Mercurial > repos > iuc > picrust2_shuffle_predictions
comparison shuffle_predictions.xml @ 0:881f2faa5fe7 draft
planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
author | iuc |
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date | Sat, 04 Mar 2023 20:28:14 +0000 |
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-1:000000000000 | 0:881f2faa5fe7 |
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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<designation>.+)" 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> |