Mercurial > repos > galaxyp > metagene_annotator
comparison metagene_annotator.xml @ 0:b04960a7abf5 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
author | galaxyp |
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date | Wed, 21 Mar 2018 17:15:25 -0400 |
parents | |
children | 17c7ab82bfbc |
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1 <tool id="metagene_annotator" name="MetaGeneAnnotator" version="1.0.0"> | |
2 <description>gene-finding program for prokaryote and phage (used by sixgill)</description> | |
3 <requirements> | |
4 <requirement type="package">metagene_annotator</requirement> | |
5 <requirement type="package">python</requirement> | |
6 </requirements> | |
7 <command detect_errors="exit_code"><![CDATA[ | |
8 #set $output_list = str($output_formats).split(',') | |
9 touch mga_output | |
10 #for $input in $inputs: | |
11 && mga ${input} $multiple_species >> mga_output | |
12 #end for | |
13 #if 'tsv' in $output_list or 'bed' in $output_list: | |
14 && python '$__tool_directory__/convert_mga.py' mga_output -v | |
15 #if 'tsv' in $output_list | |
16 --tsv '$mga_tsv' | |
17 #end if | |
18 #if 'bed' in $output_list | |
19 --bed '$mga_bed' | |
20 #end if | |
21 #end if | |
22 ]]></command> | |
23 <inputs> | |
24 <param name="inputs" type="data" format="fasta" multiple="true" label="prokaryote DNA sequences"/> | |
25 <param name="multiple_species" type="boolean" truevalue="-m" falsevalue="-s" checked="true" | |
26 label="MetaGenomic - Sequences are from multiple organisms" /> | |
27 <param name="output_formats" type="select" multiple="true" display="checkboxes" label="output formats"> | |
28 <option value="txt" selected="true">MetaGeneAnnotator text report</option> | |
29 <option value="tsv">MetaGeneAnnotator tabular report with sequence columns</option> | |
30 <option value="bed">MetaGeneAnnotator in BED format</option> | |
31 </param> | |
32 </inputs> | |
33 <outputs> | |
34 <data name="mga_txt" format="txt" from_work_dir="mga_output" label="${tool.name} on ${on_string} metagenefile"> | |
35 <filter>'txt' in output_formats</filter> | |
36 </data> | |
37 <data name="mga_tsv" format="tabular" label="${tool.name} on ${on_string} mga table"> | |
38 <filter>'tsv' in output_formats</filter> | |
39 <actions> | |
40 <action name="column_names" type="metadata" | |
41 default="seq_ID,seq_model,seq_gc,seq_rbs,gene ID,start pos,end pos,strand,frame,complete/partial,gene score,used model,rbs start,rbs end,rbs score"/> | |
42 </actions> | |
43 </data> | |
44 <data name="mga_bed" format="bed" label="${tool.name} on ${on_string} mga bed"> | |
45 <filter>'bed' in output_formats</filter> | |
46 <actions> | |
47 <action name="column_names" type="metadata" | |
48 default="chrom,chromStart,chromEnd,name,score,strand,thickStart,thickEnd,itemRgb,blockCount,blockSizes,blockStarts"/> | |
49 </actions> | |
50 </data> | |
51 </outputs> | |
52 <tests> | |
53 <test> | |
54 <param name="inputs" value="metasequences.fasta" ftype="fasta"/> | |
55 <param name="multiple_species" value="True"/> | |
56 <param name="output_formats" value="txt"/> | |
57 <output name="mga_txt"> | |
58 <assert_contents> | |
59 <has_text_matching expression="# 1/1\s# gc = 0.275862, rbs = -1\s# self: -" /> | |
60 <has_text_matching expression="gene_1\t1812\t1994\t-\t0\t11\t14.10\d+\tb\t2002\t2007\t2.11\d+" /> | |
61 </assert_contents> | |
62 </output> | |
63 </test> | |
64 <test> | |
65 <param name="inputs" value="metasequences.fasta" ftype="fasta"/> | |
66 <param name="multiple_species" value="False"/> | |
67 <param name="output_formats" value="txt"/> | |
68 <output name="mga_txt"> | |
69 <assert_contents> | |
70 <has_text_matching expression="# 1/1\s# gc = 0.275862, rbs = 0.428571\s# self: b" /> | |
71 <has_text_matching expression="gene_1\t1812\t1994\t-\t0\t11\t12.48\d+\tb\t2002\t2007\t0.49\d+" /> | |
72 </assert_contents> | |
73 </output> | |
74 </test> | |
75 <!-- Try these later | |
76 <test> | |
77 <param name="inputs" value="metasequences1.fasta,metasequences2.fasta" ftype="fasta"/> | |
78 <param name="multiple_species" value="True"/> | |
79 <param name="output_formats" value="txt"/> | |
80 <output name="mga_txt"> | |
81 <assert_contents> | |
82 <has_text_matching expression="# 1/1.*# 10/1" /> | |
83 <has_text_matching expression="gene_1\t1812\t1994\t-\t0\t11\t14.10\d+\tb\t2002\t2007\t2.11\d+" /> | |
84 </assert_contents> | |
85 </output> | |
86 </test> | |
87 <test> | |
88 <param name="inputs" value="metasequences.fasta" ftype="fasta"/> | |
89 <param name="multiple_species" value="True"/> | |
90 <param name="output_formats" value="txt,tsv,bed"/> | |
91 <output name="mga_txt"> | |
92 <assert_contents> | |
93 <has_text_matching expression="# 1/1\s# gc = 0.275862, rbs = -1\s# self: -" /> | |
94 <has_text_matching expression="gene_1\t1812\t1994\t-\t0\t11\t14.10\d+\tb\t2002\t2007\t2.11\d+" /> | |
95 </assert_contents> | |
96 </output> | |
97 <output name="mga_tsv"> | |
98 <assert_contents> | |
99 <has_text_matching expression="#seq_id\tseq_model\tseq_gc\tseq_rbs" /> | |
100 <has_text_matching expression="1/1\t-\t0.27\d+\t-1\tgene_1\t1812\t1994\t-\t0\t11\t14.1035\tb\t2002\t2007\t2.11\d+" /> | |
101 </assert_contents> | |
102 </output> | |
103 <output name="mga_bed"> | |
104 <assert_contents> | |
105 <has_text_matching expression="1/1\t1811\t1994\t1/1:gene_1\t15\t-\t1811\t1994\t0\t1\t183\t0" /> | |
106 </assert_contents> | |
107 </output> | |
108 </test> | |
109 --> | |
110 </tests> | |
111 <help><![CDATA[ | |
112 **MetaGeneAnnotator (mga)** | |
113 | |
114 A gene-finding program for prokaryote and phage. | |
115 | |
116 The gene annotations can be used by sixgill_ when generating metapeptides from metagenomics shotgun sequencing. | |
117 | |
118 .. image:: Sixgill_MetaGeneAnnotator_Workflow.png | |
119 :height: 213 | |
120 :width: 625 | |
121 | |
122 usage: | |
123 mga [multi-fasta] <-m/-s> | |
124 | |
125 -m (multiple species sequences are individually treated) | |
126 -s (single species sequences are treated as a unit) | |
127 | |
128 **Input:** | |
129 *A fasta file of metagenomic sequences* | |
130 | |
131 | |
132 **Outputs:** | |
133 | |
134 *MetaGeneAnnotator text report* | |
135 Output from the MetaGeneAnnotator mga application:: | |
136 | |
137 # 1/1 | |
138 # gc = 0.275862, rbs = -1 | |
139 # self: - | |
140 gene_1 1812 1994 - 0 11 14.1035 b 2002 2007 2.11797 | |
141 # 2/1 | |
142 # gc = 0.338877, rbs = -1 | |
143 # self: - | |
144 gene_1 1 414 + 0 01 25.748 b . . . | |
145 gene_2 614 790 + 0 11 0.774142 b . . . | |
146 gene_3 822 1079 + 0 11 20.6507 b . . . | |
147 | |
148 output format description:: | |
149 | |
150 # [sequence name] | |
151 # gc = [gc%], rbs = [rbs%] | |
152 # self: [(b)acteria/(a)rchaea/(p)hage/unused(-)] | |
153 [gene ID] [start pos.] [end pos.] [strand] [frame] [complete/partial] [gene score] [used model] [rbs start] [rbs end] [rbs score] | |
154 | |
155 explanations of output column: | |
156 *The value of [frame] (0/1/2) indicates the number of surplus (untranslated) nucleotides at the 5'-end of the predicted ORF. | |
157 *The value of [score] indicates the estimated score of predicted gene. All predicted genes are more than 0. | |
158 *The value of [complete/partial] indicates that the predicted gene structure is whether complete (contains both of start and stop codons[11]) or partial (lacks start[01] or stop[10] or both of them[00]). | |
159 *The value of [model] indicates a selected model ((s)elf/(b)acteria/(a)rchaea/(p)hage) for predicting the gene. | |
160 | |
161 | |
162 *MetaGeneAnnotator tabular report with sequence columns* | |
163 The mga output reformated as a tabular file:: | |
164 | |
165 #seq_id seq_model seq_gc seq_rbs gene ID start pos end pos strand frame complete/partial gene score used model rbs start rbs end rbs score | |
166 1/1 - 0.275862 -1 gene_1 1812 1994 - 0 11 14.1035 b 2002 2007 2.11797 | |
167 2/1 - 0.338877 -1 gene_1 1 414 + 0 01 25.748 b . . . | |
168 2/1 - 0.338877 -1 gene_2 614 790 + 0 11 0.774142 b . . . | |
169 2/1 - 0.338877 -1 gene_3 822 1079 + 0 11 20.6507 b . . . | |
170 | |
171 | |
172 *MetaGeneAnnotator in BED format* | |
173 The mga output reformatted as a BED file which can be used to extract the DNA sequences for each gene from the fasta file:: | |
174 | |
175 1/1 1811 1994 1/1:gene_1 15 - 1811 1994 0 1 183 0 | |
176 2/1 0 414 2/1:gene_1 26 + 0 414 0 1 414 0 | |
177 2/1 613 790 2/1:gene_2 1 + 613 790 0 1 177 0 | |
178 2/1 821 1079 2/1:gene_3 21 + 821 1079 0 1 258 0 | |
179 | |
180 | |
181 .. _sixgill: https://github.com/dhmay/sixgill | |
182 ]]></help> | |
183 <citations> | |
184 <citation type="doi">10.1093/dnares/dsn027</citation> | |
185 </citations> | |
186 </tool> |