Mercurial > repos > iuc > pcdl_plot_scatter

comparison pcdl_plot_scatter.xml @ 0:bc08e5879459 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/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
author iuc
date Mon, 04 Aug 2025 18:59:56 +0000
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:bc08e5879459
1 <tool id="pcdl_plot_scatter" name="pcdl_plot_scatter" version="3.0.1+galaxy0" profile="21.05">
2 <macros>
3 <import>pcdl_macros.xml</import>
4 </macros>
5 <requirements>
6 <expand macro="requirement"/>
7 </requirements>
8 <command><![CDATA[
9 #import re
10 mkdir output_pc &&
11 #for $file in $path:
12 #set $filename = re.sub('[^\w\-\.\s]', '_', str($file.element_identifier))
13 ln -s '$file' output_pc/$filename &&
14 #end for
15
16 pcdl_plot_scatter 'output_pc' '$focus_cell'
17 --custom_data_type $custom_data_type
18 --microenv $microenv
19 --physiboss $physiboss
20 --settingxml 'none'
21 --verbose $verbose
22 --z_slice $z_slice
23 --z_axis '$z_axis'
24 --alpha $alpha
25 --cmap '$cmap'
26 --title '$title'
27 --grid $grid
28 --legend_loc '$legend_loc'
29 --xlim '$xlim'
30 --ylim '$ylim'
31 --xyequal $xyequal
32 --s $s
33 --figsizepx $figsizepx_x $figsizepx_y
34 --directory 'jakku'
35 --ext $ext
36 --figbgcolor '$figbgcolor'
37 ]]></command>
38 <inputs>
39 <section name="essential" title="essential:" expanded="true">
40 <expand macro="path"/>
41 <expand macro="focus_cell"/>
42 <expand macro="custom_data_type"/>
43 <expand macro="z_slice"/>
44 <expand macro="z_axis"/>
45 <expand macro="alpha"/>
46 <expand macro="cmap"/>
47 <expand macro="title"/>
48 <expand macro="grid"/>
49 <expand macro="legend_loc"/>
50 <expand macro="xlim"/>
51 <expand macro="ylim"/>
52 <expand macro="xyequal"/>
53 <expand macro="s"/>
54 <expand macro="figsizepx_x"/>
55 <expand macro="figsizepx_y"/>
56 <expand macro="ext"/>
57 <expand macro="figbgcolor"/>
58 </section>
59 <section name="advanced" title="advanced:" expanded="false">
60 <expand macro="microenv"/>
61 <expand macro="physiboss"/>
62 <expand macro="verbose"/>
63 </section>
64 </inputs>
65 <outputs>
66 <collection name="scatter_plot" type="list">
67 <discover_datasets pattern="(?P&lt;designation&gt;output.+)\.jpeg" format="jpg" directory="jakku" visible="false"/>
68 </collection>
69 </outputs>
70 <tests>
71 <test expect_num_outputs="1">
72 <section name="essential">
73 <param name="path">
74 <expand macro="output"/>
75 </param>
76 </section>
77 <section name="advanced">
78 <param name="verbose" value="false"/>
79 </section>
80 <output_collection name="scatter_plot" count="2">
81 <element name="output00000000_cell_type">
82 <assert_contents>
83 <has_text text="JFIF"/>
84 </assert_contents>
85 </element>
86 <element name="output00000001_cell_type">
87 <assert_contents>
88 <has_text text="JFIF"/>
89 </assert_contents>
90 </element>
91 </output_collection>
92 </test>
93 </tests>
94 <help><![CDATA[
95 Function generates pandas scatter plots.
96
97 Homepage: https://github.com/elmbeech/physicelldataloader
98 ]]></help>
99 <citations>
100 <expand macro="citation"/>
101 </citations>
102 </tool>