Mercurial > repos > immport-devteam > flowtext_scatterplot

comparison getDensityPlots_text.xml @ 1:754d511df1a3 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/flowtext_scatterplot commit 2944aa6b74efcdb8d5cbf31abf27b352dcad9ac9"
author azomics
date Tue, 14 Jul 2020 09:40:13 -0400
parents
children
comparison
equal deleted inserted replaced
0:cc2266d3e611 1:754d511df1a3
1 <tool id="gen_density_plots_txt" name="Generate scatter plots" version="1.1+galaxy0" profile="18.01">
2 <description>for any given markers in a txt-converted FCS file</description>
3 <requirements>
4 <requirement type="package" version="3.3.2">r-ggplot2</requirement>
5 <requirement type="package" version="2.23_17">r-kernsmooth</requirement>
6 </requirements>
7 <stdio>
8 <exit_code range="1:9" level="fatal" />
9 <exit_code range="10" level="fatal" description="Please provide a comma separated list of channels to plot" />
10 <exit_code range="11" level="fatal" description="Please provide numeric values for the list of channels to plot" />
11 <exit_code range="12" level="fatal" description="Please provide more than one channel to plot" />
12 <exit_code range="13:" level="fatal"/>
13 </stdio>
14 <command><![CDATA[
15 Rscript $__tool_directory__/getDensityPlots_text.R '${input}' '${channels}' '${output}' '${outformat}'
16 ]]>
17 </command>
18 <inputs>
19 <param format="flowtext" name="input" type="data" label="txt-converted FCS file"/>
20 <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."/>
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="Scatter Plots of ${channels} 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" value="input.flowtext"/>
36 <param name="channels" value="i.e.:1,3,4"/>
37 <param name="outformat" value="PDF"/>
38 <output name="output" file="graph.pdf" compare="sim_size" delta="2000000"/>
39 </test>
40 <test>
41 <param name="input" value="input.flowtext"/>
42 <param name="channels" value="1,3,5"/>
43 <param name="outformat" value="PNG"/>
44 <output name="output" file="graph2.png" compare="sim_size" delta="1000000"/>
45 </test>
46 </tests>
47 <help><![CDATA[
48 This tool allows generation of density scatter plots using ggplot2.
49
50 -----
51
52 **Input files**
53
54 This tool takes txt-converted FCS files as input.
55
56 **Output files**
57
58 This tool generates a scatter plot for each marker combination in a single png file. A pdf file can optionally be generated.
59
60 class:: warningmark
61
62 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.
63
64 -----
65
66 **Example**
67
68 *Output*:
69
70 .. image:: ./static/images/flowtools/flowtextgraph.png
71 ]]>
72 </help>
73 <citations>
74 <citation type="bibtex">@BOOK{,
75 author = {Hadley Wickham},
76 title = {ggplot2: Elegant Graphics for Data Analysis},
77 publisher = {Springer-Verlag New York},
78 year = {2009},
79 isbn = {978-0-387-98140-6},
80 url = {http://ggplot2.org},
81 }</citation>
82 </citations>
83 </tool>