Mercurial > repos > yating-l > hubarchivecreator

annotate hubArchiveCreator.xml @ 85:a65e52152476 draft default tip

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 1a81ebd0ddea950b84af3fc830e9267a4814b29f
author yating-l
date Mon, 06 Nov 2017 13:13:01 -0500
parents cb62314a6297
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
83
0bc486356e2a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 82
diff changeset
1 <tool id="hubArchiveCreator" name="Hub Archive Creator" version="2.5.0">
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>
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
6 <macros>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
7 <import>macros.xml</import>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
8 </macros>
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
9
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
10 <requirements>
82
62600ac1d0f7 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents: 81
diff changeset
11 <requirement type="package" version="340">ucsc_hac</requirement>
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
12 <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
13 <requirement type="package" version="340">ucsc_bigwig</requirement>
55
ba9997c847dc planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b2894a39921adaa6a93b12523820b61a78e11f20-dirty
yating-l
parents: 54
diff changeset
14 <requirement type="package" version="340">ucsc_bigbed</requirement>
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
15 </requirements>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
16
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
17 <stdio>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
18 <regex match="^pass1"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
19 source="stderr"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
20 level="log"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
21 description="bedToBigBed"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
22 <!-- 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
23 <!-- 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
24 </stdio>
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 <!-- 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
27 <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
28 mkdir -p $output.extra_files_path;
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
29
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
30 ## Dump the tool parameters into a JSON file
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
31 python $json_file parameters.json;
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
32
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
33 python $__tool_directory__/hubArchiveCreator.py --data_json parameters.json -o $output;
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
34
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
35
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
36 ]]></command>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
37 <configfiles>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
38 <configfile name="json_file">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
39 import json
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
40 import sys
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
41
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
42 file_path = sys.argv[1]
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
43 #set global $data_parameter_dict = {}
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
44
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
45 ## Ask the user to enter the genome name
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
46 #silent $data_parameter_dict.update({"genome_name": str($genome_name)})
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
47
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
48 ## Function to retrieve the data of the inputs
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
49 #def prepare_json($datatype, $input_to_prepare, $order_index, $extra_data_dict={})
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
50 #set false_path = str($input_to_prepare)
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
51 #set $data_dict = {"false_path": $false_path}
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
52
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
53 #set name = str($input_to_prepare.name)
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
54 #silent $data_dict.update({"name": $name})
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
55 #silent $data_dict.update($extra_data_dict)
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
56 ## Add the ordering by taking the tool form indexes
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
57 #silent $data_dict.update({"order_index": $order_index})
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
58
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
59 #if $datatype in $data_parameter_dict
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
60 #silent $data_parameter_dict[$datatype].append($data_dict)
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
61 #else
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
62 #set array_inputs = []
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
63 #silent $array_inputs.append($data_dict)
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
64 #silent $data_parameter_dict.update({$datatype: $array_inputs})
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
65 #end if
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
66 #end def
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
67
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
68 ## Get the number of digits from tracks, to have a unique integer from group index and track index
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
69
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
70 #set temp_max_digit = 0
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
71
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
72 #for $g in $group
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
73 #if len($g.format) > $temp_max_digit
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
74 #silent temp_max_digit = len($g.format)
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
75 #end if
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
76 #end for
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
77
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
78
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
79 #set nb_digits_max_track = len(str($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
80
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
81 ## END Get the number of digits
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
82
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
83 #for $i_g, $g in enumerate( $group )
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
84 #for $i, $f in enumerate( $g.format )
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
85 ## Create the order index using index_group+1 concatenated with index_track
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
86 #set index_group_final = str($i_g + 1)
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
87 #set index_track_final = str($index_group_final) + str($i).zfill($nb_digits_max_track)
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
88
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
89 ## For each format, we have a few mandatory fields we store in a dict
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
90 #set track_color = str($f.formatChoice.track_color)
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
91 #set group_name = str($g.group_name)
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
92 #set longLabel = str($f.formatChoice.longLabel)
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
93 #set extra_data_dict = {"track_color": $track_color,
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
94 "group_name": $group_name,
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
95 "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
96
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
97 #if $f.formatChoice.format_select == "bam"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
98 #set bam_index = $f.formatChoice.BAM.metadata.bam_index
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
99
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
100 ## Add Bam format specific fields
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
101 #silent $extra_data_dict.update({"index": $bam_index})
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
102
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
103 #silent $prepare_json("Bam", $f.formatChoice.BAM, $index_track_final, $extra_data_dict)
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
104 #end if
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
105 #if $f.formatChoice.format_select == "bed"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
106 #if $f.formatChoice.bedChoice.bed_select == "bed_generic"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
107 #silent $prepare_json("Bed", $f.formatChoice.bedChoice.BED, $index_track_final,
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
108 $extra_data_dict)
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
109 #end if
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
110 #if $f.formatChoice.bedChoice.bed_select == "bed_cytoBand"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
111 #silent $prepare_json("CytoBand", $f.formatChoice.bedChoice.BED_cytoBand, $index_track_final,
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
112 $extra_data_dict)
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
113 #end if
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
114 #if $f.formatChoice.bedChoice.bed_select == "bed_simple_repeats_option"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
115 #silent $prepare_json("BedSimpleRepeats", $f.formatChoice.bedChoice.BED_simple_repeats, $index_track_final,
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
116 $extra_data_dict)
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
117 #end if
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
118 #if $f.formatChoice.bedChoice.bed_select == "bed_splice_junctions_option"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
119 #silent $prepare_json("BedSpliceJunctions", $f.formatChoice.bedChoice.BED_splice_junctions, $index_track_final,
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
120 $extra_data_dict)
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
121 #end if
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
122 #if $f.formatChoice.bedChoice.bed_select == "bed_blast_alignment_option"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
123 #set database = str($f.formatChoice.bedChoice.database)
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
124 #silent $extra_data_dict.update({"database": $database})
83
0bc486356e2a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 82
diff changeset
125 #if $f.formatChoice.bedChoice.add_trix_index.add_trix_index_selector == "yes"
84
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
126 #for i in $f.formatChoice.bedChoice.add_trix_index.trix_index
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
127 #if $i.element_identifier.endswith("ix")
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
128 #$extra_data_dict.update({"index_ix": str($i)})
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
129 #elif $i.element_identifier.endswith("ixx")
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
130 #$extra_data_dict.update({"index_ixx": str($i)})
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
131 #end if
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
132 #end for
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
133 ##set ix_index = str($f.formatChoice.bedChoice.add_trix_index.trix_index.index_ix)
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
134 ##set ixx_index = str($f.formatChoice.bedChoice.add_trix_index.trix_index.index_ixx)
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
135 ##silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index})
83
0bc486356e2a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 82
diff changeset
136 #end if
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
137 #silent $prepare_json("BedBlastAlignments", $f.formatChoice.bedChoice.BED_blast_alignment, $index_track_final,
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
138 $extra_data_dict)
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
139 #end if
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
140 #if $f.formatChoice.bedChoice.bed_select == "bed_blat_alignment_option"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
141 #set database = str($f.formatChoice.bedChoice.database)
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
142 #silent $extra_data_dict.update({"database": $database})
83
0bc486356e2a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 82
diff changeset
143 #if $f.formatChoice.bedChoice.add_trix_index.add_trix_index_selector == "yes"
84
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
144 #for i in $f.formatChoice.bedChoice.add_trix_index.trix_index
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
145 #if $i.element_identifier.endswith("ix")
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
146 #$extra_data_dict.update({"index_ix": str($i)})
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
147 #elif $i.element_identifier.endswith("ixx")
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
148 #$extra_data_dict.update({"index_ixx": str($i)})
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
149 #end if
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
150 #end for
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
151 ##set ix_index = str($f.formatChoice.bedChoice.add_trix_index.trix_index.index_ix)
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
152 ##set ixx_index = str($f.formatChoice.bedChoice.add_trix_index.trix_index.index_ixx)
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
153 ##silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index})
83
0bc486356e2a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 82
diff changeset
154 #end if
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
155 #silent $prepare_json("BedBlatAlignments", $f.formatChoice.bedChoice.BED_blat_alignment, $index_track_final,
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
156 $extra_data_dict)
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
157 #end if
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
158 #end if
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
159 #if $f.formatChoice.format_select == "psl"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
160 #silent $prepare_json("Psl", $f.formatChoice.PSL, $index_track_final,
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
161 $extra_data_dict)
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
162 #end if
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
163 #if $f.formatChoice.format_select == "bigwig"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
164 #silent $prepare_json("BigWig", $f.formatChoice.BIGWIG, $index_track_final,
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
165 $extra_data_dict)
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
166 #end if
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
167 #if $f.formatChoice.format_select == "bigbed"
83
0bc486356e2a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 82
diff changeset
168 #if $f.formatChoice.add_trix_index.add_trix_index_selector == "yes"
84
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
169 ##set ix_index = str($f.formatChoice.add_trix_index.trix_index.index_ix)
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
170 ##set ixx_index = str($f.formatChoice.add_trix_index.trix_index.index_ixx)
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
171 #for i in $f.formatChoice.add_trix_index.trix_index
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
172 #if $i.element_identifier.endswith("ix")
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
173 #$extra_data_dict.update({"index_ix": str($i)})
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
174 #elif $i.element_identifier.endswith("ixx")
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
175 #$extra_data_dict.update({"index_ixx": str($i)})
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
176 #end if
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
177 #end for
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
178 #$extra_data_dict.update({"trix_id": str($f.formatChoice.add_trix_index.trix_id)})
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
179 ##set trix_id = str($f.formatChoice.add_trix_index.trix_id)
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
180 ##silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index, "trix_id": $trix_id})
83
0bc486356e2a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 82
diff changeset
181 #end if
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
182 #silent $prepare_json("BigBed", $f.formatChoice.BIGBED, $index_track_final,
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
183 $extra_data_dict)
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
184 #end if
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
185 #if $f.formatChoice.format_select == "gff3"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
186 #silent $prepare_json("Gff3", $f.formatChoice.GFF3, $index_track_final,
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
187 $extra_data_dict)
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
188 #end if
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
189 #if $f.formatChoice.format_select == "gtf"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
190 ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
191 #silent $prepare_json("Gtf", $f.formatChoice.GTF, $index_track_final,
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
192 $extra_data_dict)
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
193 #end if
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
194 #end for
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
195 #end for
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
196
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
197 ## We combine the fasta file dataset name with his false path in a JSON object
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
198 #set fasta_json = {"false_path": str($fasta_file), "name": str($fasta_file.name)}
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
199 $data_parameter_dict.update({"fasta": $fasta_json})
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
200
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
201 ## Retrieve the user email
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
202 #silent $data_parameter_dict.update({"user_email": str($__user_email__)})
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
203
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
204 #silent $data_parameter_dict.update({"tool_directory": str($__tool_directory__)})
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
205
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
206 #silent $data_parameter_dict.update({"extra_files_path": str($output.extra_files_path)})
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
207
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
208 #silent $data_parameter_dict.update({"debug_mode": str($advanced_options.debug_mode)})
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
209
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
210 with open(file_path, 'w') as f:
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
211 json.dump($data_parameter_dict, f)
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
212
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
213 </configfile>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
214 </configfiles>
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
215
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
216 <inputs>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
217 <param
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
218 name="genome_name"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
219 type="text"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
220 size="30"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
221 value="unknown"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
222 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
223 />
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="fasta"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
226 name="fasta_file"
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="Reference genome"
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 <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
231 <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
232 <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
233 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
234 <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
235 <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
236 <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
237 <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
238 <option value="bigwig">BIGWIG</option>
55
ba9997c847dc planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b2894a39921adaa6a93b12523820b61a78e11f20-dirty
yating-l
parents: 54
diff changeset
239 <option value="bigbed">BIGBED</option>
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
240 <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
241 <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
242 </param>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
243
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
244 <when value="bam">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
245 <param
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
246 format="bam"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
247 name="BAM"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
248 type="data"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
249 label="BAM File"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
250 />
61
68aeb6482069 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit acefc0713163be931deb145a658c2fff18692935-dirty
yating-l
parents: 60
diff changeset
251 <param name="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" />
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
252 <!-- 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
253 <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
254 <sanitizer>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
255 <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
256 <add value="#"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
257 </valid>
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 </param>
52
c66803bff0cc planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit adc1ac50269e02570e7ce12c732637bdd3f9a547-dirty
yating-l
parents: 51
diff changeset
260 </when>
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
261 <when value="bed">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
262 <conditional name="bedChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
263 <param name="bed_select" type="select" label="Bed Choice">
62
4c4e8941feda planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 5bbecd016ad3a784ad030cb82a09a3ac40dc6060-dirty
yating-l
parents: 61
diff changeset
264 <option value="bed_generic" selected="true">BED Generic (bed4)</option>
4c4e8941feda planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 5bbecd016ad3a784ad030cb82a09a3ac40dc6060-dirty
yating-l
parents: 61
diff changeset
265 <option value="bed_cytoBand">cytoBand Track (bed4+1)</option>
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
266 <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
267 <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
268 <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
269 <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
270 </param>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
271 <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
272 <param
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
273 format="bed"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
274 name="BED"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
275 type="data"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
276 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
277 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
278
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
279 </when>
54
4a58094b051e planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 754b3f960221a68b90f9cddd98a1c3dd324d4d4e-dirty
yating-l
parents: 52
diff changeset
280 <when value="bed_cytoBand">
4a58094b051e planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 754b3f960221a68b90f9cddd98a1c3dd324d4d4e-dirty
yating-l
parents: 52
diff changeset
281 <param
4a58094b051e planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 754b3f960221a68b90f9cddd98a1c3dd324d4d4e-dirty
yating-l
parents: 52
diff changeset
282 format="bed"
4a58094b051e planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 754b3f960221a68b90f9cddd98a1c3dd324d4d4e-dirty
yating-l
parents: 52
diff changeset
283 name="BED_cytoBand"
4a58094b051e planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 754b3f960221a68b90f9cddd98a1c3dd324d4d4e-dirty
yating-l
parents: 52
diff changeset
284 type="data"
4a58094b051e planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 754b3f960221a68b90f9cddd98a1c3dd324d4d4e-dirty
yating-l
parents: 52
diff changeset
285 label="cytoBand Track (Bed4)"
4a58094b051e planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 754b3f960221a68b90f9cddd98a1c3dd324d4d4e-dirty
yating-l
parents: 52
diff changeset
286 />
4a58094b051e planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 754b3f960221a68b90f9cddd98a1c3dd324d4d4e-dirty
yating-l
parents: 52
diff changeset
287 </when>
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
288 <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
289 <param
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
290 format="bed"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
291 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
292 type="data"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
293 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
294 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
295 </when>
9
d5781fe7b782 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e42ecb807fb34a8e4ddcf96944dd74d24c695352-dirty
yating-l
parents: 8
diff changeset
296 <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
297 <param
d5781fe7b782 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e42ecb807fb34a8e4ddcf96944dd74d24c695352-dirty
yating-l
parents: 8
diff changeset
298 format="bed"
d5781fe7b782 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e42ecb807fb34a8e4ddcf96944dd74d24c695352-dirty
yating-l
parents: 8
diff changeset
299 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
300 type="data"
d5781fe7b782 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e42ecb807fb34a8e4ddcf96944dd74d24c695352-dirty
yating-l
parents: 8
diff changeset
301 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
302 />
d5781fe7b782 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e42ecb807fb34a8e4ddcf96944dd74d24c695352-dirty
yating-l
parents: 8
diff changeset
303 </when>
51
364b8db8de17 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 9
diff changeset
304 <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
305 <param
d5781fe7b782 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e42ecb807fb34a8e4ddcf96944dd74d24c695352-dirty
yating-l
parents: 8
diff changeset
306 format="bed"
51
364b8db8de17 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 9
diff changeset
307 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
308 type="data"
51
364b8db8de17 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 9
diff changeset
309 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
310 />
57
b39dd0b5a166 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ce28781f52a4f84039de300cb41e3982f2e8bf51-dirty
yating-l
parents: 55
diff changeset
311 <param name="database" type="select" label="Protein database">
b39dd0b5a166 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ce28781f52a4f84039de300cb41e3982f2e8bf51-dirty
yating-l
parents: 55
diff changeset
312 <option value="NCBI" selected="true">NCBI</option>
60
583431485006 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit acefc0713163be931deb145a658c2fff18692935
yating-l
parents: 57
diff changeset
313 <option value="UniProt">UniProt</option>
57
b39dd0b5a166 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ce28781f52a4f84039de300cb41e3982f2e8bf51-dirty
yating-l
parents: 55
diff changeset
314 <option value="FlyBase">FlyBase</option>
b39dd0b5a166 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ce28781f52a4f84039de300cb41e3982f2e8bf51-dirty
yating-l
parents: 55
diff changeset
315 <option value="Others">Others</option>
b39dd0b5a166 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ce28781f52a4f84039de300cb41e3982f2e8bf51-dirty
yating-l
parents: 55
diff changeset
316 </param>
83
0bc486356e2a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 82
diff changeset
317 <expand macro="add_trix_file"/>
51
364b8db8de17 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 9
diff changeset
318 </when>
364b8db8de17 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 9
diff changeset
319 <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
320 <param
364b8db8de17 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 9
diff changeset
321 format="bed"
364b8db8de17 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 9
diff changeset
322 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
323 type="data"
364b8db8de17 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
yating-l
parents: 9
diff changeset
324 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
325 />
57
b39dd0b5a166 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ce28781f52a4f84039de300cb41e3982f2e8bf51-dirty
yating-l
parents: 55
diff changeset
326 <param name="database" type="select" label="mRNA database">
b39dd0b5a166 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ce28781f52a4f84039de300cb41e3982f2e8bf51-dirty
yating-l
parents: 55
diff changeset
327 <option value="NCBI" selected="true">NCBI</option>
b39dd0b5a166 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ce28781f52a4f84039de300cb41e3982f2e8bf51-dirty
yating-l
parents: 55
diff changeset
328 <option value="Others">Others</option>
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
329 </param>
83
0bc486356e2a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 82
diff changeset
330 <expand macro="add_trix_file"/>
9
d5781fe7b782 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e42ecb807fb34a8e4ddcf96944dd74d24c695352-dirty
yating-l
parents: 8
diff changeset
331 </when>
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
332 </conditional>
61
68aeb6482069 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit acefc0713163be931deb145a658c2fff18692935-dirty
yating-l
parents: 60
diff changeset
333 <param name="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" />
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
334 <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
335 <sanitizer>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
336 <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
337 <add value="#"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
338 </valid>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
339 </sanitizer>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
340 </param>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
341 </when>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
342 <when value="psl">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
343 <param
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
344 format="psl"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
345 name="PSL"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
346 type="data"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
347 label="PSL File"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
348 />
61
68aeb6482069 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit acefc0713163be931deb145a658c2fff18692935-dirty
yating-l
parents: 60
diff changeset
349 <param name="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" />
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
350 <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
351 <sanitizer>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
352 <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
353 <add value="#"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
354 </valid>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
355 </sanitizer>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
356 </param>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
357 </when>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
358 <when value="bigwig">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
359 <param
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
360 format="bigwig"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
361 name="BIGWIG"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
362 type="data"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
363 label="BIGWIG File"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
364 />
61
68aeb6482069 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit acefc0713163be931deb145a658c2fff18692935-dirty
yating-l
parents: 60
diff changeset
365 <param name="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" />
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
366 <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
367 <sanitizer>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
368 <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
369 <add value="#"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
370 </valid>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
371 </sanitizer>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
372 </param>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
373 </when>
55
ba9997c847dc planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b2894a39921adaa6a93b12523820b61a78e11f20-dirty
yating-l
parents: 54
diff changeset
374 <when value="bigbed">
ba9997c847dc planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b2894a39921adaa6a93b12523820b61a78e11f20-dirty
yating-l
parents: 54
diff changeset
375 <param
ba9997c847dc planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b2894a39921adaa6a93b12523820b61a78e11f20-dirty
yating-l
parents: 54
diff changeset
376 format="bigbed"
ba9997c847dc planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b2894a39921adaa6a93b12523820b61a78e11f20-dirty
yating-l
parents: 54
diff changeset
377 name="BIGBED"
ba9997c847dc planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b2894a39921adaa6a93b12523820b61a78e11f20-dirty
yating-l
parents: 54
diff changeset
378 type="data"
ba9997c847dc planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b2894a39921adaa6a93b12523820b61a78e11f20-dirty
yating-l
parents: 54
diff changeset
379 label="BIGBED File"
ba9997c847dc planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b2894a39921adaa6a93b12523820b61a78e11f20-dirty
yating-l
parents: 54
diff changeset
380 />
83
0bc486356e2a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 82
diff changeset
381 <expand macro="add_trix_file">
0bc486356e2a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 82
diff changeset
382 <param
0bc486356e2a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 82
diff changeset
383 name="trix_id"
0bc486356e2a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 82
diff changeset
384 value="name"
0bc486356e2a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 82
diff changeset
385 type="text"
0bc486356e2a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 82
diff changeset
386 size="30"
84
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
387 label="Specify Trix identifier (The default is name)"
83
0bc486356e2a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 82
diff changeset
388 />
0bc486356e2a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 82
diff changeset
389 </expand>
61
68aeb6482069 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit acefc0713163be931deb145a658c2fff18692935-dirty
yating-l
parents: 60
diff changeset
390 <param name="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" />
55
ba9997c847dc planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b2894a39921adaa6a93b12523820b61a78e11f20-dirty
yating-l
parents: 54
diff changeset
391 <param name="track_color" type="color" label="Track color" value="#000000">
ba9997c847dc planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b2894a39921adaa6a93b12523820b61a78e11f20-dirty
yating-l
parents: 54
diff changeset
392 <sanitizer>
ba9997c847dc planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b2894a39921adaa6a93b12523820b61a78e11f20-dirty
yating-l
parents: 54
diff changeset
393 <valid initial="string.letters,string.digits">
ba9997c847dc planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b2894a39921adaa6a93b12523820b61a78e11f20-dirty
yating-l
parents: 54
diff changeset
394 <add value="#"/>
ba9997c847dc planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b2894a39921adaa6a93b12523820b61a78e11f20-dirty
yating-l
parents: 54
diff changeset
395 </valid>
ba9997c847dc planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b2894a39921adaa6a93b12523820b61a78e11f20-dirty
yating-l
parents: 54
diff changeset
396 </sanitizer>
ba9997c847dc planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b2894a39921adaa6a93b12523820b61a78e11f20-dirty
yating-l
parents: 54
diff changeset
397 </param>
ba9997c847dc planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b2894a39921adaa6a93b12523820b61a78e11f20-dirty
yating-l
parents: 54
diff changeset
398 </when>
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
399 <when value="gff3">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
400 <param
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
401 format="gff3"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
402 name="GFF3"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
403 type="data"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
404 label="GFF3 File"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
405 />
61
68aeb6482069 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit acefc0713163be931deb145a658c2fff18692935-dirty
yating-l
parents: 60
diff changeset
406 <param name="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" />
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
407 <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
408 <sanitizer>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
409 <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
410 <add value="#"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
411 </valid>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
412 </sanitizer>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
413 </param>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
414 </when>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
415 <when value="gtf">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
416 <param
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
417 format="gtf"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
418 name="GTF"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
419 type="data"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
420 label="GTF File"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
421 />
61
68aeb6482069 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit acefc0713163be931deb145a658c2fff18692935-dirty
yating-l
parents: 60
diff changeset
422 <param name="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" />
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
423 <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
424 <sanitizer>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
425 <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
426 <add value="#"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
427 </valid>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
428 </sanitizer>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
429 </param>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
430 </when>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
431 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
432 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
433 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
434 <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
435 <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
436 <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
437 <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
438 </param>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
439 <!-- 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
440 <when value="on">
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
441 <param name="debug_mode" type="select" label="Activate debug mode">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
442 <option value="false" selected="true">No</option>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
443 <option value="true">Yes</option>
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
444 <help>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
445 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
446 </help>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
447 </param>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
448 </when>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
449 <when value="off">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
450 <param name="debug_mode" type="hidden"
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
451 value="false">
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
452 </param>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
453 </when>
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
454 </conditional>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
455 </inputs>
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
456
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
457 <outputs>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
458 <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
459 </outputs>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
460
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
461 <tests>
85
a65e52152476 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 84
diff changeset
462
a65e52152476 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 84
diff changeset
463 <!-- Test with only the fasta file -->
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
464 <test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
465 <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
466 <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
467 <output name="output" file="only_genome/only_genome.html">
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
468 <!-- Use macro to check the whole common structure without repeated code -->
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
469 <expand macro="verify_hub_structure_no_track" test="only_genome" />
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
470 </output>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
471 </test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
472
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
473 <!-- Test with Bam -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
474 <test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
475 <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
476 <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
477 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
478 <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
479 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
480 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
481 <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
482 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam" />
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
483 <param name="longLabel" value="HISAT sequence alignment" />
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
484 <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
485 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
486 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
487 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
488 <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
489 <!-- 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
490 <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
491 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
492 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
493 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
494 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
495 <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
496 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
497 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
498 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
499 />
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
500 <!-- Use macro to check the whole common structure without repeated code -->
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
501 <expand macro="verify_hub_structure" test="bam" />
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
502 </output>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
503 </test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
504
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
505 <!-- 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
506 <test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
507 <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
508 <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
509 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
510 <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
511 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
512 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
513 <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
514 <conditional name="bedChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
515 <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
516 <param name="BED" ftype="bed" value="bed_generic/inputs/TBLASTN_Alignment_to_proteins"/>
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
517 <param name="longLabel" value="TBLASTN alignment" />
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
518 <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
519 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
520 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
521 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
522 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
523 <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
524 <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
525 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
526 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
527 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
528 />
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
529 <expand macro="verify_hub_structure" test="bed_generic" />
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
530 </output>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
531 </test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
532
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
533 <!-- 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
534 <test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
535 <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
536 <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
537 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
538 <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
539 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
540 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
541 <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
542 <conditional name="bedChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
543 <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
544 <param name="BED_simple_repeats" ftype="bed" value="bed_simple_repeats/inputs/Repeating_Elements_by_TrfBig"/>
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
545 <param name="longLabel" value="Simple repeat" />
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
546 <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
547 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
548 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
549 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
550 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
551 <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
552 <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
553 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
554 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
555 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
556 />
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
557 <expand macro="verify_hub_structure" test="bed_simple_repeats" />
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
558 </output>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
559 </test>
52
c66803bff0cc planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit adc1ac50269e02570e7ce12c732637bdd3f9a547-dirty
yating-l
parents: 51
diff changeset
560
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
561 <!-- 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
562 <test>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
563 <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
564 <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
565 <repeat name="group">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
566 <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
567 <repeat name="format">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
568 <conditional name="formatChoice">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
569 <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
570 <param name="PSL" value="psl/inputs/blastXmlToPsl"/>
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
571 <param name="longLabel" value="BLAST Alignment" />
2
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
572 <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
573 </conditional>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
574 </repeat>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
575 </repeat>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
576 <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
577 <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
578 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
579 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
580 compare="sim_size"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
581 />
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
582 <expand macro="verify_hub_structure" test="psl" />
2
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
583 </output>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
584 </test>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
585
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
586 <!-- Test with BigWig -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
587 <test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
588 <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
589 <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
590 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
591 <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
592 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
593 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
594 <param name="format_select" value="bigwig"/>
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
595 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
596 <param name="longLabel" value="RNA-Seq Coverage" />
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
597 <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
598 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
599 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
600 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
601 <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
602 <extra_files type="file"
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
603 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
604 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
605 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
606 />
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
607 <expand macro="verify_hub_structure" test="bigwig" />
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
608 <!-- check additional trackDb settings for BigWig -->
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
609 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
610 <assert_contents>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
611 <has_text text="autoScale"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
612 <has_text text="maxHeightPixels"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
613 <has_text text="windowingFunction"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
614 </assert_contents>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
615 </extra_files>
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
616 </output>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
617 </test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
618
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
619 <!-- Test with GFF3 -->
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 <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
622 <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
623 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
624 <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
625 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
626 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
627 <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
628 <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/>
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
629 <param name="longLabel" value="Augustus" />
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
630 <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
631 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
632 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
633 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
634 <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
635 <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
636 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
637 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
638 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
639 />
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
640 <expand macro="verify_hub_structure" test="gff3" />
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
641 </output>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
642 </test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
643
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
644 <!-- Test with GTF -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
645 <test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
646 <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
647 <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
648 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
649 <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
650 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
651 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
652 <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
653 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
654 <param name="longLabel" value="StringTie transcripts" />
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
655 <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
656 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
657 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
658 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
659 <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
660 <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
661 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
662 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
663 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
664 />
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
665 <expand macro="verify_hub_structure" test="gtf" />
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
666 </output>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
667 </test>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
668
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
669 <!-- Test with BLAT Alignment -->
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
670 <test>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
671 <param name="genome_name" value="Dbia3"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
672 <param name="fasta_file" value="common/dbia3.fa"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
673 <repeat name="group">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
674 <param name="group_name" value="Default group"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
675 <repeat name="format">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
676 <conditional name="formatChoice">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
677 <param name="format_select" value="bed" />
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
678 <conditional name="bedChoice">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
679 <param name="bed_select" value="bed_blat_alignment_option"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
680 <param name="BED_blat_alignment" ftype="bed" value="bed_blat_alignment/inputs/BLAT_alignment_bigpsl"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
681 <param name="longLabel" value="BLAT alignment" />
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
682 <param name="track_color" value="#000000"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
683 <param name="database" value="NCBI" />
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
684 </conditional>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
685 </conditional>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
686 </repeat>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
687 </repeat>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
688 <output name="output" file="bed_blat_alignment/blat_alignment_trackhub.html">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
689 <extra_files type="file"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
690 name="myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
691 value="bed_blat_alignment/myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
692 compare="sim_size"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
693 />
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
694 <expand macro="verify_hub_structure" test="bed_blat_alignment" />
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
695 <!-- check additional trackDb settings for BLAT -->
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
696 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
697 <assert_contents>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
698 <has_text text="searchIndex"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
699 <has_text text="url"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
700 <has_text text="urlLabel"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
701 <has_text text="iframeUrl"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
702 <has_text text="iframeOptions"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
703 </assert_contents>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
704 </extra_files>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
705 </output>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
706 </test>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
707
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
708 <!-- Test with BLAST Alignment -->
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
709 <test>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
710 <param name="genome_name" value="Dbia3"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
711 <param name="fasta_file" value="common/dbia3.fa"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
712 <repeat name="group">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
713 <param name="group_name" value="Default group"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
714 <repeat name="format">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
715 <conditional name="formatChoice">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
716 <param name="format_select" value="bed" />
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
717 <conditional name="bedChoice">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
718 <param name="bed_select" value="bed_blast_alignment_option"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
719 <param name="BED_blast_alignment" ftype="bed" value="bed_blast_alignment/inputs/BLAST_alignment_bigpsl"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
720 <param name="longLabel" value="BLAST alignment" />
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
721 <param name="track_color" value="#000000"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
722 <param name="database" value="NCBI" />
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
723 </conditional>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
724 </conditional>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
725 </repeat>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
726 </repeat>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
727 <output name="output" file="bed_blast_alignment/blast_alignment_trackhub.html">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
728 <extra_files type="file"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
729 name="myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
730 value="bed_blast_alignment/myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
731 compare="sim_size"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
732 />
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
733 <expand macro="verify_hub_structure" test="bed_blast_alignment" />
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
734 <!-- check additional trackDb settings for BLAST -->
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
735 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
736 <assert_contents>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
737 <has_text text="searchIndex"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
738 <has_text text="url"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
739 <has_text text="urlLabel"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
740 <has_text text="iframeUrl"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
741 <has_text text="iframeOptions"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
742 </assert_contents>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
743 </extra_files>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
744 </output>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
745 </test>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
746
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
747 <!-- Test with Regtools Splice Junctions -->
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
748 <test>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
749 <param name="genome_name" value="Dbia3"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
750 <param name="fasta_file" value="common/dbia3.fa"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
751 <repeat name="group">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
752 <param name="group_name" value="Default group"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
753 <repeat name="format">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
754 <conditional name="formatChoice">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
755 <param name="format_select" value="bed" />
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
756 <conditional name="bedChoice">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
757 <param name="bed_select" value="bed_splice_junctions_option"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
758 <param name="BED_splice_junctions" ftype="bed" value="bed_splice_junctions/inputs/regtools_junctions"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
759 <param name="longLabel" value="Splice junctions" />
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
760 <param name="track_color" value="#000000"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
761 </conditional>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
762 </conditional>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
763 </repeat>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
764 </repeat>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
765 <output name="output" file="bed_splice_junctions/splice_junctions_trackhub.html">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
766 <extra_files type="file"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
767 name="myHub/Dbia3/tracks/regtools_junctions.bb"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
768 value="bed_splice_junctions/myHub/Dbia3/tracks/regtools_junctions.bb"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
769 compare="sim_size"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
770 />
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
771 <expand macro="verify_hub_structure" test="bed_splice_junctions" />
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
772 </output>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
773 </test>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
774
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
775 <!-- Test with Cytoband -->
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
776 <test>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
777 <param name="genome_name" value="Dbia3"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
778 <param name="fasta_file" value="common/dbia3.fa"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
779 <repeat name="group">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
780 <param name="group_name" value="Default group"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
781 <repeat name="format">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
782 <conditional name="formatChoice">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
783 <param name="format_select" value="bed" />
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
784 <conditional name="bedChoice">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
785 <param name="bed_select" value="bed_cytoBand"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
786 <param name="BED_cytoBand" ftype="bed" value="bed_cytoband/inputs/Cytoband"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
787 <param name="longLabel" value="Cytoband" />
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
788 <param name="track_color" value="#000000"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
789 </conditional>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
790 </conditional>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
791 </repeat>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
792 </repeat>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
793 <output name="output" file="bed_cytoband/cytoband_trackhub.html">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
794 <extra_files type="file"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
795 name="myHub/Dbia3/tracks/Cytoband.bb"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
796 value="bed_cytoband/myHub/Dbia3/tracks/Cytoband.bb"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
797 compare="sim_size"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
798 />
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
799 <expand macro="verify_hub_structure" test="bed_cytoband" />
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
800 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
801 <assert_contents>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
802 <has_text text="track cytoBandIdeo"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
803 </assert_contents>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
804 </extra_files>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
805 </output>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
806 </test>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
807
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
808 <!-- Test with bigBed -->
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
809 <test>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
810 <param name="genome_name" value="Dbia3"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
811 <param name="fasta_file" value="common/dbia3.fa"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
812 <repeat name="group">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
813 <param name="group_name" value="Default group"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
814 <repeat name="format">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
815 <conditional name="formatChoice">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
816 <param name="format_select" value="bigbed"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
817 <param name="BIGBED" value="big_bed/inputs/BLAT_alignment_bigbed" />
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
818 <param name="longLabel" value="bigBed" />
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
819 <param name="track_color" value="#000000"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
820 </conditional>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
821 </repeat>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
822 </repeat>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
823 <output name="output" file="big_bed/bigbed_trackhub.html">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
824 <extra_files type="file"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
825 name="myHub/Dbia3/tracks/BLAT_alignment_bigbed.bigbed"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
826 value="big_bed/myHub/Dbia3/tracks/BLAT_alignment_bigbed.bigbed"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
827 compare="sim_size"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
828 />
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
829 <expand macro="verify_hub_structure" test="big_bed" />
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
830 </output>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
831 </test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
832
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
833 <!-- 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
834 <test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
835 <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
836 <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
837 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
838 <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
839 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
840 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
841 <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
842 <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
843 <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
844 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
845 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
846 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
847 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
848 <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
849 <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
850 <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
851 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
852 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
853 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
854 <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
855 <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
856 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
857 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
858 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
859 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
860 <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
861 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
862 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
863 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
864 />
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
865 <expand macro="verify_hub_structure" test="gtf_gff" />
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
866 </output>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
867 </test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
868
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
869 <!-- Test with one group and all the supported datatypes -->
2
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
870 <test>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
871 <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
872 <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
873 <repeat name="group">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
874 <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
875 <repeat name="format">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
876 <conditional name="formatChoice">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
877 <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
878 <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
879 <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
880 </conditional>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
881 </repeat>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
882 <repeat name="format">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
883 <conditional name="formatChoice">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
884 <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
885 <conditional name="bedChoice">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
886 <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
887 <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
888 <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
889 </conditional>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
890 </conditional>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
891 </repeat>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
892 <repeat name="format">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
893 <conditional name="formatChoice">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
894 <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
895 <conditional name="bedChoice">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
896 <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
897 <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
898 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
899 <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
900 </conditional>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
901 </conditional>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
902 </repeat>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
903 <repeat name="format">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
904 <conditional name="formatChoice">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
905 <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
906 <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
907 <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
908 </conditional>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
909 </repeat>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
910 <repeat name="format">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
911 <conditional name="formatChoice">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
912 <param name="format_select" value="bigwig"/>
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
913 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/>
2
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
914 <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
915 </conditional>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
916 </repeat>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
917 <repeat name="format">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
918 <conditional name="formatChoice">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
919 <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
920 <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
921 <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
922 </conditional>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
923 </repeat>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
924 <repeat name="format">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
925 <conditional name="formatChoice">
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
926 <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
927 <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
928 <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
929 </conditional>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
930 </repeat>
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
931 <repeat name="format">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
932 <conditional name="formatChoice">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
933 <param name="format_select" value="bed" />
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
934 <conditional name="bedChoice">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
935 <param name="bed_select" value="bed_cytoBand"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
936 <param name="BED_cytoBand" ftype="bed" value="bed_cytoband/inputs/Cytoband"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
937 <param name="track_color" value="#000000"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
938 </conditional>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
939 </conditional>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
940 </repeat>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
941 <repeat name="format">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
942 <conditional name="formatChoice">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
943 <param name="format_select" value="bed" />
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
944 <conditional name="bedChoice">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
945 <param name="bed_select" value="bed_splice_junctions_option"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
946 <param name="BED_splice_junctions" ftype="bed" value="bed_splice_junctions/inputs/regtools_junctions"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
947 <param name="track_color" value="#000000"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
948 </conditional>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
949 </conditional>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
950 </repeat>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
951 <repeat name="format">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
952 <conditional name="formatChoice">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
953 <param name="format_select" value="bed" />
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
954 <conditional name="bedChoice">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
955 <param name="bed_select" value="bed_blast_alignment_option"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
956 <param name="BED_blast_alignment" ftype="bed" value="bed_blast_alignment/inputs/BLAST_alignment_bigpsl"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
957 <param name="track_color" value="#000000"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
958 <param name="database" value="NCBI" />
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
959 </conditional>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
960 </conditional>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
961 </repeat>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
962 <repeat name="format">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
963 <conditional name="formatChoice">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
964 <param name="format_select" value="bed" />
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
965 <conditional name="bedChoice">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
966 <param name="bed_select" value="bed_blat_alignment_option"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
967 <param name="BED_blat_alignment" ftype="bed" value="bed_blat_alignment/inputs/BLAT_alignment_bigpsl"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
968 <param name="track_color" value="#000000"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
969 <param name="database" value="NCBI" />
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
970 </conditional>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
971 </conditional>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
972 </repeat>
2
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
973 </repeat>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
974 <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
975 <!-- 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
976 <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
977 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
978 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
979 compare="sim_size"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
980 />
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
981 <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
982 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
983 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
984 compare="sim_size"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
985 />
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
986 <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
987 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
988 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
989 compare="sim_size"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
990 />
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
991 <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
992 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
993 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
994 compare="sim_size"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
995 />
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
996 <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
997 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
998 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
999 compare="sim_size"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
1000 />
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
1001 <extra_files type="file"
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1002 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1003 value="all_datatypes/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
2
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
1004 compare="sim_size"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
1005 />
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
1006 <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
1007 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
1008 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
1009 compare="sim_size"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
1010 />
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
1011 <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
1012 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
1013 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
1014 compare="sim_size"
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
1015 />
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1016 <extra_files type="file"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1017 name="myHub/Dbia3/tracks/Cytoband.bb"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1018 value="all_datatypes/myHub/Dbia3/tracks/Cytoband.bb"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1019 compare="sim_size"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1020 />
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1021 <extra_files type="file"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1022 name="myHub/Dbia3/tracks/regtools_junctions.bb"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1023 value="all_datatypes/myHub/Dbia3/tracks/regtools_junctions.bb"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1024 compare="sim_size"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1025 />
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1026 <extra_files type="file"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1027 name="myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1028 value="all_datatypes/myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1029 compare="sim_size"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1030 />
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1031 <extra_files type="file"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1032 name="myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1033 value="all_datatypes/myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1034 compare="sim_size"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1035 />
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1036 <expand macro="verify_hub_structure" test="all_datatypes" />
2
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
1037 </output>
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
1038 </test>
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1039
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1040 <!-- Test with two groups and no tracks -->
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1041 <test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1042 <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
1043 <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
1044 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1045 <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
1046 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1047 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1048 <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
1049 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1050 <output name="output" file="two_groups_no_track/two_groups_no_track_trackhub.html">
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1051 <expand macro="verify_hub_structure_no_track" test="two_groups_no_track" />
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1052 </output>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1053 </test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1054
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1055 <!-- 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
1056 <test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1057 <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
1058 <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
1059 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1060 <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
1061 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1062 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1063 <param name="format_select" value="bigwig"/>
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1064 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/>
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1065 <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
1066 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1067 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1068 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1069 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1070 <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
1071 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1072 <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
1073 <!-- Check tracks exist -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1074 <extra_files type="file"
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1075 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1076 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1077 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1078 />
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1079 <expand macro="verify_hub_structure" test="two_groups_one_track_first" />
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1080 </output>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1081 </test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1082
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1083 <!-- 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
1084 <test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1085 <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
1086 <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
1087 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1088 <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
1089 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1090 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1091 <param name="format_select" value="bigwig"/>
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1092 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/>
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1093 <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
1094 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1095 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1096 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1097 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1098 <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
1099 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1100 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1101 <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
1102 <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
1103 <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
1104 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1105 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1106 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1107 <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
1108 <!-- Check tracks exist -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1109 <!-- First group -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1110 <extra_files type="file"
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1111 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1112 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1113 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1114 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1115
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1116 <!-- Second group -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1117 <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
1118 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
1119 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
1120 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1121 />
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1122 <expand macro="verify_hub_structure" test="two_groups_one_track_both" />
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1123 <!-- 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
1124 </output>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1125 </test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1126
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1127 <!-- 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
1128 <test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1129 <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
1130 <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
1131 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1132 <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
1133 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1134 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1135 <param name="format_select" value="bigwig"/>
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1136 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/>
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1137 <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
1138 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1139 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1140 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1141 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1142 <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
1143 <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
1144 <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
1145 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1146 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1147 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1148 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1149 <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
1150 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1151 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1152 <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
1153 <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
1154 <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
1155 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1156 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1157 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1158 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1159 <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
1160 <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
1161 <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
1162 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1163 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1164 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1165 <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
1166 <!-- Check tracks exist -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1167 <!-- First group -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1168 <extra_files type="file"
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1169 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1170 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1171 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1172 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1173 <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
1174 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
1175 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
1176 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1177 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1178 <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
1179 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
1180 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
1181 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1182 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1183
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1184 <!-- Second group -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1185 <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
1186 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
1187 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
1188 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1189 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1190 <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
1191 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
1192 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
1193 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1194 />
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1195 <expand macro="verify_hub_structure" test="two_groups_multiple_tracks" />
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1196 </output>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1197 </test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1198
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1199 <!-- 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
1200 <test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1201 <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
1202 <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
1203 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1204 <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
1205 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1206 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1207 <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
1208 <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
1209 <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
1210 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1211 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1212 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1213 <output name="output" file="default_color/default_color_trackhub.html">
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1214 <expand macro="verify_hub_structure" test="default_color" />
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1215 <!-- Verify trackDb.txt contains the color 0,0,0 -->
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1216 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1217 <assert_contents>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1218 <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
1219 </assert_contents>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1220 </extra_files>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1221
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1222 <!-- 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
1223 </output>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1224 </test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1225
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1226 <!-- 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
1227 <test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1228 <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
1229 <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
1230 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1231 <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
1232 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1233 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1234 <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
1235 <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
1236 <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
1237 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1238 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1239 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1240 <output name="output" file="changed_color/changed_color_trackhub.html">
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1241 <expand macro="verify_hub_structure" test="changed_color" />
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1242 <!-- Verify trackDb.txt contains the color 128,100,162 -->
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1243 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1244 <assert_contents>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1245 <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
1246 </assert_contents>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1247 </extra_files>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1248
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1249 <!-- 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
1250 </output>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1251 </test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1252
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1253 <!-- 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
1254 <test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1255 <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
1256 <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
1257 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1258 <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
1259 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1260 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1261 <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
1262 <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
1263 <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
1264 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1265 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1266 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1267 <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
1268 <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
1269 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
1270 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
1271 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1272 />
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1273 <expand macro="verify_hub_structure" test="stringtie_chromosome_end_coordinates" />
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1274
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1275 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1276 </output>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1277 </test>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1278
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1279 <!-- Test default label in a track -->
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1280 <test>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1281 <param name="genome_name" value="Dbia3"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1282 <param name="fasta_file" value="common/dbia3.fa"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1283 <repeat name="group">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1284 <param name="group_name" value="Default group"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1285 <repeat name="format">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1286 <conditional name="formatChoice">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1287 <param name="format_select" value="bam"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1288 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1289 <param name="track_color" value="#000000"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1290 </conditional>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1291 </repeat>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1292 </repeat>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1293 <output name="output" file="default_color/default_color_trackhub.html">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1294 <expand macro="verify_hub_structure" test="default_color" />
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1295 <!-- Verify trackDb.txt contains default label -->
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1296 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1297 <assert_contents>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1298 <has_text text="longLabel HISAT2 Accepted Hits.bam"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1299 </assert_contents>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1300 </extra_files>
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1301
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1302 <!-- 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
1303 </output>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1304 </test>
2
4ced8f116509 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
yating-l
parents: 0
diff changeset
1305
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1306 <!-- Test customized label in a track -->
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1307 <test>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1308 <param name="genome_name" value="Dbia3"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1309 <param name="fasta_file" value="common/dbia3.fa"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1310 <repeat name="group">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1311 <param name="group_name" value="Default group"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1312 <repeat name="format">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1313 <conditional name="formatChoice">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1314 <param name="format_select" value="bam"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1315 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1316 <param name="longLabel" value="HISAT sequence alignment" />
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1317 <param name="track_color" value="#000000"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1318 </conditional>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1319 </repeat>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1320 </repeat>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1321 <output name="output" file="changed_label/changed_label_trackhub.html">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1322 <expand macro="verify_hub_structure" test="changed_label" />
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1323 <!-- Verify trackDb.txt contains the customized label -->
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1324 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1325 <assert_contents>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1326 <has_text text="longLabel HISAT sequence alignment"/>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1327 </assert_contents>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1328 </extra_files>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1329
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1330 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1331 </output>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1332 </test>
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1333
84
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1334 <!-- Test TrixIndex for Blat alignment track -->
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1335 <test>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1336 <param name="genome_name" value="Dbia3"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1337 <param name="fasta_file" value="common/dbia3.fa"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1338 <repeat name="group">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1339 <param name="group_name" value="Default group"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1340 <repeat name="format">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1341 <conditional name="formatChoice">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1342 <param name="format_select" value="bed" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1343 <conditional name="bedChoice">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1344 <param name="bed_select" value="bed_blat_alignment_option"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1345 <param name="BED_blat_alignment" ftype="bed" value="bed_blat_alignment/inputs/BLAT_alignment_bigpsl"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1346 <param name="longLabel" value="BLAT alignment" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1347 <param name="track_color" value="#000000"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1348 <param name="database" value="NCBI" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1349 <conditional name="add_trix_index">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1350 <param name="add_trix_index_selector" value="yes" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1351 <param name="trix_index" value="trix_index_files/blat_out.ix,trix_index_files/blat_out.ixx" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1352 </conditional>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1353 </conditional>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1354 </conditional>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1355 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1356 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1357 <param name="debug_mode" value="true" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1358 <output name="output" file="trix_index_files/blat_alignment_trackhub.html">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1359 <extra_files type="file"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1360 name="myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1361 value="bed_blat_alignment/myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1362 compare="sim_size"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1363 />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1364 <expand macro="verify_hub_structure" test="bed_blat_alignment" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1365 <!-- check additional trackDb settings for BLAT -->
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1366 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1367 <assert_contents>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1368 <has_text text="searchIndex"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1369 <has_text text="searchTrix"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1370 <has_text text="url"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1371 <has_text text="urlLabel"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1372 <has_text text="iframeUrl"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1373 <has_text text="iframeOptions"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1374 </assert_contents>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1375 </extra_files>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1376 <!-- check Trix index directory -->
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1377 <extra_files type="file" name="myHub/Dbia3/trix/BLAT_alignment_bigpsl.bb.ix"
85
a65e52152476 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 84
diff changeset
1378 value="trix_index_files/blat_out.ix" />
84
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1379 <extra_files type="file" name="myHub/Dbia3/trix/BLAT_alignment_bigpsl.bb.ixx"
85
a65e52152476 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 84
diff changeset
1380 value="trix_index_files/blat_out.ixx" />
84
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1381 </output>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1382 </test>
66
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
yating-l
parents: 63
diff changeset
1383
84
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1384 <!-- Test TrixIndex for BLAST Alignment -->
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1385 <test>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1386 <param name="genome_name" value="Dbia3"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1387 <param name="fasta_file" value="common/dbia3.fa"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1388 <repeat name="group">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1389 <param name="group_name" value="Default group"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1390 <repeat name="format">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1391 <conditional name="formatChoice">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1392 <param name="format_select" value="bed" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1393 <conditional name="bedChoice">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1394 <param name="bed_select" value="bed_blast_alignment_option"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1395 <param name="BED_blast_alignment" ftype="bed" value="bed_blast_alignment/inputs/BLAST_alignment_bigpsl"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1396 <param name="longLabel" value="BLAST alignment" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1397 <param name="track_color" value="#000000"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1398 <param name="database" value="NCBI" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1399 <conditional name="add_trix_index">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1400 <param name="add_trix_index_selector" value="yes" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1401 <param name="trix_index" value="trix_index_files/blast_out.ix,trix_index_files/blast_out.ixx" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1402 </conditional>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1403 </conditional>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1404 </conditional>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1405 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1406 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1407 <param name="debug_mode" value="true" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1408 <output name="output" file="trix_index_files/blast_alignment_trackhub.html">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1409 <extra_files type="file"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1410 name="myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1411 value="bed_blast_alignment/myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1412 compare="sim_size"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1413 />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1414 <expand macro="verify_hub_structure" test="bed_blast_alignment" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1415 <!-- check additional trackDb settings for BLAST -->
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1416 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1417 <assert_contents>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1418 <has_text text="searchIndex"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1419 <has_text text="searchTrix"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1420 <has_text text="url"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1421 <has_text text="urlLabel"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1422 <has_text text="iframeUrl"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1423 <has_text text="iframeOptions"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1424 </assert_contents>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1425 </extra_files>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1426 <!-- check Trix index directory -->
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1427 <extra_files type="file" name="myHub/Dbia3/trix/BLAST_alignment_bigpsl.bb.ix"
85
a65e52152476 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 84
diff changeset
1428 value="trix_index_files/blast_out.ix" />
84
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1429 <extra_files type="file" name="myHub/Dbia3/trix/BLAST_alignment_bigpsl.bb.ixx"
85
a65e52152476 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 84
diff changeset
1430 value="trix_index_files/blast_out.ixx" />
84
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1431 </output>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1432 </test>
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1433
84
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1434 <!-- Test TrixIndex for BigBed -->
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1435 <test>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1436 <param name="genome_name" value="Dbia3"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1437 <param name="fasta_file" value="common/dbia3.fa"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1438 <repeat name="group">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1439 <param name="group_name" value="Default group"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1440 <repeat name="format">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1441 <conditional name="formatChoice">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1442 <param name="format_select" value="bigbed"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1443 <param name="BIGBED" value="big_bed/inputs/BLAT_alignment_bigbed" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1444 <param name="longLabel" value="bigBed" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1445 <param name="track_color" value="#000000"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1446 <conditional name="add_trix_index">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1447 <param name="add_trix_index_selector" value="yes" />
85
a65e52152476 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 84
diff changeset
1448 <param name="trix_index" value="trix_index_files/blat_out.ix,trix_index_files/blat_out.ixx" />
84
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1449 <param name="trix_id" value="name" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1450 </conditional>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1451 </conditional>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1452 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1453 </repeat>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1454 <param name="debug_mode" value="true" />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1455 <output name="output" file="trix_index_files/bigbed_trackhub.html">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1456 <extra_files type="file"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1457 name="myHub/Dbia3/tracks/BLAT_alignment_bigbed.bigbed"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1458 value="big_bed/myHub/Dbia3/tracks/BLAT_alignment_bigbed.bigbed"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1459 compare="sim_size"
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1460 />
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1461 <expand macro="verify_hub_structure" test="big_bed">
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1462 <has_text text="searchIndex"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1463 <has_text text="searchTrix"/>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1464 </expand>
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1465
84
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1466 <!-- check Trix index directory -->
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1467 <extra_files type="file" name="myHub/Dbia3/trix/BLAT_alignment_bigbed.bigbed.ix"
85
a65e52152476 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 84
diff changeset
1468 value="trix_index_files/blat_out.ix" />
84
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1469 <extra_files type="file" name="myHub/Dbia3/trix/BLAT_alignment_bigbed.bigbed.ixx"
85
a65e52152476 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents: 84
diff changeset
1470 value="trix_index_files/blat_out.ixx" />
84
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1471 </output>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1472 </test>
cb62314a6297 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
yating-l
parents: 83
diff changeset
1473
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1474 </tests>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1475
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1476 <help>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1477 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
1478 Assembly Hub visualization.
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1479 </help>
52
c66803bff0cc planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit adc1ac50269e02570e7ce12c732637bdd3f9a547-dirty
yating-l
parents: 51
diff changeset
1480
c66803bff0cc planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit adc1ac50269e02570e7ce12c732637bdd3f9a547-dirty
yating-l
parents: 51
diff changeset
1481 <citations>
c66803bff0cc planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit adc1ac50269e02570e7ce12c732637bdd3f9a547-dirty
yating-l
parents: 51
diff changeset
1482 <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
1483 </citations>
0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff changeset
1484 </tool>