="True"> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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277 <conditional name="annotation_cond"> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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278 <param label="@LABEL@" name="annotation_source" type="select"> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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279 <option selected="True" value="history">Use data from history</option> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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280 <option value="remote">Use a genome from a remote source (not recommended)</option> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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281 </param> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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282 <when value="history"> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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283 <param name="annotation" label="@LABEL@" format="@FORMAT@" type="data" multiple="@MULTIPLE@" help="@HELP@"/> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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284 </when> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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285 <when value="remote"> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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286 <param name="uri" type="text" label="URI pointing to a @LABEL@" |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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287 help="@HELP@ ⚠️ WARNING: If this URI is not available for any reason, your JBrowse track will not show up." /> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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288 <param name="label" type="text" label="Track label" /> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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289 <param name="format" type="hidden" value="@FORMAT@" /> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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290 </when> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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291 </conditional> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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292 </xml> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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293 |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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294 <xml name="input_conditional_no_remote" token_label="Track Data" token_format="data" token_help="" token_multiple="True"> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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295 <conditional name="annotation_cond"> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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296 <param label="@LABEL@" name="annotation_source" type="select"> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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297 <option selected="True" value="history">Use data from history</option> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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298 </param> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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299 <when value="history"> |
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61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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300 <param name="annotation" label="@LABEL@" format="@FORMAT@" type="data" multiple="@MULTIPLE@" help="@HELP@"/> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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301 </when> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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302 </conditional> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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303 </xml> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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304 |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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305 <xml name="citations"> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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306 <citations> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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307 <citation type="doi">10.1186/s13059-023-02914-z</citation> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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308 </citations> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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309 </xml> |
|
61add3f58f26
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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310 </macros> |