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comparison shuffle_predictions.xml @ 0:c13a42f51745 draft

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planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
author iuc
date Sat, 04 Mar 2023 20:26:04 +0000
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1 <tool id="picrust2_shuffle_predictions" name="PICRUSt2 Generation of shuffled predictions" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>for a specified number of replicates</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="bio_tool"/>
7 <expand macro="requirements"/>
8 <version_command>shuffle_predictions.py -v</version_command>
9 <command detect_errors="exit_code"><![CDATA[
10 ln -s '$input' predicted.tsv &&
11 shuffle_predictions.py
12 --input predicted.tsv
13 --outdir predicted_shuffled
14 --rep $rep
15 #if str($seed) != ''
16 --seed $seed
17 #end if
18 ]]></command>
19 <inputs>
20 <param argument="--input" type="data" format="tabular" label="Input prediction table"/>
21 <param argument="--rep" type="integer" min="1" value="1" label="Number of shuffled replicates to create"/>
22 <param argument="--seed" type="integer" optional="true" label="Random seed" help="Set this for reproducible shufflings"/>
23 </inputs>
24 <outputs>
25 <collection name="predicted_shuffled" type="list">
26 <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="predicted_shuffled/" format="tabular"/>
27 </collection>
28 </outputs>
29 <tests>
30 <test expect_num_outputs="1">
31 <param name="input" value="EC_predicted.tsv.gz"/>
32 <param name="rep" value="5"/>
33 <param name="seed" value="131"/>
34 <output_collection name="predicted_shuffled" type="list" count="5">
35 <element name="predicted_shuf1.tsv" ftype="tabular">
36 <assert_contents>
37 <has_text text="8db33d54e5184b0f448ae140f793368a"/>
38 <has_n_lines n="38"/>
39 </assert_contents>
40 </element>
41 <element name="predicted_shuf2.tsv" ftype="tabular">
42 <assert_contents>
43 <has_text text="763af2e6cfd1d573893fa6d28aafc4b5"/>
44 <has_n_lines n="38"/>
45 </assert_contents>
46 </element>
47 <element name="predicted_shuf3.tsv" ftype="tabular">
48 <assert_contents>
49 <has_text text="f5b23f626e3f2d2d1213f83c6de3e385"/>
50 <has_n_lines n="38"/>
51 </assert_contents>
52 </element>
53 <element name="predicted_shuf4.tsv" ftype="tabular">
54 <assert_contents>
55 <has_text text="ff33233ffebbe6e3720af8bba7e89f08"/>
56 <has_n_lines n="38"/>
57 </assert_contents>
58 </element>
59 <element name="predicted_shuf5.tsv" ftype="tabular">
60 <assert_contents>
61 <has_text text="691eeed271e420c8e7a91d5ea0cf5431"/>
62 <has_n_lines n="38"/>
63 </assert_contents>
64 </element>
65 </output_collection>
66 </test>
67 </tests>
68 <help><![CDATA[
69 @HELP_HEADER@
70
71 Generating shuffled predictions
72 ===============================
73 Shuffles sequence ids of prediction table for a specified number of replicates.
74
75 Note
76 ====
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.
78
79 Input
80 =====
81 Prediction table
82
83 Output
84 ======
85 Predicted shuffled table
86
87 ]]></help>
88 <citations>
89 <citation type="doi">10.1038/s41587-020-0548-6</citation>
90 </citations>
91 </tool>