Mercurial > repos > iuc > pcdl_get_conc_df

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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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b995568c667e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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1 <tool id="pcdl_get_conc_df" name="pcdl_get_conc_df" version="3.0.1+galaxy0" profile="21.05">
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2 <macros>
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3 <import>pcdl_macros.xml</import>
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4 </macros>
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5 <requirements>
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6 <expand macro="requirement"/>
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7 </requirements>
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8 <command><![CDATA[
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9 #import re
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10 mkdir output_pc &&
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11 #for $file in $path:
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12 #set $filename = re.sub('[^\w\-\.\s]', '_', str($file.element_identifier))
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13 ln -s '$file' output_pc/$filename &&
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14 #end for
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15
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16 pcdl_get_conc_df 'output_pc' $entropy
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17 --verbose $verbose
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18 --drop $drop
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19 --keep $keep
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20 --collapse $collapse
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21 ]]></command>
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22 <inputs>
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23 <section name="essential" title="essential:" expanded="true">
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24 <expand macro="path"/>
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25 <expand macro="entropy"/>
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26 <expand macro="drop"/>
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27 <expand macro="keep"/>
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28 <expand macro="collapse"/>
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29 </section>
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30 <section name="advanced" title="advanced:" expanded="false">
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31 <expand macro="verbose"/>
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32 </section>
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33 </inputs>
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34 <outputs>
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35 <collection name="conc_csv" type="list">
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36 <discover_datasets pattern="(?P&lt;designation&gt;.+_conc)\.csv" format="csv" directory="output_pc" visible="false"/>
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37 </collection>
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38 </outputs>
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39 <tests>
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40 <test expect_num_outputs="1">
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41 <section name="essential">
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42 <param name="path">
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43 <expand macro="output"/>
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44 </param>
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45 <param name="collapse" value="true"/>
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46 </section>
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47 <section name="advanced">
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48 <param name="verbose" value="true"/>
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49 </section>
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50 <output_collection name="conc_csv" count="1">
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51 <element name="timeseries_conc">
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52 <assert_contents>
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53 <has_text text="index,voxel_i,voxel_j,voxel_k,mesh_center_m,mesh_center_n,mesh_center_p"/>
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54 <has_text text=",time,runtime,xmlfile"/>
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55 </assert_contents>
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56 </element>
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57 </output_collection>
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58 </test>
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59 <test expect_num_outputs="1">
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60 <section name="essential">
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61 <param name="path">
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62 <expand macro="output"/>
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63 </param>
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64 <param name="collapse" value="false"/>
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65 </section>
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66 <section name="advanced">
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67 <param name="verbose" value="false"/>
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68 </section>
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69 <output_collection name="conc_csv" count="2">
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70 <element name="output00000000_conc">
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71 <assert_contents>
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72 <has_text text="index,voxel_i,voxel_j,voxel_k,mesh_center_m,mesh_center_n,mesh_center_p,"/>
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73 <has_text text=",time,runtime,xmlfile"/>
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74 </assert_contents>
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75 </element>
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76 <element name="output00000001_conc">
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77 <assert_contents>
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78 <has_text text="index,voxel_i,voxel_j,voxel_k,mesh_center_m,mesh_center_n,mesh_center_p,"/>
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79 <has_text text=",time,runtime,xmlfile"/>
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80 </assert_contents>
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81 </element>
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82 </output_collection>
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83 </test>
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84 </tests>
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85 <help><![CDATA[
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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.
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87
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88 Homepage: https://github.com/elmbeech/physicelldataloader
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89 ]]></help>
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90 <citations>
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91 <expand macro="citation"/>
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92 </citations>
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93 </tool>