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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 19:00:39 +0000
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1 <tool id="pcdl_get_conc_df" name="pcdl_get_conc_df" 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_get_conc_df 'output_pc' $entropy
17 --verbose $verbose
18 --drop $drop
19 --keep $keep
20 --collapse $collapse
21 ]]></command>
22 <inputs>
23 <section name="essential" title="essential:" expanded="true">
24 <expand macro="path"/>
25 <expand macro="entropy"/>
26 <expand macro="drop"/>
27 <expand macro="keep"/>
28 <expand macro="collapse"/>
29 </section>
30 <section name="advanced" title="advanced:" expanded="false">
31 <expand macro="verbose"/>
32 </section>
33 </inputs>
34 <outputs>
35 <collection name="conc_csv" type="list">
36 <discover_datasets pattern="(?P&lt;designation&gt;.+_conc)\.csv" format="csv" directory="output_pc" visible="false"/>
37 </collection>
38 </outputs>
39 <tests>
40 <test expect_num_outputs="1">
41 <section name="essential">
42 <param name="path">
43 <expand macro="output"/>
44 </param>
45 <param name="collapse" value="true"/>
46 </section>
47 <section name="advanced">
48 <param name="verbose" value="true"/>
49 </section>
50 <output_collection name="conc_csv" count="1">
51 <element name="timeseries_conc">
52 <assert_contents>
53 <has_text text="index,voxel_i,voxel_j,voxel_k,mesh_center_m,mesh_center_n,mesh_center_p"/>
54 <has_text text=",time,runtime,xmlfile"/>
55 </assert_contents>
56 </element>
57 </output_collection>
58 </test>
59 <test expect_num_outputs="1">
60 <section name="essential">
61 <param name="path">
62 <expand macro="output"/>
63 </param>
64 <param name="collapse" value="false"/>
65 </section>
66 <section name="advanced">
67 <param name="verbose" value="false"/>
68 </section>
69 <output_collection name="conc_csv" count="2">
70 <element name="output00000000_conc">
71 <assert_contents>
72 <has_text text="index,voxel_i,voxel_j,voxel_k,mesh_center_m,mesh_center_n,mesh_center_p,"/>
73 <has_text text=",time,runtime,xmlfile"/>
74 </assert_contents>
75 </element>
76 <element name="output00000001_conc">
77 <assert_contents>
78 <has_text text="index,voxel_i,voxel_j,voxel_k,mesh_center_m,mesh_center_n,mesh_center_p,"/>
79 <has_text text=",time,runtime,xmlfile"/>
80 </assert_contents>
81 </element>
82 </output_collection>
83 </test>
84 </tests>
85 <help><![CDATA[
86 This function extracts dataframes with concentration values for all chemical species in all voxels and saves them as csv files. Additionally, this dataframe lists voxel and mesh center coordinates.
87
88 Homepage: https://github.com/elmbeech/physicelldataloader
89 ]]></help>
90 <citations>
91 <expand macro="citation"/>
92 </citations>
93 </tool>