Mercurial > repos > immport-devteam > extract_pop

comparison extractpop.xml @ 1:4f28ee74079b draft default tip

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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_pop commit 117c0e4a5c00dfd2e190359badf77d5643fccefa"
author azomics
date Fri, 24 Jul 2020 19:24:49 -0400
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0:21b2dc3934ed 1:4f28ee74079b
1 <tool id="extract_pop" name="Extract populations" version="1.0+galaxy0" profile="18.01">
2 <description>of interest from FLOCK or Cross Sample output</description>
3 <requirements>
4 <requirement type="package" version="1.0.5">pandas</requirement>
5 </requirements>
6 <stdio>
7 <exit_code range="1"/>
8 <exit_code range="2" level="fatal" description="Please provide a comma separated list of populations to extract." />
9 <exit_code range="3" level="fatal" description="The populations to extract must be integers (i.e,: 1,2,4.)" />
10 <exit_code range="4:"/>
11 </stdio>
12 <command><![CDATA[
13 python '$__tool_directory__/extractpop.py' -i '${input}' -o '${output}' -p '${population}' -m '${method}'
14 ]]>
15 </command>
16 <inputs>
17 <param format="flowclr" name="input" type="data" label="Source file"/>
18 <param name="population" type="text" label="Populations:" value="i.e.:2,3,11,25"/>
19 <param name="method" type="select" label="What would you like to do?">
20 <option value="selected">Keep only these populations.</option>
21 <option value="removed">Remove these populations.</option>
22 </param>
23 </inputs>
24 <outputs>
25 <data format="flowtext" name="output" label="Populations ${population} ${method} from ${input.name}"/>
26 </outputs>
27 <tests>
28 <test>
29 <param name="input" value="input.txt"/>
30 <param name="population" value="2,4"/>
31 <param name="method" value="selected"/>
32 <output name="output" file="output.flowtext"/>
33 </test>
34 </tests>
35 <help><![CDATA[
36 This tool extracts events from given populations from FLOCK or Cross Sample outputs.
37
38 -----
39
40 **Input**
41
42 FLOCK or Cross Sample output - a table of the fluorescence intensities for each event and the population associated with each.
43
44 **Output**
45
46 The input file filtered for selected populations.
47
48 -----
49
50 **Example 1**
51
52 *Input* - fluorescence intensities per marker and population ID per event::
53
54 Marker1 Marker2 Marker3 Population
55 34 45 12 1
56 33 65 10 5
57 19 62 98 2
58 12 36 58 1
59
60 *Populations selected:* 2
61
62 *Method:* Keep only the selected populations
63
64 *Output* - fluorescence intensities per marker and population ID per event::
65
66 Marker1 Marker2 Marker3 Population
67 19 62 98 2
68
69 **Example 2**
70
71 *Input* - fluorescence intensities per marker and population ID per event::
72
73 Marker1 Marker2 Marker3 Population
74 34 45 12 1
75 33 65 10 5
76 19 62 98 2
77 12 36 58 1
78
79 *Populations selected:* 2
80
81 *Method:* Remove the selected populations
82
83 *Output* - fluorescence intensities per marker and population ID per event::
84
85 Marker1 Marker2 Marker3 Population
86 34 45 12 1
87 33 65 10 5
88 12 36 58 1
89
90 ]]>
91 </help>
92 </tool>