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comparison autogenJB2.xml @ 46:4181e97c70a7 draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
author fubar
date Mon, 04 Mar 2024 09:47:19 +0000
parents e1a3d3221ed3
children
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45:0ec526d2d8c1 46:4181e97c70a7
11 <version_command>python '${__tool_directory__}/autogenJB2.py' --version</version_command> 11 <version_command>python '${__tool_directory__}/autogenJB2.py' --version</version_command>
12 <command detect_errors="aggressive"><![CDATA[ 12 <command detect_errors="aggressive"><![CDATA[
13 export JBROWSE2_PATH=\$(dirname \$(which jbrowse))/../opt/jbrowse2 && 13 export JBROWSE2_PATH=\$(dirname \$(which jbrowse))/../opt/jbrowse2 &&
14 python '$__tool_directory__/autogenJB2.py' 14 python '$__tool_directory__/autogenJB2.py'
15 #for $key in $autoCollection.keys(): 15 #for $key in $autoCollection.keys():
16 #if $autoCollection[$key].ext == 'fasta': 16 #if $autoCollection[$key].is_collection:
17 #set subCol=$autoCollection[$key]
18 #set pafs=[($subCol[x],$subcol[x].ext,x) for x in $subCol.keys() if $subCol[x].ext == 'paf']
19 #if len($pafs) > 0:
20 --pafmeta '$pafs[0]'
21 #set refs = [($pafs[0][2],$subCol[x],x) for x in $subCol.keys() if $subCol[x].ext == 'fasta']
22 #for $ref in $refs:
23 --pafreferencemeta '$ref'
24 #end for
25 #end if
26 #else if $autoCollection[$key].ext == 'fasta':
17 --referencemeta '$autoCollection[$key],$autoCollection[$key].ext,$key' 27 --referencemeta '$autoCollection[$key],$autoCollection[$key].ext,$key'
18 #else if $autoCollection[$key].ext in ['bed', 'bigwig', 'cool', 'gff', 'gff3', 'hic', 'maf', 'mcool', 'scool', 'vcf'] 28 #else if $autoCollection[$key].ext in ['bed', 'bigwig', 'cool', 'gff', 'gff3', 'hic', 'maf', 'mcool', 'scool', 'vcf']
19 --trackmeta '$autoCollection[$key],$autoCollection[$key].ext,$key' 29 --trackmeta '$autoCollection[$key],$autoCollection[$key].ext,$key'
20 #else if $autoCollection[$key].ext in ['bam',] 30 #else if $autoCollection[$key].ext in ['bam',]
21 --trackmeta '$autoCollection[$key],$autoCollection[$key].ext,$key,$autoCollection[$key].metadata.bam_index' 31 --trackmeta '$autoCollection[$key],$autoCollection[$key].ext,$key,$autoCollection[$key].metadata.bam_index'
43 </inputs> 53 </inputs>
44 <outputs> 54 <outputs>
45 <data format="html" name="output" label="AutoJBrowse2"/> 55 <data format="html" name="output" label="AutoJBrowse2"/>
46 </outputs> 56 </outputs>
47 <tests> 57 <tests>
48 <test> 58 <test>
49 <param name="uglyTestingHack" value="enabled" /> 59 <param name="uglyTestingHack" value="enabled" />
50 <param name="autoCollection"> 60 <param name="autoCollection">
51 <collection type="list"> 61 <collection type="list">
52 <element name="Merlin" value="merlin.fa" ftype="fasta"/> 62 <element name="Merlin" value="merlin.fa" ftype="fasta"/>
53 <element name="merlin-sample.bam" value="bam/merlin-sample.bam" ftype="bam"/> 63 <element name="test-6.bed" value="bed/test-6.bed" ftype="bed"/>
54 </collection> 64 </collection>
55 </param> 65 </param>
56 <output name="output"> 66 <output name="output">
57 <assert_contents> 67 <assert_contents>
58 <has_text text='"name": "Merlin",'/> 68 <has_text text='"name": "Merlin",'/>
59 <has_text text='"name": "merlin-sample.bam",'/> 69 <has_text text='"name": "test-6.bed",'/>
60 <has_text text='"uri": "Merlin.fa.gz.fai"'/> 70 <has_text text='"uri": "Merlin.fa.gz.fai"'/>
61 <has_text text='"uri": "bam_0_merlin-sample.bam.bam.bai"'/> 71 </assert_contents>
62 72 </output>
63 </assert_contents>
64 </output>
65 </test> 73 </test>
66 </tests> 74 </tests>
67 <help><![CDATA[ 75 <help><![CDATA[
68 76
69 Autogenerated JBrowse2 77 Autogenerated JBrowse2