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comparison getOntology.xml @ 1:f70f75e89890 draft default tip

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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowcl commit d59d95d2bc6a64eb5c37b8291a7c314754c2067f"
author azomics
date Thu, 23 Jul 2020 08:50:18 -0400
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0:fb0ee82f686d 1:f70f75e89890
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>