Mercurial > repos > fubar > jbrowse2
comparison jbrowse2.xml @ 89:408781c080fc draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11
| author | fubar |
|---|---|
| date | Wed, 17 Apr 2024 22:18:47 +0000 |
| parents | efd1d41f11b4 |
| children | 51980e0dafd2 |
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| 88:efd1d41f11b4 | 89:408781c080fc |
|---|---|
| 261 #else if str($track.data_format.data_format_select) == "paf": | 261 #else if str($track.data_format.data_format_select) == "paf": |
| 262 <paf> | 262 <paf> |
| 263 #if $track.data_format.pafuseuri.insource == "history": | 263 #if $track.data_format.pafuseuri.insource == "history": |
| 264 <genome> | 264 <genome> |
| 265 #for $anno in $track.data_format.pafuseuri.annotation: | 265 #for $anno in $track.data_format.pafuseuri.annotation: |
| 266 ${anno}, | 266 ${anno}:${anno.name}, |
| 267 #end for | 267 #end for |
| 268 </genome> | 268 </genome> |
| 269 <genome_label> | |
| 270 #for $anno in $track.data_format.pafuseuri.annotation: | |
| 271 ${anno.name}, | |
| 272 #end for | |
| 273 </genome_label> | |
| 274 #else: | 269 #else: |
| 275 <genome> | 270 <genome> |
| 276 #for $refgenome in $track.data_format.pafuseuri.refuri: | 271 #for $refgenome in $track.data_format.pafuseuri.refuri: |
| 277 $refgenome.annotation, | 272 ${refgenome.annotation}:${refgenome.annoname}, |
| 278 #end for | 273 #end for |
| 279 </genome> | 274 </genome> |
| 280 <genome_label> | |
| 281 #for $refgenome in $track.data_format.pafuseuri.refuri: | |
| 282 ${refgenome.annoname}, | |
| 283 #end for | |
| 284 </genome_label> | |
| 285 #end if | 275 #end if |
| 286 </paf> | 276 </paf> |
| 287 #else if str($track.data_format.data_format_select) == "hic": | 277 #else if str($track.data_format.data_format_select) == "hic": |
| 288 <hic> | 278 <hic> |
| 289 </hic> | 279 </hic> |
| 475 </repeat> | 465 </repeat> |
| 476 <expand macro="general_options" /> | 466 <expand macro="general_options" /> |
| 477 <param type="hidden" name="uglyTestingHack" value="" /> | 467 <param type="hidden" name="uglyTestingHack" value="" /> |
| 478 </inputs> | 468 </inputs> |
| 479 <outputs> | 469 <outputs> |
| 480 <data format="html" name="output" label="JBrowse2"> | 470 <data format="html" name="output" label="JBrowse2: ${jbgen.session_name}"> |
| 481 <change_format> | 471 <change_format> |
| 482 <when input="zipOut" value="true" format="zip" /> | 472 <when input="zipOut" value="true" format="zip" /> |
| 483 </change_format> | 473 </change_format> |
| 484 </data> | 474 </data> |
| 485 </outputs> | 475 </outputs> |
| 641 </repeat> | 631 </repeat> |
| 642 </repeat> | 632 </repeat> |
| 643 </repeat> | 633 </repeat> |
| 644 <section name="jbgen"> | 634 <section name="jbgen"> |
| 645 <param name="zipOut" value="true" /> | 635 <param name="zipOut" value="true" /> |
| 636 <param name="session_name" value="New test session"/> | |
| 646 </section> | 637 </section> |
| 647 <output name="output" file="jbrowse2_result02.zip" ftype="zip" compare="sim_size"> | 638 <output name="output" file="jbrowse2_result02.zip" ftype="zip" compare="sim_size"> |
| 648 <assert_contents> | 639 <assert_contents> |
| 649 <has_archive_member path=".*" n="616" delta="10"/> | 640 <has_archive_member path=".*" n="616" delta="10"/> |
| 650 <has_archive_member path="index.html"/> | 641 <has_archive_member path="index.html"/> |
| 654 <has_text text="background_color"/> | 645 <has_text text="background_color"/> |
| 655 </has_archive_member> | 646 </has_archive_member> |
| 656 <has_archive_member path="galaxy.xml"> | 647 <has_archive_member path="galaxy.xml"> |
| 657 <is_valid_xml /> | 648 <is_valid_xml /> |
| 658 <xml_element path="./metadata/general/session_name" n="1"> | 649 <xml_element path="./metadata/general/session_name" n="1"> |
| 659 <has_text_matching expression="New session"/> | 650 <has_text_matching expression="New test session"/> |
| 660 <not_has_text text="Newton"/> | 651 <not_has_text text="Newton"/> |
| 661 </xml_element> | 652 </xml_element> |
| 662 </has_archive_member> | 653 </has_archive_member> |
| 663 <has_archive_member path="merlin.gff3_0.gff3.gz"/> | 654 <has_archive_member path="merlin.gff3_0.gz"/> |
| 664 <has_archive_member path="merlin.bw_1.bigwig"/> | 655 <has_archive_member path="merlin.bw_1"/> |
| 665 <has_archive_member path="test-6.bed_2.bed.gz"/> | 656 <has_archive_member path="test-6.bed_2.gz"/> |
| 666 <has_archive_member path="merlin.vcf_3.vcf.tbi"/> | 657 <has_archive_member path="merlin.vcf_3.tbi"/> |
| 667 <has_archive_member path="merlin.cram_4.cram"/> | 658 <has_archive_member path="merlin.cram_4"/> |
| 668 <has_archive_member path="merlin-sample.bam_5.bam"/> | 659 <has_archive_member path="merlin-sample.bam_5"/> |
| 669 <has_archive_member path="merlinlastz.maf_6.maf.sorted.bed.gz.tbi"/> | 660 <has_archive_member path="merlinlastz.maf_6.sorted.bed.gz.tbi"/> |
| 670 <has_archive_member path="merlin.blastxml_7.blastxml.gz"/> | 661 <has_archive_member path="merlin.blastxml_7.gz"/> |
| 671 <has_archive_member path="dm3test.cool_9.cool.hic"/> | 662 <has_archive_member path="dm3test.cool_9.hic"/> |
| 672 <has_archive_member path="peach-grape-map.paf_10.paf"/> | 663 <has_archive_member path="peach-grape-map.paf_10"/> |
| 673 <has_archive_member path="Merlin.fa.gz.fai"/> | 664 <has_archive_member path="Merlin.fa.gz.fai"/> |
| 674 <has_archive_member path="config.json"> | 665 <has_archive_member path="config.json"> |
| 675 <has_json_property_with_text property="name" text="Merlin" /> | 666 <has_json_property_with_text property="name" text="Merlin" /> |
| 676 </has_archive_member> | 667 </has_archive_member> |
| 677 | |
| 678 </assert_contents> | 668 </assert_contents> |
| 679 </output> | 669 </output> |
| 680 </test> | 670 </test> |
| 681 <test> | 671 <test> |
| 682 <repeat name="assemblies"> | 672 <repeat name="assemblies"> |