Mercurial > repos > yating-l > jbrowse_hub

annotate jbrowse_hub.xml @ 35:6d77d3bc0794 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
author yating-l
date Fri, 17 Mar 2017 12:54:54 -0400
parents 39a214ac35a7
children 046c5bfc0413
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
1 <tool id="jbrowse_hub" name="JBrowse Hub Creator" version="1.0">
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
2 <description>
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
3 This Galaxy tool is used to prepare your files to be ready for displaying on JBrowse
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
4 </description>
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
5
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
6 <requirements>
30
daf6a1122200 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit e81fecac281f299db00cfc88a068e056b031ae9d-dirty
yating-l
parents: 29
diff changeset
7 <requirement type="package" version="1.2">samtools</requirement>
2
d048f9f9f9df planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 1
diff changeset
8 <requirement type="package" version="1.9">numpy</requirement>
d048f9f9f9df planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 1
diff changeset
9 <requirement type="package" version="1.68">biopython</requirement>
5
e7c80e9b70ae planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 2
diff changeset
10 <requirement type="package" version="1.0">ucsc_tools_340</requirement>
7
3511d4f604a7 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 5
diff changeset
11 <requirement type="package" version="1.12.1">jbrowse_tools</requirement>
0
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
12 </requirements>
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
13
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
14 <stdio>
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
15 </stdio>
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
16
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
17 <command detect_errors="exit_code"><![CDATA[
5
e7c80e9b70ae planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 2
diff changeset
18 python $__tool_directory__/jbrowse_hub.py
0
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
19 --fasta '$reference'
31
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
20 --genome_name '$genome_name'
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
21
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
22 ## json metadata recording from Remi's hub-archive-creator.xml
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
23 #import json
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
24 #set global data_parameter_dict = {}
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
25
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
26 ## Function to retrieve the data of the inputs
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
27 #def prepare_json($input_to_prepare, $extra_data_dict={})
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
28 #set false_path = str($input_to_prepare)
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
29 #set name = $input_to_prepare.name
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
30
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
31 #set data_dict = {"name": $name}
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
32 #silent data_dict.update($extra_data_dict)
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
33
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
34 #silent $data_parameter_dict.update({$false_path: $data_dict})
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
35
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
36 #end def
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
37
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
38
0
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
39 #for $f in $format
35
6d77d3bc0794 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 33
diff changeset
40 #set track_label = str($f.formatChoice.label)
33
39a214ac35a7 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 32
diff changeset
41 #set extra_data_dict = {"label" : $track_label}
0
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
42 #if $f.formatChoice.format_select == 'bed'
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
43 #if $f.formatChoice.bedChoice.bed_select == 'bed_simple_repeats_option'
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
44 --bedSimpleRepeats $f.formatChoice.bedChoice.BED_simple_repeats
31
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
45 #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, extra_data_dict)
0
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
46 #elif $f.formatChoice.bedChoice.bed_select == 'bed_splice_junctions_option'
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
47 --bedSpliceJunctions $f.formatChoice.bedChoice.BED_splice_junctions
31
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
48 #silent $prepare_json($f.formatChoice.bedChoice.BED_splice_junctions, extra_data_dict)
0
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
49 #end if
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
50 #end if
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
51 #if $f.formatChoice.format_select == 'bam'
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
52 --bam $f.formatChoice.BAM
31
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
53 #silent $prepare_json($f.formatChoice.BAM, extra_data_dict)
17
99d66676570b planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 15
diff changeset
54 #end if
31
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
55 #if $f.formatChoice.format_select == 'gff3'
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
56 #if $f.formatChoice.gff3Choice.gff3_select == 'gff3_transcript'
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
57 --gff3_transcript $f.formatChoice.gff3Choice.GFF3_transcript
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
58 #silent $prepare_json($f.formatChoice.gff3Choice.GFF3_transcript, extra_data_dict)
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
59 #elif $f.formatChoice.gff3Choice.gff3_select == 'gff3_mrna'
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
60 --gff3_mrna $f.formatChoice.gff3Choice.GFF3_mrna
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
61 #silent $prepare_json($f.formatChoice.gff3Choice.GFF3_mrna, extra_data_dict)
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
62 #end if
0
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
63 #end if
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
64 #if $f.formatChoice.format_select == 'blastxml'
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
65 --blastxml $f.formatChoice.BlastXML
31
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
66 #silent $prepare_json($f.formatChoice.BlastXML, extra_data_dict)
0
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
67 #end if
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
68 #if $f.formatChoice.format_select == 'gtf'
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
69 --gtf $f.formatChoice.GTF
31
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
70 #silent $prepare_json($f.formatChoice.GTF, extra_data_dict)
0
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
71 #end if
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
72 #if $f.formatChoice.format_select == 'bigwig'
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
73 --bigwig $f.formatChoice.BIGWIG
31
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
74 #silent $prepare_json($f.formatChoice.BIGWIG, extra_data_dict)
0
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
75 #end if
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
76 #end for
31
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
77
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
78 #set all_data_json = json.dumps($data_parameter_dict)
32
f45a253f7c6a planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 31
diff changeset
79 -j '$all_data_json'
f45a253f7c6a planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 31
diff changeset
80 -e '$output.extra_files_path'
f45a253f7c6a planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 31
diff changeset
81 -o '$output'
31
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
82
0
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
83 ]]></command>
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
84
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
85 <inputs>
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
86 <param name="reference" type="data" format="fasta" label="Reference Genome" />
5
e7c80e9b70ae planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 2
diff changeset
87 <param name="genome_name" type="text" size="30" value="unknown" label="Genome name" />
0
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
88 <repeat name="format" title="New track">
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
89 <conditional name="formatChoice">
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
90 <param name="format_select" type="select" label="Format">
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
91 <option value="bam" selected="true">BAM</option>
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
92 <option value="bed">BED</option>
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
93 <option value="blastxml">BLASTXML</option>
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
94 <option value="bigwig">BIGWIG</option>
12
e1f188b43750 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 7
diff changeset
95 <option value="gff3_transcript">GFF3 (structure: gene->transcript->CDS)</option>
e1f188b43750 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 7
diff changeset
96 <option value="gff3_mrna">GFF3 (structure: gene->mRNA->CDS)</option>
0
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
97 <option value="gtf">GTF</option>
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
98 </param>
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
99
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
100 <when value="bam">
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
101 <param
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
102 format="bam"
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
103 name="BAM"
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
104 type="data"
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
105 label="BAM File"
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
106 />
31
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
107 <param name="label" type="text" size="30" value="${on_string}" label="Track name" />
0
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
108 </when>
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
109 <when value="bed">
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
110 <conditional name="bedChoice">
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
111 <param name="bed_select" type="select" label="Bed Choice">
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
112 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option>
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
113 <option value="bed_splice_junctions_option">BED Splice junctions (bed12+1 / spliceJunctions.as)</option>
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
114 </param>
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
115 <when value="bed_simple_repeats_option">
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
116 <param
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
117 format="bed"
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
118 name="BED_simple_repeats"
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
119 type="data"
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
120 label="Bed Simple Repeats (Bed4+12) File"
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
121 />
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
122 </when>
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
123 <when value="bed_splice_junctions_option">
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
124 <param
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
125 format="bed"
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
126 name="BED_splice_junctions"
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
127 type="data"
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
128 label="Bed Splice Junctions (Bed12+1) File"
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
129 />
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
130 </when>
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
131 </conditional>
31
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
132 <param name="label" type="text" size="30" value="${on_string}" label="Track name" />
0
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
133 </when>
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
134 <when value="blastxml">
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
135 <param
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
136 format="blastxml"
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
137 name="BlastXML"
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
138 type="data"
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
139 label="Blast Alignments File"
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
140 />
31
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
141 <param name="label" type="text" size="30" value="${on_string}" label="Track name" />
0
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
142 </when>
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
143 <when value="bigwig">
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
144 <param
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
145 format="bigwig"
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
146 name="BIGWIG"
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
147 type="data"
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
148 label="BIGWIG File"
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
149 />
31
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
150 <param name="label" type="text" size="30" value="${on_string}" label="Track name" />
0
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
151 </when>
31
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
152 <when value="gff3">
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
153 <conditional name="gff3Choice">
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
154 <param name="gff3_select" type="select" label="gff3 type">
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
155 <option value="gff3_transcript">GFF3 format, structure: gene->transcription->CDS</option>
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
156 <option value="gff3_mrna">GFF3 format, structure: gene->mRNA->CDS</option>
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
157 </param>
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
158 <when value="gff3_transcript">
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
159 <param
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
160 format="gff3"
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
161 name="GFF3_transcript"
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
162 type="data"
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
163 label="GFF3 File"
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
164 />
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
165 </when>
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
166 <when value="gff3_mrna">
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
167 <param
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
168 format="gff3"
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
169 name="GFF3_mrna"
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
170 type="data"
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
171 label="GFF3 File"
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
172 />
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
173 </when>
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
174 </conditional>
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
175 <param name="label" type="text" size="30" value="${on_string}" label="Track name" />
0
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
176 </when>
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
177 <when value="gtf">
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
178 <param
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
179 format="gtf"
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
180 name="GTF"
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
181 type="data"
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
182 label="GTF File"
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
183 />
31
d8049deb0c97 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
yating-l
parents: 30
diff changeset
184 <param name="label" type="text" size="30" value="${on_string}" label="Track name" />
0
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
185 </when>
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
186 </conditional>
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
187 </repeat>
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
188 </inputs>
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
189
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
190 <outputs>
5
e7c80e9b70ae planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 2
diff changeset
191 <data format="html" name="output" label="${tool.name}" />
0
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
192 </outputs>
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
193 <tests>
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
194 <test>
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
195 <param name="reference" value="dbia3/raw/dbia3.fa" />
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
196 <param name="output" value="hubtest" />
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
197 <repeat name="format">
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
198 <conditional name="formatChoice">
15
8627394693c6 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 14
diff changeset
199 <param name="format_select" value="gff3_transcript"/>
8627394693c6 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 14
diff changeset
200 <param name="GFF3_transcript" value="dbia3/raw/Augustus_on_data_3__GTF_GFF.gff3" />
0
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
201 </conditional>
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
202 </repeat>
5
e7c80e9b70ae planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 2
diff changeset
203 <output name="output" file="hubtest" >
e7c80e9b70ae planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents: 2
diff changeset
204 </output>
0
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
205 </test>
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
206 </tests>
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
207 <help>
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
208 This Galaxy tool will create a tar file which including raw datasets and json datasets that can be used for
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
209 JBrowse visualization.
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
210 </help>
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
211 <citations>
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
212 </citations>
e4f3f2ed4fa5 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
yating-l
parents:
diff changeset
213 </tool>