Mercurial > repos > fubar > jbrowse2
annotate macros.xml @ 20:9c7aa5885721 draft
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit b831bbba43ba42d44be2a91800f387fa868c7d9d
| author | fubar |
|---|---|
| date | Tue, 30 Jan 2024 07:49:23 +0000 |
| parents | bde6b1d09f7d |
| children | 2ddd41a0c2d5 |
| rev | line source |
|---|---|
|
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
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changeset
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1 <?xml version="1.0"?> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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2 <macros> |
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19
bde6b1d09f7d
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty
fubar
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3 <token name="@TOOL_VERSION@">2.10.1</token> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
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4 <xml name = "edamInc"> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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5 <edam_topics> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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6 <edam_topic>topic_3307</edam_topic> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
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7 <edam_topic>topic_0092</edam_topic> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
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8 </edam_topics> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
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9 <edam_operations> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
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10 <edam_operation>operation_0573</edam_operation> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
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changeset
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11 <edam_operation>operation_0564</edam_operation> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
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12 </edam_operations> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
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13 </xml> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
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14 <xml name="requirements"> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
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15 <requirements> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
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16 <requirement type="package" version="@TOOL_VERSION@">jbrowse2</requirement> |
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19
bde6b1d09f7d
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty
fubar
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17 <requirement type="package" version="1.81">biopython</requirement> |
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bde6b1d09f7d
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty
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18 <requirement type="package" version="0.7.1">bcbio-gff</requirement> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
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19 <requirement type="package" version="1.19">samtools</requirement> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
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20 <requirement type="package" version="6.0.1">pyyaml</requirement> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
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21 <requirement type="package" version="1.11">tabix</requirement> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
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22 <requirement type="package" version="4.6.0">findutils</requirement> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
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23 <yield/> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
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24 </requirements> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
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25 </xml> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
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26 <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token> |
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17
4c201a3d4755
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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27 <token name="@WRAPPER_VERSION@">galaxy2</token> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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28 <token name="@ATTRIBUTION@"><![CDATA[ |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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29 **Attribution** |
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3
2de9f585505b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b30d2e277cc360437a02fa812c577c0c8d997cff-dirty
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30 This Galaxy tool relies on the JBrowse2, maintained by the GMOD Community. The Galaxy wrapper is developed by the IUC |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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31 ]]> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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32 </token> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
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33 <xml name="genome_selector" |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
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34 token_help="" |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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35 token_label="Fasta sequences" |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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36 token_optional="False" > |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
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37 <conditional name="reference_genome"> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
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38 <param help="Built-in references" label="Reference genome to display" name="genome_type_select" type="select"> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
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39 <option selected="True" value="indexed">Use a built-in genome</option> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
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40 <option value="history">Use a genome from history</option> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
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41 </param> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
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42 <when value="indexed"> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
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43 <param |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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44 help="@HELP@" |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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45 label="@LABEL@" |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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46 name="genomes" |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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47 type="select" |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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48 optional="@OPTIONAL@" |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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49 > |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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50 <options from_data_table="all_fasta"> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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51 <filter column="2" type="sort_by" /> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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52 <validator message="No genomes are available for the selected input dataset" type="no_options" /> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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53 </options> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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54 </param> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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55 </when> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
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56 <when value="history"> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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57 <param |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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58 format="fasta" |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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59 label="@LABEL@" |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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60 help="@HELP@" |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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61 name="genomes" |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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62 type="data" |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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63 optional="@OPTIONAL@" |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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64 multiple="True" /> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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65 </when> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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66 </conditional> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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67 </xml> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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68 |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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69 <xml name="auto_manual_tk" |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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70 token_cond_label="Color" |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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71 token_cond_name="color" |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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72 token_select_label="Color Specification" |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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73 token_select_name="color_select" |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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74 token_automatic_label="Automatically selected" |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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75 token_manual_label="Manual Color Selection"> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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76 <conditional name="@COND_NAME@" label="@COND_LABEL@"> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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77 <param type="select" label="@SELECT_LABEL@" name="@SELECT_NAME@"> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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78 <option value="automatic" selected="true">@AUTOMATIC_LABEL@</option> |
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79 <option value="manual">@MANUAL_LABEL@</option> |
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d78175596286
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80 </param> |
|
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81 <when value="automatic"> |
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82 </when> |
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83 <when value="manual"> |
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84 <yield /> |
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85 </when> |
|
d78175596286
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86 </conditional> |
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87 </xml> |
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88 |
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89 <xml name="jb_color" |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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90 token_label="JBrowse style.color" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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91 token_name="style_color" |
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92 token_value="goldenrod" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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93 token_help="Basic color of features. Most glyphs interpret this as the fill color of the rectangle they draw. Color syntax is the same as that used for CSS" |
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94 > |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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95 <param label="@LABEL@" type="color" name="@NAME@" value="@VALUE@" help="@HELP@"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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96 <sanitizer> |
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97 <valid initial="string.letters,string.digits"> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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98 <add value="#" /> |
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99 </valid> |
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100 </sanitizer> |
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101 </param> |
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d78175596286
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102 </xml> |
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103 |
|
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104 <xml name="auto_color" |
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105 token_cond_label="Color" |
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106 token_cond_name="color" |
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107 token_select_label="Color Selection" |
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108 token_select_name="color_select" |
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109 token_automatic_label="Automatically selected" |
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110 token_manual_label="Manual Color Selection"> |
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111 <expand macro="auto_manual_tk" |
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112 cond_label="@COND_LABEL@" |
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113 cond_name="@COND_NAME@" |
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114 select_label="@SELECT_LABEL@" |
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115 select_name="@SELECT_NAME@" |
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116 automatic_label="@AUTOMATIC_LABEL@" |
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117 manual_label="@MANUAL_LABEL@"> |
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118 <expand macro="jb_color" /> |
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119 <yield /> |
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120 </expand> |
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121 </xml> |
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122 |
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123 |
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124 |
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125 <xml name="brewer_scheme"> |
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126 <param type="select" label="Brewer color Scheme" name="brewer_scheme"> |
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127 <option value="BrBg">BrBg: Brown - Blue Green</option> |
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128 <option value="PiYg">PiYg: Pink - Yellow Green</option> |
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129 <option value="PRGn">PRGn: Purple Red - Green</option> |
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130 <option value="PuOr">PuOr: Purple - Orange</option> |
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131 <option value="RdBu" selected="true">RdBu: Red - Blue</option> |
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132 <option value="RdGy">RdGy: Red - Gray</option> |
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133 <option value="RdYlBu">RdYlBu: Red - Yellow - Blue</option> |
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134 <option value="RdYlGn">RdYlBu: Red - Yellow - Green</option> |
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135 <option value="Spectral">Spectral</option> |
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136 </param> |
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137 </xml> |
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138 |
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139 <xml name="general_options"> |
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140 <section name="jbgen" title="General JBrowse Options [Advanced]" expanded="false"> |
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13
1d86925dbb4c
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141 <param label="Subset to display to new users" type="text" name="defaultLocation" value="" help="Initial subset to be shown for users who have never visited the browser before. Example: 'ctgA:1234..5678'"/> |
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0
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142 <param label="Session name" type="text" name="session_name" value="New session" help="Displayed at the top of the window"/> |
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143 <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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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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144 |
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145 <param name="primary_color" type="color" label="Primary color" value="#0D233F"> |
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146 <sanitizer> |
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147 <valid initial="string.ascii_letters,string.digits"> |
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148 <add value="#" /> |
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149 </valid> |
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150 </sanitizer> |
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151 </param> |
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152 <param name="secondary_color" type="color" label="Secondary color" value="#721E63"> |
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153 <sanitizer> |
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154 <valid initial="string.ascii_letters,string.digits"> |
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155 <add value="#" /> |
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156 </valid> |
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157 </sanitizer> |
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158 </param> |
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159 <param name="tertiary_color" type="color" label="Tertiary color" value="#135560"> |
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160 <sanitizer> |
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161 <valid initial="string.ascii_letters,string.digits"> |
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162 <add value="#" /> |
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163 </valid> |
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164 </sanitizer> |
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165 </param> |
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166 <param name="quaternary_color" type="color" label="Quaternary color" value="#FFB11D"> |
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167 <sanitizer> |
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168 <valid initial="string.ascii_letters,string.digits"> |
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169 <add value="#" /> |
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170 </valid> |
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171 </sanitizer> |
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172 </param> |
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173 |
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174 <param label="Font size" name="font_size" type="integer" value="10" /> |
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175 </section> |
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176 </xml> |
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177 |
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178 <xml name="color_selection_minmax"> |
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179 <section name="jbcolor" title="JBrowse Color Options [Advanced]" expanded="false"> |
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180 <!-- Abuse auto/manual for bicolor pivot. Means we'll have to handle the |
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181 auto case as well, but may be safe to just say "brewer colors? Pff, |
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182 red/blue" --> |
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183 <expand macro="auto_manual_tk" |
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184 token_cond_label="Color" |
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185 token_cond_name="color" |
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186 token_select_label="Color Selection" |
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187 token_select_name="color_select" |
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188 token_automatic_label="Automatically selected" |
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189 token_manual_label="Manual Color Selection"> |
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190 <expand macro="jb_color" |
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191 label="JBrowse style.pos_color" |
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192 name="style_pos_color" |
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193 value="blue" |
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194 help="CSS color, default 'blue'. When drawing bicolor plots, the fill color to use for values that are above the pivot point." /> |
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195 <expand macro="jb_color" |
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196 label="JBrowse style.neg_color" |
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197 name="style_neg_color" |
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198 value="red" |
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199 help=" CSS color, default 'red'. When drawing bicolor plots, the fill color to use for values that are below the pivot point." /> |
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200 </expand> |
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201 |
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202 <conditional name="bicolor_pivot" label="Bicolor Pivot"> |
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203 <param type="select" label="Bicolor Pivot" name="bicolor_pivot_select"> |
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204 <option value="zero" selected="true">Zero</option> |
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205 <option value="mean">Mean</option> |
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206 <option value="custom">Custom Value</option> |
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207 </param> |
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208 <when value="zero" /> |
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209 <when value="mean" /> |
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210 <when value="custom"> |
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211 <param label="JBrowse style.bicolor_pivot" type="float" name="pivot_point" value="0.0" help="Where to change from pos_color to neg_color when drawing bicolor plots." /> |
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212 </when> |
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213 </conditional> |
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214 </section> |
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215 </xml> |
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216 |
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217 <xml name="color_selection" |
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218 token_scaling_lin_select="true" |
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219 token_scaling_log_select="false" |
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220 > |
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221 <section name="jbcolor_scale" title="JBrowse Feature Score Scaling & Coloring Options [Advanced]" expanded="false"> |
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222 <conditional name="color_score" label="JBrowse style.color & Score relationship"> |
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223 <param type="select" label="Color Score Algorithm" name="color_score_select" help="How to color the features. If it is based on score, then features with a score attribute anywhere in their hierachy will have their color affected by the score. If you choose to ignore the score, then you'll be able to select a single solid color for every feature in the track"> |
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224 <option value="score">Based on score</option> |
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225 <option value="none" selected="true">Ignore score</option> |
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226 </param> |
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227 <when value="none"> |
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228 <!-- When no scaling is done, no scores available, then just let the |
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229 user choose a base color for the track --> |
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230 <expand macro="auto_color" /> |
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231 </when> |
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232 <when value="score"> |
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233 <!-- Scaling --> |
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234 <param type="select" label="JBrowse style.color function's score scaling" name="score_scaling" |
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235 help="How should the colors be distributed across the values? For blast results which distributes scores on the scale of approximately [1e-500, 10], it makes sense to request a logarithmic scaling of the color values. Logarithmic is indeed the default for blast. However other analysis methods may produce scores on ranges such as [0, 100] where a linear scale would be more appropriate for color distribution."> |
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236 <option value="linear" selected="@SCALING_LIN_SELECT@">Linear scaling</option> |
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237 <option value="logarithmic" selected="false">Logarithmic scaling</option> |
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238 <option value="blast" selected="@SCALING_LOG_SELECT@">Blast scaling</option> |
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239 </param> |
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240 |
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241 <!-- Scaling Bounds --> |
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242 <conditional name="score_scales" label="Minimum/Maximum values for track scores"> |
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243 <param type="select" label="How should minimum and maximum values be determined for the scores of the features" name="scale_select"> |
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244 <option value="automatic" selected="true">Automatically determined</option> |
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245 <option value="manual">Manually specify minimum and maximum expected scores for the feature track</option> |
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246 </param> |
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247 <when value="automatic" /> |
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248 <when value="manual"> |
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249 <param label="Minimum expected score" name="minimum" type="integer" value="0" /> |
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250 <param label="Maximum expected score" name="maximum" type="integer" value="100" /> |
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251 </when> |
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252 </conditional> |
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253 |
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254 <!-- Scale color --> |
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255 <conditional name="color_scheme" label="Color Scheme for scored features"> |
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256 <param type="select" label="JBrowse style.color function's color scheme for scored values" name="score_scheme"> |
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257 <option value="opacity">Opacity (high scores = 1.0 opacity)</option> |
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258 <!--<option value="brewer">Brewer Color Schemes</option>--> |
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259 </param> |
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260 <when value="opacity"> |
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261 <!-- Single color selection mode --> |
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262 <expand macro="auto_color" /> |
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263 </when> |
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264 <!--<when value="brewer">--> |
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265 <!--[> Brewer continuum selection <]--> |
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266 <!--<expand macro="brewer_scheme" />--> |
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267 <!--</when>--> |
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268 </conditional> |
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269 </when> |
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270 </conditional> |
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271 </section> |
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272 </xml> |
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273 |
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274 <xml name="track_visibility"> |
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275 <param type="select" label="Track Visibility" name="track_visibility"> |
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276 <option value="default_off">Off when browser opens</option> |
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277 <option value="default_on" selected="true">On when browser opens</option> |
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278 </param> |
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279 </xml> |
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280 |
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281 <xml name="track_styling_linear"> |
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282 <param label="Show labels" name="show_labels" type="boolean" checked="false" truevalue="true" falsevalue="false" /> |
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283 <param label="Show descriptions" name="show_descriptions" type="boolean" checked="false" truevalue="true" falsevalue="false" /> |
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284 <param name="display_mode" type="select" label="Display mode"> |
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285 <option value="normal" selected="true">normal</option> |
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286 <option value="compact">compact</option> |
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287 <option value="reducedRepresentation">reducedRepresentation</option> |
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288 <option value="collapse">collapse</option> |
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289 </param> |
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290 <param label="Max height" name="max_height" type="integer" value="600" help="Maximum height that the track is permitted to reach in pixels."/> |
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291 </xml> |
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292 |
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293 <xml name="track_styling_feature"> |
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294 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false"> |
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295 <conditional name="track_style"> |
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296 <param name="display" type="select" label="Display style" help="How the track will be displayed by default"> |
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297 <option value="LinearBasicDisplay" selected="true">LinearBasicDisplay</option> |
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298 <option value="LinearPileupDisplay">LinearPileupDisplay - good for dense tracks at scale</option> |
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299 <option value="LinearArcDisplay">LinearArcDisplay</option> |
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300 </param> |
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5
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301 <when value="LinearPileupDisplay"> |
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302 <expand macro="track_styling_linear"/> |
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303 </when> |
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0
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304 <when value="LinearBasicDisplay"> |
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305 <expand macro="track_styling_linear"/> |
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306 |
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307 <!-- examples: https://github.com/GMOD/jbrowse-components/discussions/2729 |
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308 and https://github.com/GMOD/jbrowse-components/blob/main/plugins/svg/src/SvgFeatureRenderer/configSchema.ts#L41 --> |
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309 <param label="Features label" |
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310 type="text" |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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311 name="label" |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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312 value="jexl:get(feature,'name') || get(feature,'id')" |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
313 help="See https://jbrowse.org/jb2/docs/config_guide/#configuration-callbacks for syntax"> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
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314 <sanitizer> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
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315 <valid initial="default"> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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316 <add value="|" /> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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317 <add value="{"/> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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318 <add value="}"/> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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319 <add value="!"/> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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diff
changeset
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320 <add value="?"/> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
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321 <add value="+"/> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
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322 <add value="="/> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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323 <add value="'"/> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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324 </valid> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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325 </sanitizer> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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326 </param> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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327 <param label="Features description" |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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328 type="text" |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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329 name="description" |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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330 value="jexl:get(feature,'note') || get(feature,'description')" |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
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331 help="See https://jbrowse.org/jb2/docs/config_guide/#configuration-callbacks for syntax"> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
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332 <sanitizer> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
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333 <valid initial="default"> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
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334 <add value="|" /> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
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335 <add value="{"/> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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336 <add value="}"/> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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diff
changeset
|
337 <add value="!"/> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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diff
changeset
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338 <add value="?"/> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
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339 <add value="+"/> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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diff
changeset
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340 <add value="="/> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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341 <add value="'"/> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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342 </valid> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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diff
changeset
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343 </sanitizer> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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344 </param> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
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345 </when> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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346 <when value="LinearArcDisplay"/> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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347 </conditional> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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348 </section> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
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349 </xml> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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350 |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
351 <xml name="track_styling_xam"> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
352 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false"> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
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353 <conditional name="track_style"> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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354 <param name="display" type="select" label="Display style" help="How the track will be displayed by default"> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
355 <option value="LinearAlignmentsDisplay" selected="true">LinearAlignmentsDisplay</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
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356 <option value="LinearPileupDisplay">LinearPileupDisplay</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
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357 <option value="LinearSNPCoverageDisplay">LinearSNPCoverageDisplay</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
358 </param> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
359 <when value="LinearAlignmentsDisplay"/> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
360 <when value="LinearPileupDisplay"/> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
361 <when value="LinearSNPCoverageDisplay"> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
362 <param name="displayCrossHatches" label="Draw cross hatches" type="boolean" checked="true" truevalue="true" falsevalue="false" /> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
363 <param name="minScore" label="Min score" type="integer" value="" optional="true"/> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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364 <param name="maxScore" label="Max score" type="integer" value="" optional="true"/> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
365 </when> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
366 </conditional> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
367 </section> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
368 </xml> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
369 |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
370 <xml name="track_styling_vcf"> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
371 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false"> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
372 <conditional name="track_style"> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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|
373 <param name="display" type="select" label="Display style" help="How the track will be displayed by default"> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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|
374 <option value="LinearVariantDisplay" selected="true">LinearVariantDisplay</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
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changeset
|
375 </param> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
376 <when value="LinearVariantDisplay"> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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|
377 <expand macro="track_styling_linear"/> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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|
378 </when> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
379 </conditional> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
380 </section> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
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changeset
|
381 </xml> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
382 |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
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changeset
|
383 <xml name="track_styling_bigwig"> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
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changeset
|
384 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false"> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
385 <conditional name="track_style"> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
386 <param name="display" type="select" label="Display style" help="How the track will be displayed by default"> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
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changeset
|
387 <option value="LinearWiggleDisplay" selected="true">LinearWiggleDisplay</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
388 </param> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
389 <when value="LinearWiggleDisplay"> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
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changeset
|
390 <param name="autoscale" type="select" label="Autoscale type"> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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391 <option value="local" selected="true">Local</option> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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392 <option value="global">Global</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
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393 <option value="globalsd">Global ± 3σ</option> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
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394 <option value="localsd">Local ± 3σ</option> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
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395 </param> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
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396 <param name="resolution" label="Resolution" type="integer" value="1"/> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
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397 <param name="summaryScoreMode" type="select" label="Autoscale type"> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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398 <option value="max">Max</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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399 <option value="min">Min</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
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400 <option value="avg">Avg</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
401 <option value="whiskers" selected="true">Whiskers (combines all three)</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
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402 </param> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
403 <param name="filled" label="Fill in histogram" type="boolean" checked="true" truevalue="true" falsevalue="false" /> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff
changeset
|
404 <param name="scaleType" type="select" label="Autoscale type"> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
405 <option value="linear" selected="true">Linear</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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406 <option value="log">Log</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
407 </param> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
408 <param name="displayCrossHatches" label="Draw cross hatches" type="boolean" checked="true" truevalue="true" falsevalue="false" /> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
409 <param name="minScore" label="Min score" type="integer" value="" optional="true"/> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
410 <param name="maxScore" label="Max score" type="integer" value="" optional="true"/> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
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411 </when> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
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412 </conditional> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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413 </section> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
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414 </xml> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
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415 |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
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416 <xml name="track_menu"> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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417 <section name="jbmenu" title="JBrowse Contextual Menu options [Advanced]" expanded="false"> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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418 <repeat name="track_menu" title="Track Menu"> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
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419 <param label="Menu action" |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
420 type="select" |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
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421 name="menu_action" |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
422 help="Action performed when user clicks on the menu"> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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423 <option value="iframeDialog" selected="true">iframeDialog: causes the given url to be opened in a popup dialog box within JBrowse, in an iframe element.</option> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
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424 <option value="newWindow">newWindow: causes the given url to be opened in a new browser window.</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
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425 <option value="navigateTo">navigateTo: opens the given url in the same browser window, navigating the user away from JBrowse.</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
426 </param> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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diff
changeset
|
427 <param label="Menu label" |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
428 type="text" |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
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429 name="menu_label" |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
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430 help="Will be displayed in the contextual menu on each feature ({name}, {id}, {type}, {start}, {end}, {strand} variables will be interpreted)"> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
431 <expand macro="menu_sanitize" /> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff
changeset
|
432 </param> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
433 <param label="Menu title" |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
434 type="text" |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
435 name="menu_title" |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff
changeset
|
436 help="Will be displayed in the popup title bar if displayed ({id}, {type}, {start}, {end}, {strand} variables will be interpreted)"> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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diff
changeset
|
437 <expand macro="menu_sanitize" /> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
438 </param> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
439 <param label="Menu url" |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
440 type="text" |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
441 name="menu_url" |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
442 help="Destination URL ({name}, {id}, {type}, {start}, {end}, {strand} variables will be interpreted)"> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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diff
changeset
|
443 <expand macro="menu_sanitize" /> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
444 </param> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
445 <param label="Menu icon" |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
446 type="select" |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
447 name="menu_icon" |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
448 help="Icon to display next to menu label"> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
449 <option value="dijitIconBookmark" selected="true">Bookmark</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
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450 <option value="dijitIconSave">Save</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
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451 <option value="dijitIconPrint">Print</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
452 <option value="dijitIconCut">Cut</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
453 <option value="dijitIconCopy">Copy</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
454 <option value="dijitIconClear">Clear</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
455 <option value="dijitIconDelete">Delete</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
456 <option value="dijitIconUndo">Undo</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
457 <option value="dijitIconEdit">Edit</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
458 <option value="dijitIconNewTask">New Task</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
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changeset
|
459 <option value="dijitIconEditTask">Edit Task</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
460 <option value="dijitIconEditProperty">Edit Property</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
461 <option value="dijitIconTask">Task</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
462 <option value="dijitIconFilter">Filter</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
463 <option value="dijitIconConfigure">Configure</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
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464 <option value="dijitIconSearch">Search</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
465 <option value="dijitIconApplication">Application</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
466 <option value="dijitIconChart">Chart</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
467 <option value="dijitIconConnector">Connector</option> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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468 <option value="dijitIconDatabase">Database</option> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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469 <option value="dijitIconDocuments">Documents</option> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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470 <option value="dijitIconMail">Mail</option> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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471 <option value="dijitLeaf">Leaf</option> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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472 <option value="dijitIconFile">File</option> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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473 <option value="dijitIconFunction">Function</option> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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474 <option value="dijitIconKey">Key</option> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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475 <option value="dijitIconPackage">Package</option> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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476 <option value="dijitIconSample">Sample</option> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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477 <option value="dijitIconTable">Table</option> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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478 <option value="dijitIconUsers">Users</option> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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479 <option value="dijitIconFolderClosed">Folder Closed</option> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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480 <option value="dijitIconFolderOpen">Folder Open</option> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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481 <option value="dijitIconError">Error</option> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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482 </param> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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483 </repeat> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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484 </section> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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485 </xml> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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486 |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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487 <xml name="menu_sanitize"> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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488 <sanitizer> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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489 <valid> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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490 <add value="{"/> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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491 <add value="}"/> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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492 <add value="!"/> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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493 <add value="?"/> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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494 <add value="&"/> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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495 <add value="+"/> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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496 <add value="="/> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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497 <add value="'"/> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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498 <add value='"'/> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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499 </valid> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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500 </sanitizer> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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501 </xml> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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502 |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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503 |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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504 <xml name="input_conditional" token_label="Track Data" token_format="data"> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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505 <param label="@LABEL@" format="@FORMAT@" name="annotation" type="data" multiple="True"/> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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506 </xml> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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507 <xml name="citations"> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
508 <citations> |
|
8
9a168aa68f06
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 906bfc0007c5276f4bcd4be7b3c80a1840dccaec
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diff
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509 <citation type="doi">10.1186/s13059-016-0924-1</citation> |
|
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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510 <citation type="doi">10.1101/gr.094607.109</citation> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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511 </citations> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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512 </xml> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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513 </macros> |