Mercurial > repos > immport-devteam > fcs_scatterplot
comparison getDensityPlots.xml @ 1:413f3e610295 draft default tip
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
author | azomics |
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date | Thu, 16 Jul 2020 08:00:52 -0400 |
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0:164cd5384f1d | 1:413f3e610295 |
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1 <tool id="gen_density_plots" name="Generate scatter plots" version="1.0+galaxy0"> | |
2 <description>for any given markers in FCS file</description> | |
3 <requirements> | |
4 <requirement type="package" version="1.10.0">bioconductor-flowdensity</requirement> | |
5 </requirements> | |
6 <stdio> | |
7 <exit_code range="1:9" level="fatal" /> | |
8 <exit_code range="10" level="fatal" description="Please provide a comma separated list of channels to plot" /> | |
9 <exit_code range="11" level="fatal" description="Please provide numeric values for the list of channels to plot" /> | |
10 <exit_code range="12" level="fatal" description="Please provide more than one channel to plot" /> | |
11 <exit_code range="13:" level="fatal" /> | |
12 </stdio> | |
13 <command><![CDATA[ | |
14 Rscript --slave --vanilla '$__tool_directory__/getDensityPlots.R' '${input}' '${channels}' '${output}' '${outformat}' | |
15 ]]> | |
16 </command> | |
17 <inputs> | |
18 <param format="fcs" name="input" type="data" label="FCS file"/> | |
19 <param name="channels" type="text" label="Markers to plot:" value="i.e.:1,3,4" help="By default, will plot FSC vs SSC if the channels are found."/> | |
20 <param name="outformat" type="select" label="Output Format" help="PDF will be larger files that may take some time to load."> | |
21 <option value="PNG">PNG</option> | |
22 <option value="PDF">PDF</option> | |
23 </param> | |
24 </inputs> | |
25 <outputs> | |
26 <data format="png" name="output" label="Scatter Plots of ${channels} from ${input.name} in ${outformat}"> | |
27 <change_format> | |
28 <when input="outformat" value="PDF" format="pdf" /> | |
29 </change_format> | |
30 </data> | |
31 </outputs> | |
32 <tests> | |
33 <test> | |
34 <param name="input" value="testfcs1.fcs"/> | |
35 <param name="channels" value="1,3"/> | |
36 <param name="outformat" value="PDF"/> | |
37 <output name="output" file="graph.pdf" compare="sim_size" delta="1000000"/> | |
38 </test> | |
39 <test> | |
40 <param name="input" value="testfcs1.fcs"/> | |
41 <param name="channels" value="i.e.:1,3,4"/> | |
42 <param name="outformat" value="PNG"/> | |
43 <output name="output" file="graph2.png" compare="sim_size" delta="1000000"/> | |
44 </test> | |
45 </tests> | |
46 <help><![CDATA[ | |
47 This tool allows generation of density scatter plots using flowDensity. | |
48 | |
49 ----- | |
50 | |
51 **Input files** | |
52 | |
53 This tool takes valid FCS files as input. | |
54 | |
55 **Output files** | |
56 | |
57 This tool generates a scatter plot for each marker combination in a single png file. A pdf file can optionally be generated. | |
58 | |
59 class:: warningmark | |
60 | |
61 PDF are larger files that may take some time to load. It might be faster to download the PDF output once generated to open it locally. | |
62 | |
63 ----- | |
64 | |
65 **Example** | |
66 | |
67 *Output*: | |
68 | |
69 .. image:: ./static/images/flowtools/densityplots.png | |
70 ]]> | |
71 </help> | |
72 <citations> | |
73 <citation type="doi">10.1093/bioinformatics/btu677</citation> | |
74 <citation type="doi">10.1186/1471-2105-10-106</citation> | |
75 </citations> | |
76 </tool> |