Mercurial > repos > immport-devteam > collapse_pop

comparison collapse_pops.xml @ 1:a3ae90eb1232 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/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/collapse_pop commit 1e75b0df5680c0cdd8b2b3e5d4c1f8077b430944"
author azomics
date Mon, 22 Jun 2020 16:34:35 -0400
parents
children
comparison
equal deleted inserted replaced
0:59f859ea3122 1:a3ae90eb1232
1 <tool id="collapse_populations" name="Collapse populations" version="1.0+galaxy1">
2 <description>from FLOCK or Cross Sample analysis</description>
3 <requirements>
4 <requirement type="package" version="0.17.1">pandas</requirement>
5 </requirements>
6 <stdio>
7 <exit_code range="2" level="warning" description="The color code only allows populations between 1 and 40." />
8 <exit_code range="3" level="warning" description="The same population to collapse into is being used several times." />
9 <exit_code range="4" level="fatal" description="Please provide a comma separated list of populations to collapse." />
10 <exit_code range="5" level="warning" description="The color code only allows populations between 1 and 40, and the same population to collapse into is being used several times." />
11 <exit_code range="6" level="fatal" description="The populations must be integers (i.e,: 1,2,4.)" />
12 <exit_code range="7" level="fatal" description="The same population is being collapsed into 2 different populations." />
13 </stdio>
14 <command><![CDATA[
15 python '$__tool_directory__/collapse_pops.py' -o '${output}' -i '${input}' -p '${population}' -c '${collapse}'
16 #for $repeats in $repeat_option
17 -p '${repeats.population}'
18 -c '${repeats.collapse}'
19 #end for
20 ]]>
21 </command>
22 <inputs>
23 <param format="flowclr" name="input" type="data" label="Source file"/>
24 <param name="population" type="text" label="Collapse the following populations:" value="i.e.:2,3,11,25"/>
25 <param name="collapse" type="text" label="Into population:" value="i.e.:4"/>
26 <repeat name="repeat_option" title="more populations to manipulate:">
27 <param name="population" type="text" label="Collapse the following populations:" value="i.e.:2,3,11,25"/>
28 <param name="collapse" type="text" label="Into population:" value="i.e.:4"/>
29 </repeat>
30 </inputs>
31 <outputs>
32 <data format="flowclr" name="output" label="${input.name} with renamed populations"/>
33 </outputs>
34 <tests>
35 <test>
36 <param name="input" value="input.flowclr"/>
37 <param name="population" value="2,3,4"/>
38 <param name="collapse" value="1"/>
39 <output name="output" file="output.flowclr"/>
40 </test>
41 </tests>
42 <help><![CDATA[
43 This tool collapses several populations into one.
44
45 -----
46
47 .. class:: warningmark
48
49 Tip: You can use this tool to assign specific colors to your populations in the FLOCK and Cross Sample overview tools. The color scheme we use is the following:
50
51 .. image:: ./static/images/flowtools/liz_colorcode.png
52
53 -----
54
55 **Input**
56
57 FLOCK or Cross Sample output - a table of the fluorescence intensities for each event and the population associated with each.
58
59 **Output**
60
61 The input file with selected populations replaced by the indicated population.
62
63 -----
64
65 **Example**
66
67 *Input* - fluorescence intensities per marker and population ID per event::
68
69 Marker1 Marker2 Marker3 ... Population
70 34 45 12 ... 1
71 33 65 10 ... 5
72 19 62 98 ... 2
73 12 36 58 ... 1
74 ... ... ... ... ...
75
76 *Populations selected:* 2, 5
77
78 *Collapse into population:* 3
79
80 *Output* - fluorescence intensities per marker and population ID per event::
81
82 Marker1 Marker2 Marker3 ... Population
83 34 45 12 ... 1
84 33 65 10 ... 3
85 19 62 98 ... 3
86 12 36 58 ... 1
87 ... ... ... ... ...
88
89 ]]>
90 </help>
91 </tool>