Mercurial > repos > yating-l > hubarchivecreator

annotate hubArchiveCreator.xml @ 52:c66803bff0cc draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit adc1ac50269e02570e7ce12c732637bdd3f9a547-dirty
author yating-l
date Thu, 11 May 2017 17:21:15 -0400
parents 364b8db8de17
children 4a58094b051e
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
51
364b8db8de17 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 9
diff changeset
1 <tool id="hubArchiveCreator" name="Hub Archive Creator" version="2.3.1">
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
2 <description>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
3 This Galaxy tool permits to prepare your files to be ready for
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
4 Assembly Hub visualization.
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
5 </description>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
6
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
7 <requirements>
51
364b8db8de17 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 9
diff changeset
8 <requirement type="package" version="1.0">ucsc_tools_340</requirement>
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
9 <requirement type="package" version="1.2">samtools</requirement>
52
c66803bff0cc planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit adc1ac50269e02570e7ce12c732637bdd3f9a547-dirty
yating-l
parents: 51
diff changeset
10 <requirement type="package" version="340">ucsc_bigwig</requirement>
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
11 </requirements>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
12
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
13 <stdio>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
14 <regex match="^pass1"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
15 source="stderr"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
16 level="log"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
17 description="bedToBigBed"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
18 <!-- TODO: Add the case pass1 and 0 chroms -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
19 <!-- TODO: Add the case pass2 and 0 records or 0 fields -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
20 </stdio>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
21
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
22 <!-- Idea: python \ -augustus [parameters] \ -trfBig [parameters] -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
23 <command detect_errors="exit_code"><![CDATA[
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
24 mkdir -p $output.extra_files_path;
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
25
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
26 python $__tool_directory__/hubArchiveCreator.py
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
27
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
28 ## Ask the user to enter the genome name
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
29 --genome_name '$genome_name'
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
30
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
31 #import json
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
32
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
33 #set global data_parameter_dict = {}
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
34
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
35 ## Function to retrieve the data of the inputs
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
36 #def prepare_json($input_to_prepare, $order_index, $extra_data_dict={})
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
37 #set false_path = str($input_to_prepare)
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
38 #set name = $input_to_prepare.name
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
39
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
40 #set data_dict = {"name": $name}
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
41 #silent data_dict.update($extra_data_dict)
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
42
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
43 ## Add the ordering by taking the tool form indexes
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
44 #silent $data_dict.update({"order_index": $order_index})
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
45
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
46 #silent $data_parameter_dict.update({$false_path: $data_dict})
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
47
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
48 #end def
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
49
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
50
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
51 ## Get the number of digits from tracks, to have a unique integer from group index and track index
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
52
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
53 #set temp_max_digit = 0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
54
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
55 #for $g in $group
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
56 #if len($g.format) > $temp_max_digit
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
57 #silent temp_max_digit = len($g.format)
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
58 #end if
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
59 #end for
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
60
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
61 #set nb_digits_max_track = len(str($temp_max_digit))
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
62
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
63 ## END Get the number of digits
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
64
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
65 #for $i_g, $g in enumerate( $group )
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
66 #for $i, $f in enumerate( $g.format )
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
67 ## Create the order index using index_group+1 concatenated with index_track
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
68 #set index_group_final = str($i_g + 1)
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
69 #set index_track_final = str($index_group_final) + str($i).zfill($nb_digits_max_track)
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
70
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
71 ## For each format, we have a few mandatory fields we store in a dict
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
72 #set track_color = str($f.formatChoice.track_color)
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
73 #set group_name = str($g.group_name)
52
c66803bff0cc planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit adc1ac50269e02570e7ce12c732637bdd3f9a547-dirty
yating-l
parents: 51
diff changeset
74 #set longLabel = str($f.formatChoice.longLabel)
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
75 #set extra_data_dict = {"track_color": $track_color,
52
c66803bff0cc planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit adc1ac50269e02570e7ce12c732637bdd3f9a547-dirty
yating-l
parents: 51
diff changeset
76 "group_name": $group_name,
c66803bff0cc planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit adc1ac50269e02570e7ce12c732637bdd3f9a547-dirty
yating-l
parents: 51
diff changeset
77 "long_label": $longLabel}
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
78
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
79 #if $f.formatChoice.format_select == "bam"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
80 --bam $f.formatChoice.BAM
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
81 #set bam_index = $f.formatChoice.BAM.metadata.bam_index
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
82
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
83 ## Add Bam format specific fields
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
84 #silent extra_data_dict.update({"index": $bam_index})
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
85
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
86 #silent $prepare_json($f.formatChoice.BAM, $index_track_final, extra_data_dict)
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
87 #end if
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
88 #if $f.formatChoice.format_select == "bed"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
89 #if $f.formatChoice.bedChoice.bed_select == "bed_generic"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
90 --bed $f.formatChoice.bedChoice.BED
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
91 #silent $prepare_json($f.formatChoice.bedChoice.BED, $index_track_final,
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
92 extra_data_dict)
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
93 #end if
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
94 #if $f.formatChoice.bedChoice.bed_select == "bed_simple_repeats_option"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
95 --bedSimpleRepeats $f.formatChoice.bedChoice.BED_simple_repeats
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
96 #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, $index_track_final,
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
97 extra_data_dict)
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
98 #end if
9
d5781fe7b782 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e42ecb807fb34a8e4ddcf96944dd74d24c695352-dirty
yating-l
parents: 8
diff changeset
99 #if $f.formatChoice.bedChoice.bed_select == "bed_splice_junctions_option"
d5781fe7b782 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e42ecb807fb34a8e4ddcf96944dd74d24c695352-dirty
yating-l
parents: 8
diff changeset
100 --bedSpliceJunctions $f.formatChoice.bedChoice.BED_splice_junctions
d5781fe7b782 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e42ecb807fb34a8e4ddcf96944dd74d24c695352-dirty
yating-l
parents: 8
diff changeset
101 #silent $prepare_json($f.formatChoice.bedChoice.BED_splice_junctions, $index_track_final,
d5781fe7b782 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e42ecb807fb34a8e4ddcf96944dd74d24c695352-dirty
yating-l
parents: 8
diff changeset
102 extra_data_dict)
d5781fe7b782 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e42ecb807fb34a8e4ddcf96944dd74d24c695352-dirty
yating-l
parents: 8
diff changeset
103 #end if
51
364b8db8de17 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 9
diff changeset
104 #if $f.formatChoice.bedChoice.bed_select == "bed_blast_alignment_option"
364b8db8de17 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 9
diff changeset
105 --bedBlastAlignments $f.formatChoice.bedChoice.BED_blast_alignment
52
c66803bff0cc planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit adc1ac50269e02570e7ce12c732637bdd3f9a547-dirty
yating-l
parents: 51
diff changeset
106 #silent $prepare_json($f.formatChoice.bedChoice.BED_blast_alignment, $index_track_final,
51
364b8db8de17 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 9
diff changeset
107 extra_data_dict)
364b8db8de17 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 9
diff changeset
108 #end if
364b8db8de17 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 9
diff changeset
109 #if $f.formatChoice.bedChoice.bed_select == "bed_blat_alignment_option"
364b8db8de17 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 9
diff changeset
110 --bigpsl $f.formatChoice.bedChoice.BED_blat_alignment
52
c66803bff0cc planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit adc1ac50269e02570e7ce12c732637bdd3f9a547-dirty
yating-l
parents: 51
diff changeset
111 #silent $prepare_json($f.formatChoice.bedChoice.BED_blat_alignment, $index_track_final,
51
364b8db8de17 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 9
diff changeset
112 extra_data_dict)
9
d5781fe7b782 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e42ecb807fb34a8e4ddcf96944dd74d24c695352-dirty
yating-l
parents: 8
diff changeset
113 #end if
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
114 #end if
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
115 #if $f.formatChoice.format_select == "psl"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
116 --psl $f.formatChoice.PSL
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
117 #silent $prepare_json($f.formatChoice.PSL, $index_track_final,
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
118 extra_data_dict)
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
119 #end if
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
120 #if $f.formatChoice.format_select == "bigwig"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
121 --bigwig $f.formatChoice.BIGWIG
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
122 #silent $prepare_json($f.formatChoice.BIGWIG, $index_track_final,
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
123 extra_data_dict)
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
124 #end if
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
125 #if $f.formatChoice.format_select == "gff3"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
126 --gff3 $f.formatChoice.GFF3
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
127 #silent $prepare_json($f.formatChoice.GFF3, $index_track_final,
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
128 extra_data_dict)
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
129 #end if
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
130 #if $f.formatChoice.format_select == "gtf"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
131 ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
132 --gtf $f.formatChoice.GTF
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
133 #silent $prepare_json($f.formatChoice.GTF, $index_track_final,
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
134 extra_data_dict)
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
135 #end if
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
136 #end for
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
137 #end for
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
138
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
139 ## We combine the fasta file dataset name with his false path in a JSON object
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
140 #set fasta_json = json.dumps({"false_path": str($fasta_file), "name": $fasta_file.name})
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
141 -f '$fasta_json'
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
142
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
143 ## Dump the final json
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
144 #set all_data_json = json.dumps($data_parameter_dict)
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
145
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
146 --data_json '$all_data_json'
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
147
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
148 ## Retrieve the user email
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
149 --user_email $__user_email__
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
150
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
151 -d $__tool_directory__
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
152
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
153 -e $output.extra_files_path
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
154
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
155 $advanced_options.debug_mode
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
156
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
157 -o $output;
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
158
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
159 ]]></command>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
160
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
161 <inputs>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
162 <param
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
163 name="genome_name"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
164 type="text"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
165 size="30"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
166 value="unknown"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
167 label="UCSC Genome Browser assembly ID"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
168 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
169 <param
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
170 format="fasta"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
171 name="fasta_file"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
172 type="data"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
173 label="Reference genome"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
174 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
175 <repeat name="group" title="New group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
176 <param type="text" name="group_name" label="Group name" value="Default group"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
177 <repeat name="format" title="New track">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
178 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
179 <param name="format_select" type="select" label="Format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
180 <option value="bam" selected="true">BAM</option>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
181 <option value="bed">BED</option>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
182 <option value="psl">PSL</option>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
183 <option value="bigwig">BIGWIG</option>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
184 <option value="gff3">GFF3</option>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
185 <option value="gtf">GTF</option>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
186 </param>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
187
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
188 <when value="bam">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
189 <param
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
190 format="bam"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
191 name="BAM"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
192 type="data"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
193 label="BAM File"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
194 />
52
c66803bff0cc planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit adc1ac50269e02570e7ce12c732637bdd3f9a547-dirty
yating-l
parents: 51
diff changeset
195 <param name="longLabel" type="text" size="80" label="Track label" />
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
196 <!-- TODO: Find a solution to avoid repetition and to generate a new color depending on the others -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
197 <param name="track_color" type="color" label="Track color" value="#000000">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
198 <sanitizer>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
199 <valid initial="string.letters,string.digits">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
200 <add value="#"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
201 </valid>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
202 </sanitizer>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
203 </param>
52
c66803bff0cc planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit adc1ac50269e02570e7ce12c732637bdd3f9a547-dirty
yating-l
parents: 51
diff changeset
204 </when>
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
205 <when value="bed">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
206 <conditional name="bedChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
207 <param name="bed_select" type="select" label="Bed Choice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
208 <option value="bed_generic" selected="true">BED Generic (bed3+)</option>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
209 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option>
9
d5781fe7b782 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e42ecb807fb34a8e4ddcf96944dd74d24c695352-dirty
yating-l
parents: 8
diff changeset
210 <option value="bed_splice_junctions_option">BED Splice junctions (bed12+1 / spliceJunctions.as)</option>
51
364b8db8de17 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 9
diff changeset
211 <option value="bed_blast_alignment_option">Blast alignments (bed12+12 / bigPsl.as)</option>
364b8db8de17 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 9
diff changeset
212 <option value="bed_blat_alignment_option">BLAT alignments (bigPsl / bigPsl.as)</option>
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
213 </param>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
214 <when value="bed_generic">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
215 <param
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
216 format="bed"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
217 name="BED"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
218 type="data"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
219 label="Generic Bed File Choice"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
220 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
221
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
222 </when>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
223 <when value="bed_simple_repeats_option">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
224 <param
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
225 format="bed"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
226 name="BED_simple_repeats"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
227 type="data"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
228 label="Bed Simple Repeats (Bed4+12) File"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
229 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
230 </when>
9
d5781fe7b782 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e42ecb807fb34a8e4ddcf96944dd74d24c695352-dirty
yating-l
parents: 8
diff changeset
231 <when value="bed_splice_junctions_option">
d5781fe7b782 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e42ecb807fb34a8e4ddcf96944dd74d24c695352-dirty
yating-l
parents: 8
diff changeset
232 <param
d5781fe7b782 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e42ecb807fb34a8e4ddcf96944dd74d24c695352-dirty
yating-l
parents: 8
diff changeset
233 format="bed"
d5781fe7b782 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e42ecb807fb34a8e4ddcf96944dd74d24c695352-dirty
yating-l
parents: 8
diff changeset
234 name="BED_splice_junctions"
d5781fe7b782 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e42ecb807fb34a8e4ddcf96944dd74d24c695352-dirty
yating-l
parents: 8
diff changeset
235 type="data"
d5781fe7b782 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e42ecb807fb34a8e4ddcf96944dd74d24c695352-dirty
yating-l
parents: 8
diff changeset
236 label="Bed Splice Junctions (Bed12+1) File"
d5781fe7b782 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e42ecb807fb34a8e4ddcf96944dd74d24c695352-dirty
yating-l
parents: 8
diff changeset
237 />
d5781fe7b782 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e42ecb807fb34a8e4ddcf96944dd74d24c695352-dirty
yating-l
parents: 8
diff changeset
238 </when>
51
364b8db8de17 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 9
diff changeset
239 <when value="bed_blast_alignment_option">
9
d5781fe7b782 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e42ecb807fb34a8e4ddcf96944dd74d24c695352-dirty
yating-l
parents: 8
diff changeset
240 <param
d5781fe7b782 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e42ecb807fb34a8e4ddcf96944dd74d24c695352-dirty
yating-l
parents: 8
diff changeset
241 format="bed"
51
364b8db8de17 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 9
diff changeset
242 name="BED_blast_alignment"
9
d5781fe7b782 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e42ecb807fb34a8e4ddcf96944dd74d24c695352-dirty
yating-l
parents: 8
diff changeset
243 type="data"
51
364b8db8de17 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 9
diff changeset
244 label="Bed Blast Alignments (Bed12+12) File"
364b8db8de17 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 9
diff changeset
245 />
364b8db8de17 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 9
diff changeset
246 </when>
364b8db8de17 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 9
diff changeset
247 <when value="bed_blat_alignment_option">
364b8db8de17 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 9
diff changeset
248 <param
364b8db8de17 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 9
diff changeset
249 format="bed"
364b8db8de17 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 9
diff changeset
250 name="BED_blat_alignment"
364b8db8de17 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 9
diff changeset
251 type="data"
364b8db8de17 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 9
diff changeset
252 label="Bed BLAT Alignments (bigPsl) File"
9
d5781fe7b782 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e42ecb807fb34a8e4ddcf96944dd74d24c695352-dirty
yating-l
parents: 8
diff changeset
253 />
d5781fe7b782 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e42ecb807fb34a8e4ddcf96944dd74d24c695352-dirty
yating-l
parents: 8
diff changeset
254 </when>
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
255 </conditional>
52
c66803bff0cc planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit adc1ac50269e02570e7ce12c732637bdd3f9a547-dirty
yating-l
parents: 51
diff changeset
256 <param name="longLabel" type="text" size="30" label="Track name" />
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
257 <param name="track_color" type="color" label="Track color" value="#000000">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
258 <sanitizer>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
259 <valid initial="string.letters,string.digits">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
260 <add value="#"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
261 </valid>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
262 </sanitizer>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
263 </param>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
264 </when>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
265 <when value="psl">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
266 <param
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
267 format="psl"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
268 name="PSL"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
269 type="data"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
270 label="PSL File"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
271 />
52
c66803bff0cc planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit adc1ac50269e02570e7ce12c732637bdd3f9a547-dirty
yating-l
parents: 51
diff changeset
272 <param name="longLabel" type="text" size="30" label="Track name" />
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
273 <param name="track_color" type="color" label="Track color" value="#000000">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
274 <sanitizer>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
275 <valid initial="string.letters,string.digits">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
276 <add value="#"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
277 </valid>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
278 </sanitizer>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
279 </param>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
280 </when>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
281 <when value="bigwig">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
282 <param
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
283 format="bigwig"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
284 name="BIGWIG"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
285 type="data"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
286 label="BIGWIG File"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
287 />
52
c66803bff0cc planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit adc1ac50269e02570e7ce12c732637bdd3f9a547-dirty
yating-l
parents: 51
diff changeset
288 <param name="longLabel" type="text" size="30" label="Track name" />
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
289 <param name="track_color" type="color" label="Track color" value="#000000">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
290 <sanitizer>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
291 <valid initial="string.letters,string.digits">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
292 <add value="#"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
293 </valid>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
294 </sanitizer>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
295 </param>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
296 </when>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
297 <when value="gff3">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
298 <param
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
299 format="gff3"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
300 name="GFF3"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
301 type="data"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
302 label="GFF3 File"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
303 />
52
c66803bff0cc planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit adc1ac50269e02570e7ce12c732637bdd3f9a547-dirty
yating-l
parents: 51
diff changeset
304 <param name="longLabel" type="text" size="30" label="Track name" />
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
305 <param name="track_color" type="color" label="Track color" value="#000000">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
306 <sanitizer>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
307 <valid initial="string.letters,string.digits">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
308 <add value="#"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
309 </valid>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
310 </sanitizer>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
311 </param>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
312 </when>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
313 <when value="gtf">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
314 <param
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
315 format="gtf"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
316 name="GTF"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
317 type="data"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
318 label="GTF File"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
319 />
52
c66803bff0cc planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit adc1ac50269e02570e7ce12c732637bdd3f9a547-dirty
yating-l
parents: 51
diff changeset
320 <param name="longLabel" type="text" size="30" label="Track name" />
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
321 <param name="track_color" type="color" label="Track color" value="#000000">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
322 <sanitizer>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
323 <valid initial="string.letters,string.digits">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
324 <add value="#"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
325 </valid>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
326 </sanitizer>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
327 </param>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
328 </when>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
329 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
330 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
331 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
332 <conditional name="advanced_options">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
333 <param name="advanced_options_selector" type="select" label="Advanced options">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
334 <option value="off" selected="true">Hide advanced options</option>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
335 <option value="on">Display advanced options</option>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
336 </param>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
337 <!-- TODO: Avoid redundancy here -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
338 <when value="on">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
339 <param name="debug_mode" type="boolean"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
340 label="Activate debug mode" checked="false"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
341 truevalue="--debug_mode" falsevalue="">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
342 <help>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
343 Use this option if you are a G-OnRamp developer
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
344 </help>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
345 </param>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
346 </when>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
347 <when value="off">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
348 <param name="debug_mode" type="hidden"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
349 value="">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
350 </param>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
351 </when>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
352 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
353 </inputs>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
354
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
355 <outputs>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
356 <data format="trackhub" name="output"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
357 </outputs>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
358
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
359 <tests>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
360 <!-- Test with only the fasta file -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
361 <test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
362 <param name="genome_name" value="Dbia3"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
363 <param name="fasta_file" value="common/dbia3.fa"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
364 <output name="output" file="only_genome/only_genome.html">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
365 <extra_files type="file" name="__main__.log" value="only_genome/__main__.log" />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
366 <extra_files type="file" name="myHub/genomes.txt" value="only_genome/myHub/genomes.txt" />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
367 <extra_files type="file" name="myHub/Dbia3.html" value="only_genome/myHub/Dbia3.html"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
368 <!-- Email could be different, but we need to ensure we still have the email line -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
369 <extra_files type="file" name="myHub/hub.txt" value="only_genome/myHub/hub.txt" lines_diff="2">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
370 <assert_contents>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
371 <has_text text="email"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
372 </assert_contents>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
373 </extra_files>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
374 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
375 </extra_files>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
376 <extra_files type="file" name="myHub/Dbia3/description.html" value="only_genome/myHub/Dbia3/description.html"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
377 </output>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
378 </test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
379
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
380 <!-- Test with Bam -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
381 <test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
382 <param name="genome_name" value="Dbia3"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
383 <param name="fasta_file" value="common/dbia3.fa"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
384 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
385 <param name="group_name" value="Default group"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
386 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
387 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
388 <param name="format_select" value="bam"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
389 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam" />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
390 <param name="track_color" value="#000000"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
391 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
392 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
393 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
394 <output name="output" file="bam/bam.html">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
395 <!-- Verify tracks folder contains bam and bai -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
396 <extra_files type="file"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
397 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
398 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
399 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
400 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
401 <extra_files type="file"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
402 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
403 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
404 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
405 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
406 <!-- Verify trackDb.txt contains the basic fields for a bam -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
407 <extra_files type="file" name="myHub/Dbia3/trackDb.txt" value="bam/myHub/Dbia3/trackDb.txt">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
408 <assert_contents>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
409 <has_text text="track"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
410 <has_text text="longLabel"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
411 <has_text text="shortLabel"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
412 <has_text text="bigDataUrl"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
413 <has_text text="type"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
414 <has_text text="visibility"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
415 <has_text text="thickDrawItem"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
416 <has_text text="priority"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
417 <has_text text="color"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
418 <has_text text="group"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
419 </assert_contents>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
420 </extra_files>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
421 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
422 </output>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
423 </test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
424
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
425 <!-- Test with Bed Generic -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
426 <test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
427 <param name="genome_name" value="Dbia3"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
428 <param name="fasta_file" value="common/dbia3.fa"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
429 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
430 <param name="group_name" value="Default group"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
431 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
432 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
433 <param name="format_select" value="bed" />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
434 <conditional name="bedChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
435 <param name="bed_select" value="bed_generic"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
436 <param name="BED" ftype="bed" value="bed_generic/inputs/TBLASTN_Alignment_to_proteins"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
437 <param name="track_color" value="#000000"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
438 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
439 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
440 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
441 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
442 <output name="output" file="bed_generic/bed_generic.html">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
443 <!-- Verify tracks folder contains bam and bai -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
444 <extra_files type="file"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
445 name="myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
446 value="bed_generic/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
447 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
448 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
449 </output>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
450 </test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
451
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
452 <!-- Test with Bed Simple repeat -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
453 <test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
454 <param name="genome_name" value="Dbia3"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
455 <param name="fasta_file" value="common/dbia3.fa"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
456 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
457 <param name="group_name" value="Default group"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
458 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
459 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
460 <param name="format_select" value="bed" />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
461 <conditional name="bedChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
462 <param name="bed_select" value="bed_simple_repeats_option"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
463 <param name="BED_simple_repeats" ftype="bed" value="bed_simple_repeats/inputs/Repeating_Elements_by_TrfBig"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
464 <param name="track_color" value="#000000"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
465 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
466 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
467 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
468 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
469 <output name="output" file="bed_simple_repeats/bed_simple_repeats_trackhub.html">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
470 <!-- Verify tracks folder contains bam and bai -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
471 <extra_files type="file"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
472 name="myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
473 value="bed_simple_repeats/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
474 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
475 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
476 </output>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
477 </test>
52
c66803bff0cc planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit adc1ac50269e02570e7ce12c732637bdd3f9a547-dirty
yating-l
parents: 51
diff changeset
478
2
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
479
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
480 <!-- Test with Psl -->
2
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
481 <test>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
482 <param name="genome_name" value="Dbia3"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
483 <param name="fasta_file" value="common/dbia3.fa"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
484 <repeat name="group">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
485 <param name="group_name" value="Default group"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
486 <repeat name="format">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
487 <conditional name="formatChoice">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
488 <param name="format_select" value="psl"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
489 <param name="PSL" value="psl/inputs/blastXmlToPsl"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
490 <param name="track_color" value="#000000"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
491 </conditional>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
492 </repeat>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
493 </repeat>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
494 <output name="output" file="psl/psl_trackhub.html">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
495 <!-- Verify tracks folder contains bam and bai -->
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
496 <extra_files type="file"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
497 name="myHub/Dbia3/tracks/blastXmlToPsl.bb"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
498 value="psl/myHub/Dbia3/tracks/blastXmlToPsl.bb"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
499 compare="sim_size"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
500 />
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
501 <!-- Verify trackDb.txt contains the basic fields for a bam -->
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
502 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
503 </output>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
504 </test>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
505
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
506 <!-- Test with BigWig -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
507 <test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
508 <param name="genome_name" value="Dbia3"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
509 <param name="fasta_file" value="common/dbia3.fa"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
510 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
511 <param name="group_name" value="Default group"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
512 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
513 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
514 <param name="format_select" value="bigwig"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
515 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
516 <param name="track_color" value="#000000"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
517 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
518 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
519 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
520 <output name="output" file="bigwig/bigwig.html">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
521 <!-- Verify tracks folder contains bam and bai -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
522 <extra_files type="file"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
523 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
524 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
525 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
526 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
527 <!-- Verify trackDb.txt contains the basic fields for a bam -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
528 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
529 </output>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
530 </test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
531
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
532 <!-- Test with GFF3 -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
533 <test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
534 <param name="genome_name" value="Dbia3"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
535 <param name="fasta_file" value="common/dbia3.fa"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
536 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
537 <param name="group_name" value="Default group"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
538 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
539 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
540 <param name="format_select" value="gff3"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
541 <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
542 <param name="track_color" value="#000000"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
543 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
544 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
545 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
546 <output name="output" file="gff3/gff3_trackhub.html">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
547 <!-- Verify tracks folder contains bam and bai -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
548 <extra_files type="file"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
549 name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
550 value="gff3/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
551 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
552 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
553 <!-- Verify trackDb.txt contains the basic fields for a bam -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
554 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
555 </output>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
556 </test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
557
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
558 <!-- Test with GTF -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
559 <test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
560 <param name="genome_name" value="Dbia3"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
561 <param name="fasta_file" value="common/dbia3.fa"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
562 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
563 <param name="group_name" value="Default group"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
564 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
565 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
566 <param name="format_select" value="gtf"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
567 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
568 <param name="track_color" value="#000000"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
569 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
570 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
571 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
572 <output name="output" file="gtf/gtf_trackhub.html">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
573 <!-- Verify tracks folder contains bam and bai -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
574 <extra_files type="file"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
575 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
576 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
577 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
578 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
579 <!-- Verify trackDb.txt contains the basic fields for a bam -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
580 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
581 </output>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
582 </test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
583
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
584 <!-- Test with one group and multiple tracks -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
585 <test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
586 <param name="genome_name" value="Dbia3"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
587 <param name="fasta_file" value="common/dbia3.fa"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
588 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
589 <param name="group_name" value="Default group"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
590 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
591 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
592 <param name="format_select" value="gtf"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
593 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
594 <param name="track_color" value="#000000"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
595 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
596 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
597 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
598 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
599 <param name="format_select" value="gff3"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
600 <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
601 <param name="track_color" value="#000000"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
602 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
603 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
604 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
605 <output name="output" file="gtf_gff/gtf_gff_trackhub.html">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
606 <!-- verify tracks folder contains bam and bai -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
607 <extra_files type="file"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
608 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
609 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
610 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
611 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
612 <extra_files type="file"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
613 name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
614 value="gff3/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
615 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
616 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
617 <!-- verify trackdb.txt contains the basic fields for a bam -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
618 <!-- todo: find a way to check also that the whole common structure is intact too, without too much repetition -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
619 </output>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
620 </test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
621
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
622 <!-- Test with one group and all the supported datatypes on 10/04/2016 -->
2
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
623 <test>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
624 <param name="genome_name" value="Dbia3"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
625 <param name="fasta_file" value="common/dbia3.fa"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
626 <repeat name="group">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
627 <param name="group_name" value="Default group"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
628 <repeat name="format">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
629 <conditional name="formatChoice">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
630 <param name="format_select" value="bam"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
631 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
632 <param name="track_color" value="#000000"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
633 </conditional>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
634 </repeat>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
635 <repeat name="format">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
636 <conditional name="formatChoice">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
637 <param name="format_select" value="bed"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
638 <conditional name="bedChoice">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
639 <param name="bed_select" value="bed_generic"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
640 <param name="BED" ftype="bed" value="bed_generic/inputs/TBLASTN_Alignment_to_proteins"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
641 <param name="track_color" value="#000000"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
642 </conditional>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
643 </conditional>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
644 </repeat>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
645 <repeat name="format">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
646 <conditional name="formatChoice">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
647 <param name="format_select" value="bed"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
648 <conditional name="bedChoice">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
649 <param name="bed_select" value="bed_simple_repeats_option"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
650 <param name="BED_simple_repeats" ftype="bed"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
651 value="bed_simple_repeats/inputs/Repeating_Elements_by_TrfBig"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
652 <param name="track_color" value="#000000"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
653 </conditional>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
654 </conditional>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
655 </repeat>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
656 <repeat name="format">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
657 <conditional name="formatChoice">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
658 <param name="format_select" value="psl"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
659 <param name="PSL" value="psl/inputs/blastXmlToPsl"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
660 <param name="track_color" value="#000000"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
661 </conditional>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
662 </repeat>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
663 <repeat name="format">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
664 <conditional name="formatChoice">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
665 <param name="format_select" value="bigwig"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
666 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
667 <param name="track_color" value="#000000"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
668 </conditional>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
669 </repeat>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
670 <repeat name="format">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
671 <conditional name="formatChoice">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
672 <param name="format_select" value="gff3"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
673 <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
674 <param name="track_color" value="#000000"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
675 </conditional>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
676 </repeat>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
677 <repeat name="format">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
678 <conditional name="formatChoice">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
679 <param name="format_select" value="gtf"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
680 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
681 <param name="track_color" value="#000000"/>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
682 </conditional>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
683 </repeat>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
684 </repeat>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
685 <output name="output" file="all_datatypes/all_datatypes_trackhub.html">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
686 <!-- verify tracks folder contains all the files -->
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
687 <extra_files type="file"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
688 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
689 value="all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
690 compare="sim_size"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
691 />
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
692 <extra_files type="file"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
693 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
694 value="all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
695 compare="sim_size"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
696 />
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
697 <extra_files type="file"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
698 name="myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
699 value="all_datatypes/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
700 compare="sim_size"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
701 />
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
702 <extra_files type="file"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
703 name="myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
704 value="all_datatypes/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
705 compare="sim_size"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
706 />
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
707 <extra_files type="file"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
708 name="myHub/Dbia3/tracks/blastXmlToPsl.bb"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
709 value="all_datatypes/myHub/Dbia3/tracks/blastXmlToPsl.bb"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
710 compare="sim_size"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
711 />
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
712 <extra_files type="file"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
713 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
714 value="all_datatypes/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
715 compare="sim_size"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
716 />
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
717 <extra_files type="file"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
718 name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
719 value="all_datatypes/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
720 compare="sim_size"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
721 />
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
722 <extra_files type="file"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
723 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
724 value="all_datatypes/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
725 compare="sim_size"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
726 />
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
727 <!-- verify trackdb.txt contains the basic fields for a bam -->
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
728 <!-- todo: find a way to check also that the whole common structure is intact too, without too much repetition -->
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
729 </output>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
730 </test>
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
731
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
732 <!-- Test with two groups and no tracks -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
733 <test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
734 <param name="genome_name" value="Dbia3"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
735 <param name="fasta_file" value="common/dbia3.fa"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
736 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
737 <param name="group_name" value="Default group"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
738 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
739 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
740 <param name="group_name" value="Other group"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
741 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
742 <output name="output" file="two_groups_no_track/two_groups_no_track_trackhub.html">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
743 <extra_files type="file" name="myHub/genomes.txt" value="two_groups_no_track/myHub/genomes.txt"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
744 <extra_files type="file" name="myHub/Dbia3.html" value="two_groups_no_track/myHub/Dbia3.html"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
745 <!-- Email could be different, but we need to ensure we still have the email line -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
746 <extra_files type="file" name="myHub/hub.txt" value="two_groups_no_track/myHub/hub.txt" lines_diff="2">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
747 <assert_contents>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
748 <has_text text="email"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
749 </assert_contents>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
750 </extra_files>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
751 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
752 </extra_files>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
753 <extra_files type="file" name="myHub/Dbia3/description.html"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
754 value="two_groups_no_track/myHub/Dbia3/description.html"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
755 </output>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
756 </test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
757
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
758 <!-- Test with two groups and one track in first -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
759 <test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
760 <param name="genome_name" value="Dbia3"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
761 <param name="fasta_file" value="common/dbia3.fa"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
762 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
763 <param name="group_name" value="Default group"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
764 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
765 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
766 <param name="format_select" value="bigwig"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
767 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
768 <param name="track_color" value="#000000"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
769 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
770 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
771 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
772 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
773 <param name="group_name" value="Other group"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
774 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
775 <output name="output" file="two_groups_one_track_first/two_groups_one_track_first_trackhub.html">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
776 <!-- Check myHub structure -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
777 <extra_files type="file" name="myHub/genomes.txt" value="two_groups_one_track_first/myHub/genomes.txt"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
778 <extra_files type="file" name="myHub/Dbia3.html" value="two_groups_one_track_first/myHub/Dbia3.html"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
779 <!-- Email could be different, but we need to ensure we still have the email line -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
780 <extra_files type="file" name="myHub/hub.txt" value="two_groups_one_track_first/myHub/hub.txt" lines_diff="2">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
781 <assert_contents>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
782 <has_text text="email"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
783 </assert_contents>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
784 </extra_files>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
785 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
786 </extra_files>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
787 <extra_files type="file" name="myHub/Dbia3/description.html"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
788 value="two_groups_one_track_first/myHub/Dbia3/description.html"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
789
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
790 <!-- Check tracks exist -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
791 <extra_files type="file"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
792 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
793 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
794 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
795 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
796
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
797 <!-- Check the groups.txt exists and is properly populated -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
798 </output>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
799 </test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
800
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
801 <!-- Test with two groups and one track in both -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
802 <test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
803 <param name="genome_name" value="Dbia3"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
804 <param name="fasta_file" value="common/dbia3.fa"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
805 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
806 <param name="group_name" value="Default group"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
807 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
808 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
809 <param name="format_select" value="bigwig"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
810 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
811 <param name="track_color" value="#000000"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
812 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
813 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
814 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
815 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
816 <param name="group_name" value="Other group"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
817 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
818 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
819 <param name="format_select" value="gtf"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
820 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
821 <param name="track_color" value="#000000"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
822 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
823 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
824 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
825 <output name="output" file="two_groups_one_track_both/two_groups_one_track_both_trackhub.html">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
826 <!-- Check myHub structure -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
827 <extra_files type="file" name="myHub/genomes.txt" value="two_groups_one_track_both/myHub/genomes.txt"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
828 <extra_files type="file" name="myHub/Dbia3.html" value="two_groups_one_track_both/myHub/Dbia3.html"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
829 <!-- Email could be different, but we need to ensure we still have the email line -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
830 <extra_files type="file" name="myHub/hub.txt" value="two_groups_one_track_both/myHub/hub.txt"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
831 lines_diff="2">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
832 <assert_contents>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
833 <has_text text="email"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
834 </assert_contents>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
835 </extra_files>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
836 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
837 </extra_files>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
838 <extra_files type="file" name="myHub/Dbia3/description.html"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
839 value="two_groups_one_track_both/myHub/Dbia3/description.html"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
840
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
841 <!-- Check tracks exist -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
842 <!-- First group -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
843 <extra_files type="file"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
844 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
845 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
846 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
847 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
848
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
849 <!-- Second group -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
850 <extra_files type="file"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
851 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
852 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
853 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
854 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
855 <!-- Check the groups.txt exists and is properly populated -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
856 </output>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
857 </test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
858
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
859 <!-- Test with two groups and multiple tracks in both -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
860 <test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
861 <param name="genome_name" value="Dbia3"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
862 <param name="fasta_file" value="common/dbia3.fa"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
863 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
864 <param name="group_name" value="Default group"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
865 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
866 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
867 <param name="format_select" value="bigwig"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
868 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
869 <param name="track_color" value="#000000"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
870 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
871 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
872 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
873 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
874 <param name="format_select" value="bam"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
875 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
876 <param name="track_color" value="#000000"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
877 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
878 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
879 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
880 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
881 <param name="group_name" value="Other group"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
882 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
883 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
884 <param name="format_select" value="gtf"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
885 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
886 <param name="track_color" value="#000000"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
887 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
888 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
889 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
890 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
891 <param name="format_select" value="gff3"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
892 <param name="GFF3" value="gff3_multi_fasta/inputs/Multi-Fasta_GlimmerHMM_Gene_Predictions"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
893 <param name="track_color" value="#000000"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
894 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
895 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
896 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
897 <output name="output" file="two_groups_multiple_tracks/two_groups_multiple_tracks_trackhub.html">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
898 <!-- Check myHub structure -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
899 <extra_files type="file" name="myHub/genomes.txt" value="two_groups_multiple_tracks/myHub/genomes.txt"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
900 <extra_files type="file" name="myHub/Dbia3.html" value="two_groups_multiple_tracks/myHub/Dbia3.html"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
901 <!-- Email could be different, but we need to ensure we still have the email line -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
902 <extra_files type="file" name="myHub/hub.txt" value="two_groups_multiple_tracks/myHub/hub.txt"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
903 lines_diff="2">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
904 <assert_contents>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
905 <has_text text="email"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
906 </assert_contents>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
907 </extra_files>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
908 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
909 </extra_files>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
910 <extra_files type="file" name="myHub/Dbia3/description.html"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
911 value="two_groups_multiple_tracks/myHub/Dbia3/description.html"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
912
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
913 <!-- Check tracks exist -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
914 <!-- First group -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
915 <extra_files type="file"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
916 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
917 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
918 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
919 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
920 <extra_files type="file"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
921 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
922 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
923 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
924 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
925 <extra_files type="file"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
926 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
927 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
928 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
929 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
930
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
931 <!-- Second group -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
932 <extra_files type="file"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
933 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
934 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
935 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
936 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
937 <extra_files type="file"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
938 name="myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
939 value="gff3_multi_fasta/myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
940 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
941 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
942 <!-- Check the groups.txt exists and is properly populated -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
943 </output>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
944 </test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
945
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
946 <!-- Test default color in a track -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
947 <test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
948 <param name="genome_name" value="Dbia3"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
949 <param name="fasta_file" value="common/dbia3.fa"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
950 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
951 <param name="group_name" value="Default group"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
952 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
953 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
954 <param name="format_select" value="bam"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
955 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
956 <param name="track_color" value="#000000"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
957 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
958 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
959 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
960 <output name="output" file="default_color/default_color_trackhub.html">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
961 <!-- Verify trackDb.txt contains the color 0,0,0 -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
962 <extra_files type="file" name="myHub/Dbia3/trackDb.txt" value="default_color/myHub/Dbia3/trackDb.txt">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
963 <assert_contents>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
964 <has_text text="color 0,0,0"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
965 </assert_contents>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
966 </extra_files>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
967
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
968 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
969 </output>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
970 </test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
971
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
972 <!-- Test changed color in a track -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
973 <test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
974 <param name="genome_name" value="Dbia3"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
975 <param name="fasta_file" value="common/dbia3.fa"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
976 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
977 <param name="group_name" value="Default group"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
978 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
979 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
980 <param name="format_select" value="bam"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
981 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
982 <param name="track_color" value="#8064a2"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
983 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
984 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
985 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
986 <output name="output" file="changed_color/changed_color_trackhub.html">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
987 <!-- Verify trackDb.txt contains the color 128,100,162 -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
988 <extra_files type="file" name="myHub/Dbia3/trackDb.txt" value="changed_color/myHub/Dbia3/trackDb.txt">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
989 <assert_contents>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
990 <has_text text="color 128,100,162"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
991 </assert_contents>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
992 </extra_files>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
993
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
994 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
995 </output>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
996 </test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
997
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
998 <!-- Test for StringTie Chromosome end coordinates -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
999 <test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1000 <param name="genome_name" value="Dbia3"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1001 <param name="fasta_file" value="common/dbia3.fa"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1002 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1003 <param name="group_name" value="Default group"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1004 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1005 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1006 <param name="format_select" value="gtf"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1007 <param name="GTF" ftype="gtf" value="stringtie_chromosome_end_coordinates/inputs/StringTie_Assembled_Transcripts"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1008 <param name="track_color" value="#000000"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1009 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1010 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1011 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1012 <output name="output" file="stringtie_chromosome_end_coordinates/stringtie_chromosome_end_coordinates_trackhub.html">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1013 <extra_files type="file"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1014 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1015 value="stringtie_chromosome_end_coordinates/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1016 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1017 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1018
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1019 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1020 </output>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1021 </test>
2
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
1022
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
1023 <!-- Test for big files? -->
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1024
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1025 <!-- Find tests that should fail -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1026
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1027 </tests>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1028
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1029 <help>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1030 This Galaxy tool permits to prepare your files to be ready for
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1031 Assembly Hub visualization.
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1032 </help>
52
c66803bff0cc planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit adc1ac50269e02570e7ce12c732637bdd3f9a547-dirty
yating-l
parents: 51
diff changeset
1033
c66803bff0cc planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit adc1ac50269e02570e7ce12c732637bdd3f9a547-dirty
yating-l
parents: 51
diff changeset
1034 <citations>
c66803bff0cc planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit adc1ac50269e02570e7ce12c732637bdd3f9a547-dirty
yating-l
parents: 51
diff changeset
1035 <citation type="doi">10.7490/f1000research.1112719.1</citation>
c66803bff0cc planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit adc1ac50269e02570e7ce12c732637bdd3f9a547-dirty
yating-l
parents: 51
diff changeset
1036 </citations>
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1037 </tool>