Mercurial > repos > azomics > flowviz_density_plots

comparison FCSflowViz.xml @ 0:23c0af6be9a7 draft default tip

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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
author azomics
date Mon, 22 Jun 2020 20:48:47 -0400
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1 <tool id="flowviz_density_plots" name="Generate stacked density plots" version="1.0+galaxy0">
2 <description>for a set of FCS files</description>
3 <requirements>
4 <requirement type="package" version="1.40.0">bioconductor-flowviz</requirement>
5 </requirements>
6 <stdio>
7 <exit_code range="10" level="fatal" description="Please provide a comma separated list of channels to plot" />
8 <exit_code range="11" level="fatal" description="Please provide numeric values for the list of channels to plot" />
9 <exit_code range="12" level="fatal" description="The set of FCS files must have the same set of channels" />
10 </stdio>
11 <command><![CDATA[
12 Rscript $__tool_directory__/FCSflowViz.R '${channels}' '${output}' '${outformat}'
13 #for $f in $input
14 '${f}' '${f.name}'
15 #end for
16 ]]>
17 </command>
18 <inputs>
19 <param format="fcs" name="input" type="data_collection" collection_type="list" label="FCS files Collection"/>
20 <param name="channels" type="text" label="Markers to plot:" value="i.e.:1,3,4" help="By default, will plot all channels."/>
21 <param name="outformat" type="select" label="Output Format" help="PDF will be larger files that may take some time to load.">
22 <option value="PNG">PNG</option>
23 <option value="PDF">PDF</option>
24 </param>
25 </inputs>
26 <outputs>
27 <data format="png" name="output" label="Stacked Density Plots from ${input.name} in ${outformat}">
28 <change_format>
29 <when input="outformat" value="PDF" format="pdf" />
30 </change_format>
31 </data>
32 </outputs>
33 <tests>
34 <test>
35 <param name="input">
36 <collection type="list">
37 <element name="input1.fcs" value="input1.fcs"/>
38 <element name="input2.fcs" value="input2.fcs"/>
39 <element name="input3.fcs" value="input3.fcs"/>
40 </collection>
41 </param>
42 <param name="channels" value="1,3"/>
43 <param name="outformat" value="PDF"/>
44 <output name="output" file="graph.pdf" compare="sim_size"/>
45 </test>
46 <test>
47 <param name="input">
48 <collection type="list">
49 <element name="input1.fcs" value="input1.fcs"/>
50 <element name="input2.fcs" value="input2.fcs"/>
51 <element name="input3.fcs" value="input3.fcs"/>
52 </collection>
53 </param>
54 <param name="channels" value="i.e.:1,3,4"/>
55 <param name="outformat" value="PNG"/>
56 <output name="output" file="graph.png" compare="sim_size"/>
57 </test>
58 </tests>
59 <help><![CDATA[
60 FlowViz stacked 1D density plots
61 --------------------------------
62
63 This tool generates stacked 1D density plots using flowViz.
64
65 **Input files**
66
67 This tool takes a collection of valid FCS files as input.
68
69 .. class:: warningmark
70
71 Each FCS file in the input data collection should have the SAME set of channels.
72
73 **Output files**
74
75 This tool generates stacked 1D density plots for each channel. A pdf file can optionally be generated.
76
77 class:: warningmark
78
79 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.
80
81 -----
82
83 **Example**
84
85 *Output*:
86
87 .. image:: ./static/images/flowtools/flowviz.png
88
89 -----
90
91 **flowViz reference**
92
93 Ellis B, Gentleman R, Hahne F, Le Meur N, Sarkar D and Jiang M (2017). flowViz: Visualization for flow cytometry. R package version 1.40.0.
94
95 ]]>
96 </help>
97 <citations>
98 <citation type="doi">10.1186/1471-2105-10-106</citation>
99 </citations>
100 </tool>