Mercurial > repos > iuc > picrust2_shuffle_predictions

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planemo upload for repository https://github.com/picrust/picrust2 commit f8c32a316582ff102c9b7edf3817000691ef9eea
author iuc
date Tue, 13 Aug 2024 12:09:58 +0000
parents c13a42f51745
children
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c13a42f51745 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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1 <tool id="picrust2_shuffle_predictions" name="PICRUSt2 Generation of shuffled predictions" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>for a specified number of replicates</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="bio_tool"/>
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7 <expand macro="requirements"/>
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8 <version_command>shuffle_predictions.py -v</version_command>
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9 <command detect_errors="exit_code"><![CDATA[
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10 ln -s '$input' predicted.tsv &&
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11 shuffle_predictions.py
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12 --input predicted.tsv
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13 --outdir predicted_shuffled
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14 --rep $rep
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15 #if str($seed) != ''
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16 --seed $seed
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17 #end if
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18 ]]></command>
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19 <inputs>
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20 <param argument="--input" type="data" format="tabular" label="Input prediction table"/>
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21 <param argument="--rep" type="integer" min="1" value="1" label="Number of shuffled replicates to create"/>
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22 <param argument="--seed" type="integer" optional="true" label="Random seed" help="Set this for reproducible shufflings"/>
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23 </inputs>
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24 <outputs>
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25 <collection name="predicted_shuffled" type="list">
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26 <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="predicted_shuffled/" format="tabular"/>
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27 </collection>
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28 </outputs>
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29 <tests>
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30 <test expect_num_outputs="1">
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31 <param name="input" value="EC_predicted.tsv.gz"/>
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32 <param name="rep" value="5"/>
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33 <param name="seed" value="131"/>
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34 <output_collection name="predicted_shuffled" type="list" count="5">
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35 <element name="predicted_shuf1.tsv" ftype="tabular">
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36 <assert_contents>
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37 <has_text text="8db33d54e5184b0f448ae140f793368a"/>
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38 <has_n_lines n="38"/>
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39 </assert_contents>
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40 </element>
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41 <element name="predicted_shuf2.tsv" ftype="tabular">
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42 <assert_contents>
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43 <has_text text="763af2e6cfd1d573893fa6d28aafc4b5"/>
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44 <has_n_lines n="38"/>
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45 </assert_contents>
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46 </element>
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47 <element name="predicted_shuf3.tsv" ftype="tabular">
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48 <assert_contents>
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49 <has_text text="f5b23f626e3f2d2d1213f83c6de3e385"/>
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50 <has_n_lines n="38"/>
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51 </assert_contents>
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52 </element>
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53 <element name="predicted_shuf4.tsv" ftype="tabular">
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54 <assert_contents>
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55 <has_text text="ff33233ffebbe6e3720af8bba7e89f08"/>
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56 <has_n_lines n="38"/>
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57 </assert_contents>
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58 </element>
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59 <element name="predicted_shuf5.tsv" ftype="tabular">
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60 <assert_contents>
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61 <has_text text="691eeed271e420c8e7a91d5ea0cf5431"/>
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62 <has_n_lines n="38"/>
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63 </assert_contents>
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64 </element>
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65 </output_collection>
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66 </test>
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67 </tests>
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68 <help><![CDATA[
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69 @HELP_HEADER@
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70
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71 Generating shuffled predictions
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72 ===============================
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73 Shuffles sequence ids of prediction table for a specified number of replicates.
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74
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75 Note
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76 ====
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77 This means that the prediction table is not totally scrambled across all colunmns: each predicted genome is still the same, but the sequence ids (e.g. the ASV id) linked with each predicted genome is randomized.
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78
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79 Input
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80 =====
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81 Prediction table
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82
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83 Output
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84 ======
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85 Predicted shuffled table
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86
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87 ]]></help>
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88 <citations>
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89 <citation type="doi">10.1038/s41587-020-0548-6</citation>
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90 </citations>
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91 </tool>