Mercurial > repos > fubar > jbrowse2

comparison jbrowse2.xml @ 38:07849bf248e3 draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a74e469a81b38c7142f63de510ae31d3754d1767
author fubar
date Fri, 01 Mar 2024 00:40:38 +0000
parents 5f39f745682f
children e1a3d3221ed3
comparison
equal deleted inserted replaced
37:7adde511daa1 38:07849bf248e3
12 <command detect_errors="aggressive"><![CDATA[ 12 <command detect_errors="aggressive"><![CDATA[
13 mkdir -p '$output.files_path' && 13 mkdir -p '$output.files_path' &&
14 ## Copy the XML file into the directory, mostly for debugging 14 ## Copy the XML file into the directory, mostly for debugging
15 ## but nice if users want to reproduce locally 15 ## but nice if users want to reproduce locally
16 cp '$trackxml' '$output.files_path/galaxy.xml' && 16 cp '$trackxml' '$output.files_path/galaxy.xml' &&
17
18 export JBROWSE2_PATH=\$(dirname \$(which jbrowse))/../opt/jbrowse2 &&
19
20 ## Once that's done, we run the python script to handle the real work
17 python '$__tool_directory__/jbrowse2.py' 21 python '$__tool_directory__/jbrowse2.py'
22 --jbrowse2path \${JBROWSE2_PATH}
18 --outdir '$output.files_path' 23 --outdir '$output.files_path'
19 --xml '$trackxml' && 24 --xml '$trackxml' &&
20 #if $jbgen.zipOut == "true": 25 #if $jbgen.zipOut == "true":
21 (cd '$output.files_path' && zip -r - . ) > '$output' 26 (cd '$output.files_path' && zip -r - . ) > '$output'
22 #else 27 #else
354 <param name="reference_genome|genome" value="merlin.fa"/> 359 <param name="reference_genome|genome" value="merlin.fa"/>
355 <repeat name="track_groups"> 360 <repeat name="track_groups">
356 <param name="category" value="Default" /> 361 <param name="category" value="Default" />
357 <repeat name="data_tracks"> 362 <repeat name="data_tracks">
358 <conditional name="data_format"> 363 <conditional name="data_format">
359 <param name="data_format_select" value="wiggle"/> 364 <param name="data_format_select" value="bigwig"/>
360 <param name="annotation" value="bw/merlin.bw"/> 365 <param name="annotation" value="bw/merlin.bw"/>
361 </conditional> 366 </conditional>
362 </repeat> 367 </repeat>
363 </repeat> 368 </repeat>
364 <param name="uglyTestingHack" value="enabled" /> 369 <param name="uglyTestingHack" value="enabled" />
369 <has_text text="history id="></has_text> 374 <has_text text="history id="></has_text>
370 <has_text text="metadata"></has_text> 375 <has_text text="metadata"></has_text>
371 <has_text text="tool_id"></has_text> 376 <has_text text="tool_id"></has_text>
372 <has_text text="trackFile path="></has_text> 377 <has_text text="trackFile path="></has_text>
373 <has_text text="file_ext=&quot;bigwig&quot;"></has_text> 378 <has_text text="file_ext=&quot;bigwig&quot;"></has_text>
374 <has_text text="format=&quot;wiggle&quot;"></has_text> 379 <has_text text="format=&quot;bigwig&quot;"></has_text>
375 </assert_contents> 380 </assert_contents>
376 </output> 381 </output>
377 </test> 382 </test>
378
379 <test> 383 <test>
380 <param name="reference_genome|genome_type_select" value="history"/> 384 <param name="reference_genome|genome_type_select" value="history"/>
381 <param name="reference_genome|genome" value="merlin.fa"/> 385 <param name="reference_genome|genome" value="merlin.fa"/>
382 <repeat name="track_groups"> 386 <repeat name="track_groups">
383 <param name="category" value="Default" /> 387 <param name="category" value="Default" />
708 <has_text text="With menu or index"/> 712 <has_text text="With menu or index"/>
709 <has_text text="gene_calls"/> 713 <has_text text="gene_calls"/>
710 </assert_contents> 714 </assert_contents>
711 </output> 715 </output>
712 </test> 716 </test>
713
714 <!-- TODO add a synteny test --> 717 <!-- TODO add a synteny test -->
715 <!-- TODO add a bam and a cram test --> 718 <!-- TODO add a bam and a cram test -->
716 <!-- TODO add an hic test --> 719 <!-- TODO add an hic test -->
717 <!-- TODO add a vcf_bgzip test --> 720 <!-- TODO add a vcf_bgzip test -->
718 </tests> 721 </tests>