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comparison macros.xml @ 93:4c517a0041a8 draft

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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
comparison
equal deleted inserted replaced
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>