Mercurial > repos > immport-devteam > flowcl
comparison getOntology.xml @ 1:f70f75e89890 draft default tip
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowcl commit d59d95d2bc6a64eb5c37b8291a7c314754c2067f"
author | azomics |
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date | Thu, 23 Jul 2020 08:50:18 -0400 |
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0:fb0ee82f686d | 1:f70f75e89890 |
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1 <tool id="get_cell_ontology" name="Explore cell ontology" version="1.0+galaxy0" profile="18.01"> | |
2 <description>given a phenotype using flowCL</description> | |
3 <requirements> | |
4 <requirement type="package" version="2.11.2">jinja2</requirement> | |
5 <requirement type="package" version="1.26.0">bioconductor-flowcl</requirement> | |
6 </requirements> | |
7 <stdio> | |
8 <exit_code range="1" level="fatal"/> | |
9 <exit_code range="2" level="fatal" description="There was a problem running flowCL. You might want to check your marker names - See stderr for more details." /> | |
10 <exit_code range="3:" level="fatal" description="See stderr for more details." /> | |
11 </stdio> | |
12 <command><![CDATA[ | |
13 python '$__tool_directory__/getOntology.py' -o '${html_file}' -d '${html_file.files_path}' -t '$__tool_directory__' -m '${marker1}' -y '${type1}' | |
14 #for $mrkrs in $Markers | |
15 -m '${mrkrs.markername}' | |
16 -y '${mrkrs.markertype}' | |
17 #end for | |
18 ]]> | |
19 </command> | |
20 <inputs> | |
21 <param name="marker1" type="text" label="First marker"/> | |
22 <param name="type1" type="select" label="First marker type"> | |
23 <option value="+">+</option> | |
24 <option value="-">-</option> | |
25 <option value="lo">lo</option> | |
26 <option value="lo">low</option> | |
27 <option value="lo">dim</option> | |
28 <option value="lo">--</option> | |
29 <option value="hi">hi</option> | |
30 <option value="hi">high</option> | |
31 <option value="hi">bri</option> | |
32 <option value="hi">bright</option> | |
33 <option value="hi">++</option> | |
34 </param> | |
35 <repeat name="Markers" title="Marker"> | |
36 <param name="markername" type="text" label="Add marker"/> | |
37 <param name="markertype" type="select" label="Marker type"> | |
38 <option value="+">+</option> | |
39 <option value="-">-</option> | |
40 <option value="lo">lo</option> | |
41 <option value="lo">low</option> | |
42 <option value="lo">dim</option> | |
43 <option value="lo">--</option> | |
44 <option value="hi">hi</option> | |
45 <option value="hi">high</option> | |
46 <option value="hi">bri</option> | |
47 <option value="hi">bright</option> | |
48 <option value="hi">++</option> | |
49 </param> | |
50 </repeat> | |
51 </inputs> | |
52 <outputs> | |
53 <data format="html" name="html_file" label="flowCL run"/> | |
54 </outputs> | |
55 <tests> | |
56 <test> | |
57 <param name="marker1" value="CD4"/> | |
58 <param name="type1" value="+"/> | |
59 <output name="html_file" file="out.html" compare="sim_size"> | |
60 <extra_files type="file" name="flowCL_res.pdf" value="flowCL_res.pdf" compare="sim_size"/> | |
61 <extra_files type="file" name="flowCL_run_summary.txt" value="flowCL_run_summary.txt" compare="sim_size"/> | |
62 <extra_files type="file" name="flowCL_table.txt" value="flowCL_table.txt" compare="sim_size"/> | |
63 </output> | |
64 </test> | |
65 </tests> | |
66 <help><![CDATA[ | |
67 This tool uses flowCL to find the most likely match to a given set a markers. | |
68 | |
69 ----- | |
70 | |
71 **Input** | |
72 | |
73 Type in the marker names and select the expression level in the drop-down menu. Marker names need to be in the Cell Ontology for this to work. | |
74 | |
75 **Output** | |
76 | |
77 A summary of the ouptut of flowCL is captured in a txt file. For more details, please refer to the flowCL documentation. | |
78 | |
79 **Graphical output** | |
80 | |
81 FlowCL generates a plot for the most likely matches to ontology. | |
82 | |
83 ----- | |
84 | |
85 **Example** | |
86 | |
87 *Output summary* | |
88 | |
89 The CL terms hyperlink to their representation in the Immport Cell Ontology browser. | |
90 | |
91 .. image:: ./static/images/flowtools/flowcl_summary.png | |
92 | |
93 *Graphical output* | |
94 | |
95 .. image:: ./static/images/flowtools/flowcl_graph.png | |
96 | |
97 ]]> | |
98 </help> | |
99 <citations> | |
100 <citation type="doi">10.1093/bioinformatics/btu807</citation> | |
101 </citations> | |
102 </tool> |