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comparison getDensityPlots.xml @ 1:413f3e610295 draft default tip

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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"
author azomics
date Thu, 16 Jul 2020 08:00:52 -0400
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0:164cd5384f1d 1:413f3e610295
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>