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comparison pcdl_plot_timeseries.xml @ 0:c8c9631bec71 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
author iuc
date Mon, 04 Aug 2025 19:00:59 +0000
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-1:000000000000 0:c8c9631bec71
1 <tool id="pcdl_plot_timeseries" name="pcdl_plot_timeseries" 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_timeseries output_pc '$focus_cat' '$focus_num' '$aggregate_num'
17 --custom_data_type $custom_data_type
18 --microenv $microenv
19 --physiboss $physiboss
20 --settingxml 'none'
21 --verbose $verbose
22 --frame $frame
23 --z_slice '$z_slice'
24 --logy $logy
25 --ylim '$ylim'
26 --secondary_y $secondary_y
27 --subplots $subplots
28 --sharex $sharex
29 --sharey $sharey
30 --linestyle $linestyle
31 --linewidth '$linewidth'
32 --cmap '$cmap'
33 --color '$color'
34 --grid $grid
35 --legend $legend
36 --yunit '$yunit'
37 --title '$title'
38 --figsizepx $figsizepx_x $figsizepx_y
39 --ext $ext
40 --figbgcolor '$figbgcolor'
41 ]]></command>
42 <inputs>
43 <section name="essential" title="essential:" expanded="true">
44 <expand macro="path"/>
45 <expand macro="focus_cat"/>
46 <expand macro="focus_num"/>
47 <expand macro="aggregate_num"/>
48 <expand macro="custom_data_type"/>
49 <expand macro="frame"/>
50 <expand macro="z_slice"/>
51 <expand macro="logy"/>
52 <expand macro="ylim"/>
53 <expand macro="secondary_y"/>
54 <expand macro="subplots"/>
55 <expand macro="sharex"/>
56 <expand macro="sharey"/>
57 <expand macro="linestyle"/>
58 <expand macro="linewidth"/>
59 <expand macro="cmap"/>
60 <expand macro="color"/>
61 <expand macro="grid"/>
62 <expand macro="legend"/>
63 <expand macro="yunit"/>
64 <expand macro="title"/>
65 <expand macro="figsizepx_x"/>
66 <expand macro="figsizepx_y"/>
67 <expand macro="ext"/>
68 <expand macro="figbgcolor"/>
69 </section>
70 <section name="advanced" title="advanced:" expanded="false">
71 <expand macro="microenv"/>
72 <expand macro="physiboss"/>
73 <expand macro="verbose"/>
74 </section>
75 </inputs>
76 <outputs>
77 <collection name="timeseries_plot" type="list">
78 <discover_datasets pattern="(?P&lt;designation&gt;timeseries_.+)\.jpeg" format="jpg" directory="output_pc" visible="false"/>
79 </collection>
80 </outputs>
81 <tests>
82 <test expect_num_outputs="1">
83 <section name="essential">
84 <param name="path">
85 <expand macro="output"/>
86 </param>
87 </section>
88 <section name="advanced">
89 <param name="verbose" value="true"/>
90 </section>
91 <output_collection name="timeseries_plot" count="1">
92 <element name="timeseries_cell_total_count">
93 <assert_contents>
94 <has_text text="JFIF"/>
95 </assert_contents>
96 </element>
97 </output_collection>
98 </test>
99 </tests>
100 <help><![CDATA[
101 This function to generate a timeseries plot and either returns a matplotlib figure or an image file (jpeg, png, tiff).
102
103 Homepage: https://github.com/elmbeech/physicelldataloader
104 ]]></help>
105 <citations>
106 <expand macro="citation"/>
107 </citations>
108 </tool>