Mercurial > repos > fubar > jbrowse2

comparison autogenJB2.xml @ 36:5f39f745682f draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
author fubar
date Thu, 29 Feb 2024 00:47:58 +0000
parents 15da358c3108
children bc57164eb270
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35:15da358c3108 36:5f39f745682f
1 <tool id="autogenjb2" name="autogenjb2" version="2.10.2_0" profile="22.05"> 1 <tool id="autogenjb2" name="autogenjb2" version="2.10.2.0" profile="22.05">
2 <description>Track collection to JBrowse2</description> 2 <description>Track collection to JBrowse2</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="edamInc"/> 6 <expand macro="edamInc"/>
24 #end for 24 #end for
25 --outdir '$output.files_path' 25 --outdir '$output.files_path'
26 --sessName "Autogen JBrowse" && 26 --sessName "Autogen JBrowse" &&
27 27
28 cp '$output.files_path/index.html' '$output' 28 cp '$output.files_path/index.html' '$output'
29
30 ## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph. 29 ## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph.
31 30 #if str($uglyTestingHack) == "enabled":
32 31 && cp '$output.files_path/config.json' '$output'
32 #end if
33 ]]></command> 33 ]]></command>
34 <inputs> 34 <inputs>
35 <param 35 <param
36 label="Collection of files to become tracks - they must have short, informative names" 36 label="Collection of files to become tracks - they must have short, informative names"
37 name="autoCollection" 37 name="autoCollection"
38 type="data_collection"> 38 type="data_collection">
39 </param> 39 </param>
40 <param type="hidden" name="uglyTestingHack" value="" />
40 </inputs> 41 </inputs>
41 <outputs> 42 <outputs>
42 <data format="html" name="output" label="AutoJBrowse2"/> 43 <data format="html" name="output" label="AutoJBrowse2"/>
43 </outputs> 44 </outputs>
45 <tests>
46 <test>
47 <param name="uglyTestingHack" value="enabled" />
48 <param name="autoCollection">
49 <collection type="list">
50 <element name="Merlin" value="merlin.fa" ftype="fasta"/>
51 <element name="merlin-sample.bam" value="bam/merlin-sample.bam" ftype="bam"/>
52 </collection>
53 </param>
54 <output name="output">
55 <assert_contents>
56 <has_text text='"name": "Merlin",'/>
57 <has_text text='"name": "merlin-sample.bam",'/>
58 <has_text text='"uri": "Merlin.fa.gz.fai"'/>
59 <has_text text='"uri": "bam_0_merlin-sample.bam.bam.bai"'/>
44 60
61 </assert_contents>
62 </output>
63 </test>
64 </tests>
45 <help><![CDATA[ 65 <help><![CDATA[
46 66
47 JBrowse2-in-Galaxy 67 JBrowse2-in-Galaxy
48 ================== 68 ==================
49 69