Mercurial > repos > bgruening > tiara
annotate tiara.xml @ 0:3f33a8ac8891 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
author | bgruening |
---|---|
date | Thu, 30 May 2024 11:10:39 +0000 |
parents | |
children |
rev | line source |
---|---|
0
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
1 <tool id="tiara" name="tiara" version="@TOOL_VERSION@+galaxy0" profile="21.05"> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
2 <description>Deep-learning-based approach for identification of eukaryotic sequences in the metagenomic data </description> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
3 <macros> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
4 <import>macros.xml</import> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
5 </macros> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
6 <expand macro="biotools"/> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
7 <expand macro="requirements"/> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
8 <command detect_errors="exit_code"><![CDATA[ |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
9 |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
10 tiara |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
11 -t \${GALAXY_SLOTS:-4} |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
12 -i '$input' |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
13 -o '$output' |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
14 |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
15 #if $taxonomy_filter |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
16 --tf #for $tf in $taxonomy_filter |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
17 $tf |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
18 #end for |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
19 #end if |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
20 #if $probabilities |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
21 --pr '$probabilities' |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
22 #end if |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
23 #if $min_len |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
24 -m '$min_len' |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
25 #end if |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
26 #if $cutoff_stage1 |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
27 -p $cutoff_stage1 |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
28 #if $cutoff_stage2 |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
29 $cutoff_stage2 |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
30 #end if |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
31 #end if |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
32 #if $advanced_options.advance.customize_kmer_length == 'customize' |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
33 --k1 $advanced_options.advance.first_stage_kmer |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
34 --k2 $advanced_options.advance.second_stage_kmer |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
35 #end if |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
36 |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
37 ]]></command> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
38 <inputs> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
39 <param name="input" type="data" format="fasta" label="input fasta,fasta.gz file"/> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
40 <param name="taxonomy_filter" type="select" multiple="true" optional="true" label="Write sequences to fasta,fasta.gz files specified in the arguments to this option." help="all refers to all classes present in input fasta (to separate fasta files)."> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
41 <option value="mit">mitochondria</option> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
42 <option value="pla">plastid</option> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
43 <option value="bac">bacteria</option> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
44 <option value="arc">archea</option> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
45 <option value="euk">eukarya</option> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
46 <option value="unk">unknown</option> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
47 <option value="pro">prokarya</option> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
48 <option value="all">all</option> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
49 </param> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
50 <param argument="probabilities" type="boolean" truevalue="--pr" falsevalue="" checked="false" label="Add probabilities of individual classes for each sequence."/> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
51 <param argument="min_len" type="integer" value="3000" min="1000" optional="true" label="Minimum length of a sequence. Default: 3000 bp." help="Specify the desired minimum length in base pairs.Default value is 3000 bp and we do not recommend classifying sequences shorter than 1000 bp. "/> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
52 <param argument="cutoff_stage1" type="float" value="0.65" min="0.5" max="1" optional="true" label="Probability threshold for the first stage." help="Probability threshold needed for classification in the first stage. Default: 0.65." /> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
53 <param argument="cutoff_stage2" type="float" value="0.65" min="0.5" max="1" optional="true" label="Probability threshold for the second stage." help="Probability threshold needed for classification in the second stage. Default: 0.65." /> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
54 <section name="advanced_options" title="k-mer" expanded="true"> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
55 <conditional name="advance"> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
56 <param argument="customize_kmer_length" type="select" label="Advanced options"> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
57 <option value="default_options">No, Use param defaults</option> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
58 <option value="customize">Yes, See full parameter list</option> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
59 </param> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
60 <when value="customize"> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
61 <param argument="first_stage_kmer" type="select" label="Select k-mer length used in the first stage of classification (Default: 6)."> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
62 <option value="4">k-mer length 4</option> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
63 <option value="5">k-mer length 5</option> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
64 <option value="6" selected="True">default k-mer length</option> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
65 </param> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
66 <param argument="second_stage_kmer" type="select" label="k-mer length used in the second stage of classification (Default: 7)."> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
67 <option value="4">k-mer length 4</option> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
68 <option value="5">k-mer length 5</option> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
69 <option value="6">k-mer length 6</option> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
70 <option value="7" selected="True">default k-mer length</option> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
71 </param> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
72 </when> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
73 <when value="default_options"> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
74 <!-- Define actions or defaults for the default option if necessary --> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
75 </when> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
76 </conditional> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
77 </section> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
78 </inputs> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
79 <outputs> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
80 <data name="output" format="txt" label="${tool.name} on ${on_string}: sequence ID, classification results"/> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
81 </outputs> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
82 <tests> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
83 <test expect_num_outputs="1"> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
84 <param name="input" value="plast_fr.fasta.gz"/> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
85 <param name="taxonomy_filter" value="pla"/> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
86 <output name="output" ftype="txt"> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
87 <assert_contents> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
88 <has_text_matching expression=".*sequence_id*"/> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
89 <has_n_lines n="11" delta="5"/> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
90 </assert_contents> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
91 </output> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
92 </test> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
93 <test expect_num_outputs="1"> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
94 <param name="input" value="mitplas1.fasta"/> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
95 <param name="taxonomy_filter" value="pla,mit"/> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
96 <output name="output" ftype="txt"> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
97 <assert_contents> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
98 <has_text_matching expression=".*sequence_id*"/> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
99 <has_n_lines n="30" delta="5"/> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
100 </assert_contents> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
101 </output> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
102 </test> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
103 <test expect_num_outputs="1"> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
104 <param name="input" value="sample_all.fasta"/> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
105 <param name="taxonomy_filter" value="all"/> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
106 <output name="output" ftype="txt"> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
107 <assert_contents> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
108 <has_text_matching expression=".*sequence_id*"/> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
109 <has_n_lines n="51" delta="5"/> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
110 </assert_contents> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
111 </output> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
112 </test> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
113 <test expect_num_outputs="1"> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
114 <param name="input" value="sample_all.fasta"/> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
115 <param name="taxonomy_filter" value="euk,bac,arc,unk"/> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
116 <output name="output" ftype="txt"> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
117 <assert_contents> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
118 <has_text_matching expression=".*sequence_id*"/> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
119 <has_n_lines n="51" delta="5"/> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
120 </assert_contents> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
121 </output> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
122 </test> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
123 <test expect_num_outputs="1"> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
124 <param name="input" value="eukarya_fr.fasta"/> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
125 <param name="taxonomy_filter" value="euk"/> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
126 <param name="min_len" value="5000"/> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
127 <param name="cutoff_stage1" value="0.65"/> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
128 <param name="cutoff_stage2" value="0.60"/> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
129 <output name="output" ftype="txt"> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
130 <assert_contents> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
131 <has_text_matching expression=".*sequence_id*"/> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
132 <has_n_lines n="11" delta="5"/> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
133 </assert_contents> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
134 </output> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
135 </test> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
136 <test expect_num_outputs="1"> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
137 <param name="input" value="bacteria_fr.fasta"/> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
138 <param name="taxonomy_filter" value="bac"/> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
139 <param name="min_len" value="5000"/> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
140 <param name="cutoff_stage1" value="0.65"/> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
141 <param name="cutoff_stage2" value="0.60"/> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
142 <param name="probabilities" value="true"/> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
143 <output name="output" ftype="txt"> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
144 <assert_contents> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
145 <has_text_matching expression=".*bac*"/> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
146 <has_n_lines n="11" delta="5"/> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
147 </assert_contents> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
148 </output> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
149 </test> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
150 </tests> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
151 <help><![CDATA[ |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
152 What it does |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
153 ============ |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
154 Tiara is a Deep-learning-based approach for identification of eukaryotic sequences in the metagenomic data powered by PyTorch. |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
155 |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
156 How it works |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
157 ============ |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
158 The sequences are classified in two stages: |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
159 |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
160 First Stage: |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
161 Input: Sequences are classified into classes: archaea, bacteria, prokarya, eukarya, organelle, and unknown. |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
162 Output: Classifications for each sequence into one of the above classes. |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
163 |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
164 Second Stage: |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
165 Input: Sequences labeled as organelle from the first stage. |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
166 Output: Further classification into mitochondria, plastid, or unknown. |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
167 |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
168 Required Inputs |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
169 =============== |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
170 The primary input for Tiara is metagenomic sequence data that needs classification. |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
171 |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
172 Generated Outputs |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
173 ================= |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
174 The output will be the sequences categorized into specific classes as described above. |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
175 |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
176 Additional Resources |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
177 ==================== |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
178 For a more comprehensive understanding of tiara and detailed usage instructions, please visit the tiara GitHub repository: |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
179 tiara GitHub Repository: [https://github.com/ibe-uw/tiara] |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
180 |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
181 ]]></help> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
182 <expand macro="citations"/> |
3f33a8ac8891
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tiara commit 3e174d7bc4280c835f5092a44d259cc33f0b54b6
bgruening
parents:
diff
changeset
|
183 </tool> |