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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
author iuc
date Wed, 25 May 2022 14:53:03 +0000
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1 <tool id="orfipy" name="ORFipy" version="@TOOL_VERSION@+galaxy0" profile="21.05">
2 <description>a versatile ORF finder</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="xrefs"/>
7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">orfipy</requirement>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[
11 orfipy
12 --procs "\${GALAXY_SLOTS:-1}"
13 --outdir ./
14 #for $o in str($out_files).split(','):
15 #if $o == 'BED':
16 --bed '$out_bed'
17 #else if $o == 'BED12':
18 --bed12 '$out_bed12'
19 #else if $o == 'DNA':
20 --dna '$out_dna'
21 #else if $o == 'RNA':
22 --rna '$out_rna'
23 #else if $o == 'PEP':
24 --pep '$out_pep'
25 #end if
26 #end for
27 --strand $strand
28 #if $min:
29 --min $min
30 #end if
31 --table $table
32 #if $start:
33 --start '$start'
34 #end if
35 #if $stop:
36 --stop '$stop'
37 #end if
38 $ignore_case
39 $partial_3
40 $partial_5
41 $between_stops
42 $include_stop
43 '$input1'
44 ]]></command>
45 <inputs>
46 <param name="input1" type="data" format="fasta,fasta.gz" label="Find ORFs in:" help="ORFs will be detected in this sequence"/>
47 <param type="select" argument="--table" label="Specify genetic code">
48 <option value="1" selected="true">1 Standard</option>
49 <option value="2">2 Vertebrate mitochondrial</option>
50 <option value="3">3 Yeast mitochondrial</option>
51 <option value="4">4 Mold, Protozoan, Coelenterate, Mycoplasma, Spiroplasma mitochondrial</option>
52 <option value="5">5 Invertebrate Mitochondrial</option>
53 <option value="6">6 Ciliate, Dasycladacean, Hexamita Nuclear</option>
54 <option value="7">7 Echinoderm and Flatworm Mitochondrial</option>
55 <option value="8">8 Euplotid Nuclear</option>
56 <option value="9">9 Bacterial, Archaeal and Plant Plastid</option>
57 <option value="10">10 Alternative Yeast nuclear</option>
58 <option value="11">11 Ascidian mitochondrial</option>
59 <option value="12">12 Alternative Flatworm mitochondrial</option>
60 <option value="13">13 Chlorophycean mitochondrial</option>
61 <option value="14">14 Trematode mitochondrial</option>
62 <option value="15">15 Scenedesmus obliquus mitochondrial</option>
63 <option value="16">16 Thraustochytrium mitochondrial code</option>
64 <option value="17">17 Pterobranchia mitochondrial</option>
65 <option value="18">18 Candidate Division SR1 and Gracilibacteria</option>
66 <option value="19">19 Pachysolen tannophilus Nuclear Code</option>
67 <option value="20">20 Karyorelict nuclear</option>
68 <option value="21">21 Condylostoma nuclear</option>
69 <option value="22">22 Mesodinium nuclear</option>
70 <option value="23">23 Peritrich nuclear</option>
71 </param>
72 <param name="out_files" argument="--bed,--bed12,--dna,--rna,--pep" type="select" multiple="true" display="checkboxes" label="Select outputs"
73 help="DNA, RNA, and Peptide options will produce FASTA outputs">
74 <option value="BED" selected="true">BED</option>
75 <option value="BED12">BED12</option>
76 <option value="DNA">DNA</option>
77 <option value="RNA">RNA</option>
78 <option value="PEP">Peptides</option>
79 </param>
80 <param argument="--strand" type="select" display="radio" label="Select strand" help="Identify ORFs on which strand">
81 <option value="b" selected="true">Both</option>
82 <option value="f">Forward</option>
83 <option value="r">Reverse</option>
84 </param>
85 <param argument="--min" type="integer" min="0" optional="true" label="Minimum length of ORFs"
86 help="No ORFs below this value will be reported. All ORFs will be reported if this parameter is not set. Default is 30"/>
87 <param argument="--start" type="text" optional="true" label="Start codon(s) to use"
88 help="A comma-separated list without spaces. Only ATCG and comma are allowed">
89 <validator type="regex" message="Only 'ATCGatcg' and ',' are allowed in this field">^[ATGCatcg,]*$</validator>
90 </param>
91 <param argument="--stop" type="text" optional="true" label="Stop codon(s) to use"
92 help="A commma separated list without spaces. Only ATCG and comma are allowed">
93 <validator type="regex" message="Only 'ATCGatcg' and ',' are allowed in this field">^[ATGCatcg,]*$</validator>
94 </param>
95 <param argument="--ignore-case" type="boolean" truevalue="--ignore-case" falsevalue="" display="radio" label="Ignore case?"
96 help="Ignore case and find ORFs in lower case sequences too. NO = do not ignore (use upper case only). YES = ignore"/>
97 <param argument="--partial-3" type="boolean" truevalue="--partial-3" falsevalue="" display="radio" label="Output ORFs with Start but no Stop?"
98 help="Output ORFs with a start codon but lacking an inframe stop codon. NO = do not output. YES = do output"/>
99 <param argument="--partial-5" type="boolean" truevalue="--partial-5" falsevalue="" display="radio" label="Output ORFs with Stop but no Start?"
100 help="Output ORFs with an inframe stop codon lacking an inframe start codon. NO = do not output. YES = do output"/>
101 <param argument="--between-stops" type="boolean" display="radio" truevalue="--between-stops" falsevalue="" label="Output ORFs bound by Stop codons?"
102 help="Output ORFs defined as regions between stop codons (regions free of stop codon). This will set --partial-3 and --partial-5 true"/>
103 <param argument="--include-stop" type="boolean" truevalue="--include-stop" falsevalue="" display="radio" label="Include stop codon in the results?"
104 help="Output ORFs with an inframe stop codon lacking an inframe start codon. NO = do not include. YES = include"/>
105 </inputs>
106 <outputs>
107 <data name="out_bed" format="bed6" label="ORFs on ${on_string} (BED format)">
108 <filter>"BED" in out_files</filter>
109 </data>
110 <data name="out_bed12" format="bed12" label="ORFs on ${on_string} (BED12 format)">
111 <filter>"BED12" in out_files</filter>
112 </data>
113 <data name="out_dna" format="fasta" label="ORFs on ${on_string} (FASTA DNA)">
114 <filter>"DNA" in out_files</filter>
115 </data>
116 <data name="out_rna" format="fasta" label="ORFs on ${on_string} (FASTA RNA)">
117 <filter>"RNA" in out_files</filter>
118 </data>
119 <data name="out_pep" format="fasta" label="ORFs on ${on_string} (FASTA Protein)">
120 <filter>"PEP" in out_files</filter>
121 </data>
122 </outputs>
123 <tests>
124 <test expect_num_outputs="1">
125 <param name="input1" value="orfipy.fa"/>
126 <param name="out_files" value="BED"/>
127 <output name="out_bed" file="test1.bed"/>
128 </test>
129 <test expect_num_outputs="1">
130 <param name="input1" value="orfipy.fa"/>
131 <param name="out_files" value="DNA"/>
132 <param name="min" value="100"/>
133 <param name="partial_5" value="true"/>
134 <output name="out_dna" file="test2.fa"/>
135 </test>
136 <test expect_num_outputs="1">
137 <param name="input1" value="orfipy.fa.gz"/>
138 <param name="out_files" value="DNA"/>
139 <param name="min" value="100"/>
140 <param name="partial_5" value="true"/>
141 <output name="out_dna" file="test2.fa"/>
142 </test>
143 </tests>
144 <help><![CDATA[
145 **What it does**
146
147 Orfipy is a tool for finding open reading frames (ORFs).
148
149 **Parameters**
150
151 Galaxy interface of Orfipy supports the following parameters (the following is taken from the tool help)::
152
153 --table TABLE The codon table number to use or path to .json file
154 with codon table. Use --show-tables to see available
155 tables compiled from: https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?chapter=cgencodes Default: 1
156 --start START Comma-separated list of start-codons. This will
157 override start codons described in translation table.
158 E.g. "--start ATG,ATT" Default: Derived from the
159 translation table selected
160 --stop STOP Comma-separated list of stop codons. This will
161 override stop codons described in translation table.
162 E.g. "--start TAG,TTT" Default: Derived from the
163 translation table selected
164 --outdir OUTDIR Path to outdir default: orfipy_<infasta>_out
165 --bed12 BED12 bed12 out file Default: None
166 --bed BED bed out file Default: None
167 --dna DNA fasta (DNA) out file Default: None
168 --rna RNA fasta (RNA) out file Default: None
169 --pep PEP fasta (peptide) out file Default: None
170 --min MIN Minimum length of ORF, excluding stop codon
171 (nucleotide) Default: 30
172 --max MAX Maximum length of ORF, excluding stop codon
173 (nucleotide) Default: 1,000,000,000
174 --strand {f,r,b} Strands to find ORFs [(f)orward,(r)everse,(b)oth]
175 Default: b
176 --ignore-case Ignore case and find ORFs in lower case sequences too.
177 Useful for soft-masked sequences. Default: False
178 --partial-3 Output ORFs with a start codon but lacking an inframe
179 stop codon. E.g. "ATG TTT AAA" Default: False
180 --partial-5 Output ORFs with an inframe stop codon lacking an
181 inframe start codon. E.g. "TTT AAA TAG" Default: False
182 --between-stops Output ORFs defined as regions between stop codons
183 (regions free of stop codon). This will set
184 --partial-3 and --partial-5 true. Default: False
185 --include-stop Include stop codon in the results, if a stop codon
186 exists. This output format is compatible with
187 TransDecoder's which includes stop codon coordinates
188 Default: False
189 ]]></help>
190 <citations>
191 <citation type="doi">10.1093/bioinformatics/btab090</citation>
192 </citations>
193 </tool>