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