Mercurial > repos > fubar > jbrowse2
comparison macros.xml @ 93:4c517a0041a8 draft
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
| author | fubar |
|---|---|
| date | Wed, 24 Apr 2024 02:29:32 +0000 |
| parents | 408781c080fc |
| children | 74074746ccd8 |
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| 92:3c4db8203fad | 93:4c517a0041a8 |
|---|---|
| 1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
| 2 <macros> | 2 <macros> |
| 3 <token name="@TOOL_VERSION@">2.10.1</token> | 3 <token name="@TOOL_VERSION@">2.11.0</token> |
| 4 <xml name = "edamInc"> | 4 <xml name = "edamInc"> |
| 5 <edam_topics> | 5 <edam_topics> |
| 6 <edam_topic>topic_3307</edam_topic> | 6 <edam_topic>topic_3307</edam_topic> |
| 7 <edam_topic>topic_0092</edam_topic> | 7 <edam_topic>topic_0092</edam_topic> |
| 8 </edam_topics> | 8 </edam_topics> |
| 18 <requirement type="package" version="0.7.1">bcbio-gff</requirement> | 18 <requirement type="package" version="0.7.1">bcbio-gff</requirement> |
| 19 <requirement type="package" version="1.19">samtools</requirement> | 19 <requirement type="package" version="1.19">samtools</requirement> |
| 20 <requirement type="package" version="6.0.1">pyyaml</requirement> | 20 <requirement type="package" version="6.0.1">pyyaml</requirement> |
| 21 <requirement type="package" version="1.11">tabix</requirement> | 21 <requirement type="package" version="1.11">tabix</requirement> |
| 22 <requirement type="package" version="4.6.0">findutils</requirement> | 22 <requirement type="package" version="4.6.0">findutils</requirement> |
| 23 <requirement type="package" version="0.0.8">hictk</requirement> | 23 <requirement type="package" version="0.0.12-0">hictk</requirement> |
| 24 <requirement type="package" version="3.0">zip</requirement> | |
| 24 <yield/> | 25 <yield/> |
| 25 </requirements> | 26 </requirements> |
| 26 </xml> | 27 </xml> |
| 27 <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token> | 28 <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token> |
| 28 <token name="@WRAPPER_VERSION@">galaxy2</token> | 29 <token name="@WRAPPER_VERSION@">galaxy2</token> |
| 537 </sanitizer> | 538 </sanitizer> |
| 538 </xml> | 539 </xml> |
| 539 | 540 |
| 540 <xml name="input_conditional" token_label="Track Data" token_format="data"> | 541 <xml name="input_conditional" token_label="Track Data" token_format="data"> |
| 541 <conditional name="useuri"> | 542 <conditional name="useuri"> |
| 542 <param name="insource" type="select" label="Define track data as a history file or an internet URI" | 543 <param name="insource" type="select" label="Define track data as a history file or an internet URI" |
| 543 help="A public URI implies that all the associated tabix files are also in place. They are created for history files"> | 544 help="A public URI implies that all the associated tabix files are also in place. They are created for history files"> |
| 544 <option value="history" selected="true">Track data from a history file</option> | 545 <option value="history" selected="true">Track data from a history file</option> |
| 545 <option value="uri" >Tabix data URI - index files must be available at corresponding URI</option> | 546 <option value="uri" >Tabix data URI - index files must be available at corresponding URI</option> |
| 546 </param> | 547 </param> |
| 547 <when value="history"> | 548 <when value="history"> |
| 548 <param label="@LABEL@" format="@FORMAT@" name="annotation" multiple="True" optional="true" type="data" /> | 549 <param label="@LABEL@" format="@FORMAT@" name="annotation" multiple="True" optional="true" type="data" /> |
| 549 </when> | 550 </when> |
| 550 <when value="uri"> | 551 <when value="uri"> |
| 551 <param label="@LABEL@" name="annouri" type="text" /> | 552 <param label="@LABEL@" name="annouri" type="text" /> |
| 552 <param label="Short name for track display" name="annoname" type="text" > | 553 <param label="Short name for track display" name="annoname" type="text" > |
| 553 <sanitizer invalid_char="_"> | 554 <sanitizer invalid_char="_"> |
| 555 <valid initial="string.printable" > | |
| 556 <remove value="'" /> | |
| 557 </valid> | |
| 558 </sanitizer> | |
| 559 </param> | |
| 560 </when> | |
| 561 </conditional> | |
| 562 </xml> | |
| 563 <xml name="pafref_conditional" token_label="Track Data" token_format="data"> | |
| 564 <conditional name="pafuseuri"> | |
| 565 <param name="insource" type="select" label="PAF reference data from a history file or an internet URI?" | |
| 566 help="Multiple references can be used for mashmap PAF. A URI source requires all the associated tabix index files to be in place."> | |
| 567 <option value="history" selected="true">PAF reference comparison genome from a history file</option> | |
| 568 <option value="uri">PAF reference comparison genome tabix .gz URI with index files at the corresponding URIs</option> | |
| 569 </param> | |
| 570 <when value="history"> | |
| 571 <param label="@LABEL@" format="@FORMAT@" name="annotation" type="data" | |
| 572 help="Add all PAF reference comparison genomes used to make the PAF" multiple="true" /> | |
| 573 </when> | |
| 574 <when value="uri"> | |
| 575 <repeat name="refuri" title="PAF reference comparison genome URI" min="1"> | |
| 576 <param label="@LABEL@" name="annotation" type="text" /> | |
| 577 <param label="Short name for this reference" name="annoname" type="text" help="Short names take less track space"> | |
| 578 <sanitizer invalid_char="_"> | |
| 554 <valid initial="string.printable" > | 579 <valid initial="string.printable" > |
| 555 <remove value="'" /> | 580 <remove value="'" /> |
| 556 </valid> | 581 </valid> |
| 557 </sanitizer> | 582 </sanitizer> |
| 558 </param> | 583 </param> |
| 559 </when> | 584 </repeat> |
| 560 </conditional> | 585 </when> |
| 561 </xml> | 586 </conditional> |
| 562 <xml name="pafref_conditional" token_label="Track Data" token_format="data"> | 587 </xml> |
| 563 <conditional name="pafuseuri"> | |
| 564 <param name="insource" type="select" label="PAF reference data from a history file or an internet URI?" | |
| 565 help="Multiple references can be used for mashmap PAF. A URI source requires all the associated tabix index files to be in place."> | |
| 566 <option value="history" selected="true">PAF reference comparison genome from a history file</option> | |
| 567 <option value="uri">PAF reference comparison genome tabix .gz URI with index files at the corresponding URIs</option> | |
| 568 </param> | |
| 569 <when value="history"> | |
| 570 <param label="@LABEL@" format="@FORMAT@" name="annotation" type="data" | |
| 571 help="Add all PAF reference comparison genomes used to make the PAF" multiple="true" /> | |
| 572 </when> | |
| 573 <when value="uri"> | |
| 574 <repeat name="refuri" title="PAF reference comparison genome URI" min="1"> | |
| 575 <param label="@LABEL@" name="annotation" type="text" /> | |
| 576 <param label="Short name for this reference" name="annoname" type="text" help="Short names take less track space"> | |
| 577 <sanitizer invalid_char="_"> | |
| 578 <valid initial="string.printable" > | |
| 579 <remove value="'" /> | |
| 580 </valid> | |
| 581 </sanitizer> | |
| 582 </param> | |
| 583 </repeat> | |
| 584 </when> | |
| 585 </conditional> | |
| 586 </xml> | |
| 587 <xml name="citations"> | 588 <xml name="citations"> |
| 588 <citations> | 589 <citations> |
| 589 <citation type="doi">10.1186/s13059-016-0924-1</citation> | 590 <citation type="doi">10.1186/s13059-016-0924-1</citation> |
| 590 <citation type="doi">10.1101/gr.094607.109</citation> | 591 <citation type="doi">10.1101/gr.094607.109</citation> |
| 591 </citations> | 592 </citations> |