Mercurial > repos > iuc > dram_annotate
comparison dram_annotate.xml @ 0:cf3f6929b52c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
author | iuc |
---|---|
date | Sat, 10 Dec 2022 21:14:46 +0000 |
parents | |
children | 4058af4457c0 |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:cf3f6929b52c |
---|---|
1 <tool id="dram_annotate" name="DRAM annotate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> | |
2 <description>metagenome-assembled-genomes (MAGs)</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements"/> | |
7 <expand macro="stdio"/> | |
8 <command detect_errors="exit_code"><![CDATA[ | |
9 #import os | |
10 | |
11 ## DRAM names the genbank output based on the input_fasta file name | |
12 #set input_fasta_file_name = $os.path.splitext($os.path.basename(str($input_fasta)))[0] | |
13 #set output_gbk_file_name = $input_fasta_file_name + '.gbk' | |
14 | |
15 DRAM.py annotate | |
16 --input_fasta '$input_fasta' | |
17 --output_dir 'output_dir' | |
18 --min_contig_size $min_contig_size | |
19 --prodigal_mode '$prodigal_mode' | |
20 --trans_table $trans_table | |
21 --bit_score_threshold $bit_score_threshold | |
22 --rbh_bit_score_threshold $rbh_bit_score_threshold | |
23 $kofam_use_dbcan2_thresholds | |
24 #if str($custom_fasta_dbs_cond.custom_dbs_fasta) == 'yes': | |
25 #for additional_db in $custom_fasta_dbs_cond.custom_fasta_dbs: | |
26 --custom_db_name '$additional_db.custom_db_name' | |
27 --custom_fasta_loc '$additional_db.custom_fasta_loc' | |
28 #end for | |
29 #end if | |
30 #if str($custom_hmm_dbs_cond.custom_dbs_hmm) == 'yes': | |
31 #for additional_db in $custom_hmm_dbs_cond.custom_hmm_dbs: | |
32 --custom_hmm_name '$additional_db.custom_hmm_name' | |
33 --custom_hmm_loc '$additional_db.custom_hmm_loc' | |
34 #if $additional_db.custom_hmm_cutoffs_loc: | |
35 --custom_hmm_cutoffs_loc '$additional_db.custom_hmm_cutoffs_loc' | |
36 #end if | |
37 #end for | |
38 #end if | |
39 $use_uniref | |
40 $use_vogdb | |
41 $low_mem_mode | |
42 $skip_trnascan | |
43 --threads \${GALAXY_SLOTS:-10} | |
44 && test -f 'output_dir/genes.faa' && mv 'output_dir/genes.faa' '$output_genes_faa' || echo 'No genes.faa output produced' | |
45 && test -f 'output_dir/genes.fna' && mv 'output_dir/genes.fna' '$output_genes_fna' || echo 'No genes.fna output produced' | |
46 && test -f 'output_dir/genes.gff' && mv 'output_dir/genes.gff' '$output_genes_gff' || echo 'No genes.gff output produced' | |
47 && test -f 'output_dir/scaffolds.fna' && mv 'output_dir/scaffolds.fna' '$output_scaffolds_fna' || echo 'No scaffolds.fna output produced' | |
48 && test -f 'output_dir/rrnas.tsv' && mv 'output_dir/rrnas.tsv' '$output_rrnas' || echo 'No rrnas.tsv output produced' | |
49 && test -f 'output_dir/trnas.tsv' && mv 'output_dir/trnas.tsv' '$output_trnas' || echo 'No trnas.tsv output produced' | |
50 && test -f 'output_dir/genbank/$output_gbk_file_name' && mv 'output_dir/genbank/$output_gbk_file_name' '$output_genbank' || echo 'No genbank output produced' | |
51 && test -f 'output_dir/annotations.tsv' && mv 'output_dir/annotations.tsv' '$output_annotations' || echo 'No annotations.tsv output produced' | |
52 ]]></command> | |
53 <inputs> | |
54 <param argument="--input_fasta" type="data" format="fasta,fasta.gz" label="FASTA file"/> | |
55 <param argument="--min_contig_size" type="integer" value="2500" min="0" label="Minimum contig size to be used for gene prediction"/> | |
56 <param argument="--prodigal_mode" type="select" label="Select mode of prodigal to use for gene calling" help="Single mode requires genomes which are high quality with low contamination and long contigs (average length >3 Kbp)"> | |
57 <option value="single" selected="true">single</option> | |
58 <option value="meta">meta</option> | |
59 <option value="train">train</option> | |
60 </param> | |
61 <param argument="--trans_table" type="integer" value="11" min="1" max="25" label="Translation table for prodigal to use for gene calling"/> | |
62 <param argument="--bit_score_threshold" type="integer" value="60" min="1" label="Minimum bitScore of search to retain hits"/> | |
63 <param argument="--rbh_bit_score_threshold" type="integer" value="350" min="1" label="Minimum bitScore of reverse best hits to retain hits"/> | |
64 <param argument="--kofam_use_dbcan2_thresholds" type="boolean" truevalue="--kofam_use_dbcan2_thresholds" falsevalue="" checked="false" label="Use dbcan2 suggested HMM cutoffs for KOfam annotation instead of KOfam recommended cutoffs?"/> | |
65 <conditional name="custom_fasta_dbs_cond"> | |
66 <param name="custom_dbs_fasta" type="select" label="Specify additional fasta files against which to annotate?"> | |
67 <option value="no" selected="true">No</option> | |
68 <option value="yes">Yes</option> | |
69 </param> | |
70 <when value="no"/> | |
71 <when value="yes"> | |
72 <repeat name="custom_fasta_dbs" title="FASTA file" min="1"> | |
73 <param argument="--custom_db_name" type="text" value="CF1" label="Custom FASTA database name"> | |
74 <validator type="empty_field"/> | |
75 <expand macro="sanitizer"/> | |
76 </param> | |
77 <param argument="--custom_fasta_loc" type="data" format="fasta,fasta.gz" label="Custom database FASTA file"/> | |
78 </repeat> | |
79 </when> | |
80 </conditional> | |
81 <conditional name="custom_hmm_dbs_cond"> | |
82 <param name="custom_dbs_hmm" type="select" label="Specify additional hmm files against which to annotate?"> | |
83 <option value="no" selected="true">No</option> | |
84 <option value="yes">Yes</option> | |
85 </param> | |
86 <when value="no"/> | |
87 <when value="yes"> | |
88 <repeat name="custom_hmm_dbs" title="HMM file" min="1"> | |
89 <param argument="--custom_hmm_name" type="text" value="CH1" label="Custom HMM database name"> | |
90 <validator type="empty_field"/> | |
91 <expand macro="sanitizer"/> | |
92 </param> | |
93 <param argument="--custom_hmm_loc" type="data" format="hmm2,hmm3" label="Custom database HMM file"/> | |
94 <param argument="--custom_hmm_cutoffs_loc" type="data" format="tabular,tsv" optional="true" label="Custom HMM cutoffs and descriptions file" help="Optional, leave blank to ignore"/> | |
95 </repeat> | |
96 </when> | |
97 </conditional> | |
98 <param argument="--use_uniref" type="boolean" truevalue="--use_uniref" falsevalue="" checked="false" label="Annotate the input FASTA files against UniRef?" help="Increases run time and memory requirements"/> | |
99 <param argument="--use_vogdb" type="boolean" truevalue="--use_vogdb" falsevalue="" checked="false" label="Annotate the input FASTA files against VOGDB?" help="Decreases run time"/> | |
100 <param argument="--low_mem_mode" type="boolean" truevalue="--low_mem_mode" falsevalue="" checked="false" label="Skip annotating with uniref and use kofam?" help="Decreases memory requirements"/> | |
101 <param argument="--skip_trnascan" type="boolean" truevalue="--skip_trnascan" falsevalue="" checked="false" label="Skip transcan"/> | |
102 </inputs> | |
103 <outputs> | |
104 <data name="output_genes_faa" format="fasta" label="${tool.name} on ${on_string}: genes.faa"/> | |
105 <data name="output_genes_fna" format="fasta" label="${tool.name} on ${on_string}: genes.fna"/> | |
106 <data name="output_genes_gff" format="gff3" label="${tool.name} on ${on_string}: genes.gff"/> | |
107 <data name="output_scaffolds_fna" format="fasta" label="${tool.name} on ${on_string}: scaffolds"/> | |
108 <data name="output_rrnas" format="tabular" label="${tool.name} on ${on_string}: rrnas"/> | |
109 <data name="output_trnas" format="tabular" label="${tool.name} on ${on_string}: trnas"/> | |
110 <data name="output_genbank" format="genbank" label="${tool.name} on ${on_string}: genbank"/> | |
111 <data name="output_annotations" format="tabular" label="${tool.name} on ${on_string}: annotations"/> | |
112 </outputs> | |
113 <tests> | |
114 <test expect_num_outputs="8"> | |
115 <param name="input_fasta" value="input_annotate1.fasta.gz" ftype="fasta.gz"/> | |
116 <param name="prodigal_mode" value="meta"/> | |
117 <output name="output_genes_faa"> | |
118 <assert_contents> | |
119 <has_text text="rank"/> | |
120 </assert_contents> | |
121 </output> | |
122 <output name="output_genes_fna"> | |
123 <assert_contents> | |
124 <has_text text="rank"/> | |
125 </assert_contents> | |
126 </output> | |
127 <output name="output_genes_gff"> | |
128 <assert_contents> | |
129 <has_text text="gff-version 3"/> | |
130 </assert_contents> | |
131 </output> | |
132 <output name="output_scaffolds_fna"> | |
133 <assert_contents> | |
134 <has_text text="scaffold"/> | |
135 </assert_contents> | |
136 </output> | |
137 <output name="output_rrnas"> | |
138 <assert_contents> | |
139 <has_text text="scaffold"/> | |
140 </assert_contents> | |
141 </output> | |
142 <output name="output_trnas"> | |
143 <assert_contents> | |
144 <has_text text="fasta"/> | |
145 </assert_contents> | |
146 </output> | |
147 <output name="output_genbank"> | |
148 <assert_contents> | |
149 <has_text text="LOCUS"/> | |
150 </assert_contents> | |
151 </output> | |
152 <output name="output_annotations"> | |
153 <assert_contents> | |
154 <has_text text="fasta"/> | |
155 </assert_contents> | |
156 </output> | |
157 </test> | |
158 <!-- These settings require a db which doesn't exist in the test environment --> | |
159 <test expect_failure="true"> | |
160 <param name="input_fasta" value="input_annotate1.fasta.gz" ftype="fasta.gz"/> | |
161 <param name="custom_dbs_fasta" value="yes"/> | |
162 <repeat name="custom_fasta_dbs"> | |
163 <param name="custom_db_name" value="CF1"/> | |
164 <param name="custom_fasta_loc" value="annotate_custom.fasta" ftype="fasta"/> | |
165 </repeat> | |
166 <param name="custom_dbs_hmm" value="yes"/> | |
167 <repeat name="custom_hmm_dbs"> | |
168 <param name="custom_hmm_name" value="CH1"/> | |
169 <param name="custom_hmm_loc" value="annotate_custom.hmm" ftype="hmm3"/> | |
170 </repeat> | |
171 <param name="prodigal_mode" value="meta"/> | |
172 <assert_stderr> | |
173 <has_text text="returned non-zero exit status"/> | |
174 </assert_stderr> | |
175 </test> | |
176 </tests> | |
177 <help> | |
178 **What it does** | |
179 | |
180 @WHATITDOESHEADER@ | |
181 | |
182 This tool annotates genes by assigning database identifiers to them. Short contigs (default less than 2,500 bp) are initially | |
183 removed and then Prodigal is used to detect open reading frames (ORFs) and to predict their amino acid sequences. Next, DRAM | |
184 searches all amino acid sequences against multiple databases, providing a single Raw output. When gene annotation is complete, | |
185 all results are merged in a single tabular annotation table, including the best hit for each database, for user comparison. | |
186 | |
187 This tool accepts assembly-derived fastA files which may come from unbinned data (metagenome contig or scaffold files) or | |
188 genome-resolved data from one or many organisms (isolate genomes, single-amplified genome (SAGs), MAGs). | |
189 | |
190 This tool produces the following outputs. | |
191 | |
192 * A tabular file with all annotations from Pfam, UniProt, dbCAN and MEROPS databases for all genes in the input genomes | |
193 * Genbank files for each genome | |
194 * A gff file of all annotations across genomes | |
195 * A fasta file of each open reading frame amino acid sequence and best ranked annotation | |
196 * Tabular files with tRNAs and rRNAs | |
197 | |
198 @WHATITDOESFOOTER@ | |
199 </help> | |
200 <expand macro="citations"/> | |
201 </tool> |