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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 02b217857afbabac1f86b825a902a5cc20fcf5ed
author iuc
date Tue, 04 Jun 2024 10:56:16 +0000
parents 45d4d26e01b5
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1:45d4d26e01b5 2:f5114c60dc95
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
11 orfipy 11 orfipy
12 --procs "\${GALAXY_SLOTS:-1}" 12 --procs "\${GALAXY_SLOTS:-1}"
13 --outdir ./ 13 --outdir ./
14 #for $o in str($out_files).split(','): 14 #if 'BED' in $out_files or $longest:
15 #if $o == 'BED': 15 --bed '$out_bed'
16 --bed '$out_bed' 16 #end if
17 #else if $o == 'BED12': 17 #if 'BED12' in $out_files:
18 --bed12 '$out_bed12' 18 --bed12 '$out_bed12'
19 #else if $o == 'DNA': 19 #end if
20 --dna '$out_dna' 20 #if 'DNA' in $out_files:
21 #else if $o == 'RNA': 21 --dna '$out_dna'
22 --rna '$out_rna' 22 #end if
23 #else if $o == 'PEP': 23 #if 'RNA' in $out_files:
24 --pep '$out_pep' 24 --rna '$out_rna'
25 #end if 25 #end if
26 #end for 26 #if 'PEP' in $out_files:
27 --pep '$out_pep'
28 #end if
27 --strand $strand 29 --strand $strand
28 #if $min: 30 #if $min:
29 --min $min 31 --min $min
30 #end if 32 #end if
31 #if $max: 33 #if $max:
41 $ignore_case 43 $ignore_case
42 $partial_3 44 $partial_3
43 $partial_5 45 $partial_5
44 $between_stops 46 $between_stops
45 $include_stop 47 $include_stop
48 $longest
46 '$input1' 49 '$input1'
47 ]]></command> 50 ]]></command>
48 <inputs> 51 <inputs>
49 <param name="input1" type="data" format="fasta,fasta.gz" label="Find ORFs in:" help="ORFs will be detected in this sequence"/> 52 <param name="input1" type="data" format="fasta,fasta.gz" label="Find ORFs in:" help="ORFs will be detected in this sequence"/>
50 <param type="select" argument="--table" label="Specify genetic code"> 53 <param argument="--table" type="select" label="Specify genetic code">
51 <option value="1" selected="true">1 Standard</option> 54 <option value="1" selected="true">1 Standard</option>
52 <option value="2">2 Vertebrate mitochondrial</option> 55 <option value="2">2 Vertebrate mitochondrial</option>
53 <option value="3">3 Yeast mitochondrial</option> 56 <option value="3">3 Yeast mitochondrial</option>
54 <option value="4">4 Mold, Protozoan, Coelenterate, Mycoplasma, Spiroplasma mitochondrial</option> 57 <option value="4">4 Mold, Protozoan, Coelenterate, Mycoplasma, Spiroplasma mitochondrial</option>
55 <option value="5">5 Invertebrate Mitochondrial</option> 58 <option value="5">5 Invertebrate Mitochondrial</option>
70 <option value="20">20 Karyorelict nuclear</option> 73 <option value="20">20 Karyorelict nuclear</option>
71 <option value="21">21 Condylostoma nuclear</option> 74 <option value="21">21 Condylostoma nuclear</option>
72 <option value="22">22 Mesodinium nuclear</option> 75 <option value="22">22 Mesodinium nuclear</option>
73 <option value="23">23 Peritrich nuclear</option> 76 <option value="23">23 Peritrich nuclear</option>
74 </param> 77 </param>
75 <param name="out_files" argument="--bed,--bed12,--dna,--rna,--pep" type="select" multiple="true" display="checkboxes" label="Select outputs" 78 <param name="out_files" type="select" label="Select outputs" help="DNA, RNA, and Peptide options will produce FASTA outputs" multiple="true" display="checkboxes">
76 help="DNA, RNA, and Peptide options will produce FASTA outputs">
77 <option value="BED" selected="true">BED</option> 79 <option value="BED" selected="true">BED</option>
78 <option value="BED12">BED12</option> 80 <option value="BED12">BED12</option>
79 <option value="DNA">DNA</option> 81 <option value="DNA">DNA</option>
80 <option value="RNA">RNA</option> 82 <option value="RNA">RNA</option>
81 <option value="PEP">Peptides</option> 83 <option value="PEP">Peptides</option>
82 </param> 84 </param>
83 <param argument="--strand" type="select" display="radio" label="Select strand" help="Identify ORFs on which strand"> 85 <param argument="--strand" type="select" label="Select strand" help="Identify ORFs on which strand" display="radio">
84 <option value="b" selected="true">Both</option> 86 <option value="b" selected="true">Both</option>
85 <option value="f">Forward</option> 87 <option value="f">Forward</option>
86 <option value="r">Reverse</option> 88 <option value="r">Reverse</option>
87 </param> 89 </param>
88 <param argument="--min" type="integer" min="0" optional="true" label="Minimum length of ORFs" 90 <param argument="--min" type="integer" min="0" optional="true" label="Minimum length of ORFs"
95 </param> 97 </param>
96 <param argument="--stop" type="text" optional="true" label="Stop codon(s) to use" 98 <param argument="--stop" type="text" optional="true" label="Stop codon(s) to use"
97 help="A commma separated list without spaces. Only ATCG and comma are allowed"> 99 help="A commma separated list without spaces. Only ATCG and comma are allowed">
98 <validator type="regex" message="Only 'ATCGatcg' and ',' are allowed in this field">^[ATGCatcg,]*$</validator> 100 <validator type="regex" message="Only 'ATCGatcg' and ',' are allowed in this field">^[ATGCatcg,]*$</validator>
99 </param> 101 </param>
100 <param argument="--ignore-case" type="boolean" truevalue="--ignore-case" falsevalue="" display="radio" label="Ignore case?" 102 <param argument="--ignore-case" type="boolean" truevalue="--ignore-case" falsevalue="" label="Ignore case?" help="Ignore case and find ORFs in lower case sequences too. NO = do not ignore (use upper case only). YES = ignore" display="radio"/>
101 help="Ignore case and find ORFs in lower case sequences too. NO = do not ignore (use upper case only). YES = ignore"/> 103 <param argument="--partial-3" type="boolean" truevalue="--partial-3" falsevalue="" label="Output ORFs with Start but no Stop?" help="Output ORFs with a start codon but lacking an inframe stop codon. NO = do not output. YES = do output" display="radio"/>
102 <param argument="--partial-3" type="boolean" truevalue="--partial-3" falsevalue="" display="radio" label="Output ORFs with Start but no Stop?" 104 <param argument="--partial-5" type="boolean" truevalue="--partial-5" falsevalue="" label="Output ORFs with Stop but no Start?" help="Output ORFs with an inframe stop codon lacking an inframe start codon. NO = do not output. YES = do output" display="radio"/>
103 help="Output ORFs with a start codon but lacking an inframe stop codon. NO = do not output. YES = do output"/> 105 <param argument="--between-stops" type="boolean" truevalue="--between-stops" falsevalue="" label="Output ORFs bound by Stop codons?" help="Output ORFs defined as regions between stop codons (regions free of stop codon). This will set --partial-3 and --partial-5 true" display="radio"/>
104 <param argument="--partial-5" type="boolean" truevalue="--partial-5" falsevalue="" display="radio" label="Output ORFs with Stop but no Start?" 106 <param argument="--include-stop" type="boolean" truevalue="--include-stop" falsevalue="" label="Include stop codon in the results?" help="Output ORFs with an inframe stop codon lacking an inframe start codon. NO = do not include. YES = include" display="radio"/>
105 help="Output ORFs with an inframe stop codon lacking an inframe start codon. NO = do not output. YES = do output"/> 107 <param argument="--longest" type="boolean" truevalue="--longest" falsevalue="" label="Output separate BED file with longest ORFs per sequence" help="Setting this option will automatically enable the BED option."/>
106 <param argument="--between-stops" type="boolean" display="radio" truevalue="--between-stops" falsevalue="" label="Output ORFs bound by Stop codons?"
107 help="Output ORFs defined as regions between stop codons (regions free of stop codon). This will set --partial-3 and --partial-5 true"/>
108 <param argument="--include-stop" type="boolean" truevalue="--include-stop" falsevalue="" display="radio" label="Include stop codon in the results?"
109 help="Output ORFs with an inframe stop codon lacking an inframe start codon. NO = do not include. YES = include"/>
110 </inputs> 108 </inputs>
111 <outputs> 109 <outputs>
112 <data name="out_bed" format="bed6" label="ORFs on ${on_string} (BED format)"> 110 <data name="out_bed" format="bed6" label="ORFs on ${on_string} (BED format)">
113 <filter>"BED" in out_files</filter> 111 <filter>"BED" in out_files or longest</filter>
114 </data> 112 </data>
115 <data name="out_bed12" format="bed12" label="ORFs on ${on_string} (BED12 format)"> 113 <data name="out_bed12" format="bed12" label="ORFs on ${on_string} (BED12 format)">
116 <filter>"BED12" in out_files</filter> 114 <filter>"BED12" in out_files</filter>
117 </data> 115 </data>
118 <data name="out_dna" format="fasta" label="ORFs on ${on_string} (FASTA DNA)"> 116 <data name="out_dna" format="fasta" label="ORFs on ${on_string} (FASTA DNA)">
149 <param name="input1" value="orfipy.fa.gz"/> 147 <param name="input1" value="orfipy.fa.gz"/>
150 <param name="out_files" value="DNA"/> 148 <param name="out_files" value="DNA"/>
151 <param name="max" value="100000000"/> 149 <param name="max" value="100000000"/>
152 <output name="out_dna" file="test3.fa"/> 150 <output name="out_dna" file="test3.fa"/>
153 </test> 151 </test>
152 <test expect_num_outputs="2">
153 <param name="input1" value="orfipy.fa.gz"/>
154 <param name="out_files" value="DNA"/>
155 <param name="max" value="100000000"/>
156 <param name="longest" value="true"/>
157 <output name="out_dna" file="test3.fa"/>
158 <output name="out_bed" file="test1.bed"/>
159 </test>
160 <test expect_num_outputs="1">
161 <param name="input1" value="orfipy.fa"/>
162 <param name="out_files" value="BED"/>
163 <param name="longest" value="true"/>
164 <output name="out_bed" file="test1.bed"/>
165 </test>
154 </tests> 166 </tests>
155 <help><![CDATA[ 167 <help><![CDATA[
156 **What it does** 168 **What it does**
157 169
158 Orfipy is a tool for finding open reading frames (ORFs). 170 Orfipy is a tool for finding open reading frames (ORFs) in sequences (FASTA files).
159 171
160 **Parameters**
161 172
162 Galaxy interface of Orfipy supports the following parameters (the following is taken from the tool help)::
163
164 --table TABLE The codon table number to use or path to .json file
165 with codon table. Use --show-tables to see available
166 tables compiled from: https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?chapter=cgencodes Default: 1
167 --start START Comma-separated list of start-codons. This will
168 override start codons described in translation table.
169 E.g. "--start ATG,ATT" Default: Derived from the
170 translation table selected
171 --stop STOP Comma-separated list of stop codons. This will
172 override stop codons described in translation table.
173 E.g. "--start TAG,TTT" Default: Derived from the
174 translation table selected
175 --outdir OUTDIR Path to outdir default: orfipy_<infasta>_out
176 --bed12 BED12 bed12 out file Default: None
177 --bed BED bed out file Default: None
178 --dna DNA fasta (DNA) out file Default: None
179 --rna RNA fasta (RNA) out file Default: None
180 --pep PEP fasta (peptide) out file Default: None
181 --min MIN Minimum length of ORF, excluding stop codon
182 (nucleotide) Default: 30
183 --max MAX Maximum length of ORF, excluding stop codon
184 (nucleotide) Default: 1,000,000,000
185 --strand {f,r,b} Strands to find ORFs [(f)orward,(r)everse,(b)oth]
186 Default: b
187 --ignore-case Ignore case and find ORFs in lower case sequences too.
188 Useful for soft-masked sequences. Default: False
189 --partial-3 Output ORFs with a start codon but lacking an inframe
190 stop codon. E.g. "ATG TTT AAA" Default: False
191 --partial-5 Output ORFs with an inframe stop codon lacking an
192 inframe start codon. E.g. "TTT AAA TAG" Default: False
193 --between-stops Output ORFs defined as regions between stop codons
194 (regions free of stop codon). This will set
195 --partial-3 and --partial-5 true. Default: False
196 --include-stop Include stop codon in the results, if a stop codon
197 exists. This output format is compatible with
198 TransDecoder's which includes stop codon coordinates
199 Default: False
200 ]]></help> 173 ]]></help>
201 <citations> 174 <citations>
202 <citation type="doi">10.1093/bioinformatics/btab090</citation> 175 <citation type="doi">10.1093/bioinformatics/btab090</citation>
203 </citations> 176 </citations>
204 </tool> 177 </tool>