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comparison FCS1Dplotggcyto.xml @ 0:b73fc4860906 draft default tip

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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
author azomics
date Mon, 22 Jun 2020 17:53:11 -0400
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-1:000000000000 0:b73fc4860906
1 <tool id="ggcyto_1d_density_plots" name="Generate 1D density plots" version="1.1+galaxy0">
2 <description>for FCS file</description>
3 <requirements>
4 <requirement type="package" version="1.14.0">bioconductor-ggcyto</requirement>
5 <!-- to fix https://github.com/RGLab/ggcyto/issues/64 and not able to install ggcyto 1.16.0-->
6 <requirement type="package" version="3.2.1">r-ggplot2</requirement>
7 </requirements>
8 <stdio>
9 <exit_code range="1:" />
10 </stdio>
11 <command><![CDATA[
12 Rscript $__tool_directory__/FCS1Dplotggcyto.R '${input}' '${output}' $outformat '${transform.trans_method}'
13 #if $transform.trans_method == "arcsinh"
14 $transform.scaling_factor
15 #else if $transform.trans_method == "logicle"
16 $transform.w $transform.t $transform.m
17 #end if
18 ]]>
19 </command>
20 <inputs>
21 <param format="fcs" name="input" type="data" label="FCS file"/>
22 <conditional name="transform">
23 <param name="trans_method" type="select" label="Apply transformation to plot:" help="by default, no transformation">
24 <option value="None">no transformation please.</option>
25 <option value="logicle">logicle</option>
26 <option value="arcsinh">arcsinh</option>
27 </param>
28 <when value="arcsinh">
29 <param name="scaling_factor" type="integer" min="1" max="200" value="150" label="Scaling factor b for arcsinh transform:" help="The default value is 150 for standard FCM data. The recommended value for cyTOF data is 5.">
30 </param>
31 </when>
32 <when value="logicle">
33 <param name="w" type="float" value="0.5" label="Linearization width w for logicle transform:" help="w should be positive and determines the slope of transformation at zero. The default value is 0.5.">
34 </param>
35 <param name="t" type="integer" value="262144" label="Top of the scale data value t for logicle transform:" help=" t should be greater than zero. Recommended values are 10000 for common 4 decade data or 262144 for a 18 bit data range. The default value is 262144.">
36 </param>
37 <param name="m" type="float" value="4.5" label="Full width of the transformed display m for logicle transform:" help="m is expressed in asymptotic decades and should be positive. The default value is 4.5 .">
38 </param>
39 </when>
40 </conditional>
41 <param name="outformat" type="select" label="Output Format" help="PDF will be larger files that may take some time to load.">
42 <option value="PNG">PNG</option>
43 <option value="PDF">PDF</option>
44 </param>
45 </inputs>
46 <outputs>
47 <data format="png" name="output" label="1D Density Plots for ${input.name} with ${transform.trans_method} in ${outformat}">
48 <change_format>
49 <when input="outformat" value="PDF" format="pdf" />
50 </change_format>
51 </data>
52 </outputs>
53 <tests>
54 <test>
55 <param name="input" value="testfcs1.fcs"/>
56 <param name="outformat" value="PDF"/>
57 <param name="trans_method" value="None"/>
58 <output name="output" file="graph.pdf" compare="sim_size"/>
59 </test>
60 <test>
61 <param name="input" value="testfcs1.fcs"/>
62 <param name="outformat" value="PNG"/>
63 <param name="trans_method" value="logicle"/>
64 <param name="w" value="0.4"/>
65 <param name="m" value="4.5"/>
66 <param name="t" value="10000"/>
67 <output name="output" file="graph1.png" compare="sim_size"/>
68 </test>
69 <test>
70 <param name="input" value="testfcs1.fcs"/>
71 <param name="outformat" value="PNG"/>
72 <param name="trans_method" value="arcsinh"/>
73 <param name="scaling_factor" value="150"/>
74 <output name="output" file="graph2.png" compare="sim_size"/>
75 </test>
76 </tests>
77 <help><![CDATA[
78 Scatterplots of fcs sample
79 -------------------
80
81 This tool allows generation of density scatter plots using ggcyto.
82
83 **Input files**
84
85 This tool takes valid FCS files as input.
86
87 **Output files**
88
89 This tool generates a series of 1D density plot using ggcyto and produces a png file. A pdf file can optionally be generated.
90
91 class:: warningmark
92
93 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.
94
95 -----
96
97 **Transformation**
98
99 This tools currently supports 2 transformation algorithms: arcsinh and logicle, implemented using flowCore. Transformation applied are color-coded: black is no transformation, blue is arcinsh, and green is logicle.
100
101 -----
102
103 **Example**
104
105 *Output*:
106
107 .. image:: ./static/images/flowtools/testoutputggcyto.png
108
109 -----
110
111 **ggcyto reference**
112 Jiang M (2015). ggcyto: Visualize Cytometry data with ggplot. R package version 1.4.0, https://github.com/RGLab/ggcyto/issues.
113
114 ]]>
115 </help>
116 <citations>
117 <citation type="doi">10.1186/1471-2105-10-106</citation>
118 </citations>
119 </tool>