Mercurial > repos > jkanche > epiviz

annotate epiviz_export.xml @ 0:78367907d256 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
author jkanche
date Fri, 20 Sep 2019 07:23:50 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
1 <tool id="epiviz_export" name="Interactively visualize genomic data with Epiviz" version="0.1.0" python_template_version="3.5">
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
2 <requirements>
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
3 </requirements>
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
4 <command detect_errors="exit_code"><![CDATA[
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
5 python $script_file
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
6 ]]></command>
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
7 <configfiles>
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
8 <configfile name="script_file">
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
9 import os
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
10 import sys
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
11 import json
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
12 file_location = []
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
13 file_type = []
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
14 file_annotations = []
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
15 #for $i, $s in enumerate($files)
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
16 tloc = '${s.input}'
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
17 tlocs = tloc.split("/")
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
18 file_location.append("/data/" + tlocs[len(tlocs)-1])
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
19 file_type.append('${s.format}')
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
20 tanno = '${s.fileanno}'
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
21 print(tanno)
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
22 tanno = tanno.split(",")
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
23 print(tanno)
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
24 ttanno = {}
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
25 for i in tanno:
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
26 ti = i.split(":")
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
27 ttanno[ti[0]] = ti[1]
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
28
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
29 file_annotations.append(ttanno)
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
30 #end for
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
31 epiviz_json = []
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
32 for i in range(0,len(file_location)):
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
33 fdatatype = "bp" if file_type[i] == "BigWig" else "annotation"
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
34 epiviz_json.append(
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
35 {
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
36 "url": file_location[i],
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
37 "file_type": file_type[i],
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
38 "datatype": fdatatype,
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
39 "name": file_location[i],
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
40 "id": file_location[i],
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
41 "annotation": file_annotations[i],
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
42 "metadata": []
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
43 }
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
44 )
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
45 print epiviz_json
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
46 fout = open('$output', "w")
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
47 json.dump(epiviz_json, fout)
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
48 fout.close()
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
49 </configfile>
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
50 </configfiles>
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
51 <inputs>
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
52 <repeat name="files" title="Add File">
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
53 <param type="data" name="input" format="bigbed,bigwig"/>
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
54 <param name="format" type="select" label="Data Format">
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
55 <option value="BigWig" selected="true">BigWig</option>
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
56 <option value="BigBed">BigBed</option>
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
57 <option value="tbx">tbx</option>
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
58 </param>
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
59 <param type ="text" name="fileanno" format="json" />
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
60 </repeat>
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
61 </inputs>
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
62 <outputs>
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
63 <data name="output" format="json" from_work_dir="output.json" />
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
64 </outputs>
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
65 <tests>
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
66 <test>
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
67 <param name="input" value="/test"/>
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
68 <param name="format" value="bigbed"/>
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
69 <param name="fileanno" value="annotation"/>
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
70 <output name="output">
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
71 <assert_contents>
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
72 <has_line line="datatype" />
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
73 </assert_contents>
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
74 </output>
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
75 </test>
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
76 </tests>
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
77 <help><![CDATA[
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
78 Usage: Choose files to interactively visualize with epiviz.
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
79 ]]></help>
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
80 <citations>
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
81 <citation type="bibtex">
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
82 @misc{epiviz,
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
83 author = {epiviz},
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
84 year = {2019},
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
85 title = {epiviz},
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
86 publisher = {GitHub},
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
87 journal = {GitHub repository},
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
88 url = {https://github.com/epiviz/epivizGalaxyTool},
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
89 }</citation>
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
90 </citations>
78367907d256 planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30
jkanche
parents:
diff changeset
91 </tool>