Mercurial > repos > iuc > orfipy

annotate orfipy.xml @ 1:45d4d26e01b5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 472277ff42e1d7018e0d2921bd51a018572793c5
author iuc
date Thu, 22 Sep 2022 14:03:42 +0000
parents c147914c9f02
children f5114c60dc95
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45d4d26e01b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 472277ff42e1d7018e0d2921bd51a018572793c5
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1 <tool id="orfipy" name="ORFipy" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
0
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
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2 <description>a versatile ORF finder</description>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
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3 <macros>
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4 <import>macros.xml</import>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
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5 </macros>
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6 <expand macro="xrefs"/>
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">orfipy</requirement>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
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11 orfipy
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12 --procs "\${GALAXY_SLOTS:-1}"
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
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13 --outdir ./
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
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14 #for $o in str($out_files).split(','):
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
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15 #if $o == 'BED':
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16 --bed '$out_bed'
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
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17 #else if $o == 'BED12':
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
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18 --bed12 '$out_bed12'
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19 #else if $o == 'DNA':
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20 --dna '$out_dna'
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
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21 #else if $o == 'RNA':
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22 --rna '$out_rna'
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
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23 #else if $o == 'PEP':
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24 --pep '$out_pep'
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25 #end if
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26 #end for
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27 --strand $strand
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28 #if $min:
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29 --min $min
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
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30 #end if
1
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31 #if $max:
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32 --max $max
45d4d26e01b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 472277ff42e1d7018e0d2921bd51a018572793c5
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33 #end if
0
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34 --table $table
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35 #if $start:
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36 --start '$start'
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37 #end if
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38 #if $stop:
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39 --stop '$stop'
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40 #end if
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41 $ignore_case
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42 $partial_3
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43 $partial_5
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44 $between_stops
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45 $include_stop
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46 '$input1'
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47 ]]></command>
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48 <inputs>
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49 <param name="input1" type="data" format="fasta,fasta.gz" label="Find ORFs in:" help="ORFs will be detected in this sequence"/>
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50 <param type="select" argument="--table" label="Specify genetic code">
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51 <option value="1" selected="true">1 Standard</option>
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52 <option value="2">2 Vertebrate mitochondrial</option>
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53 <option value="3">3 Yeast mitochondrial</option>
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54 <option value="4">4 Mold, Protozoan, Coelenterate, Mycoplasma, Spiroplasma mitochondrial</option>
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55 <option value="5">5 Invertebrate Mitochondrial</option>
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56 <option value="6">6 Ciliate, Dasycladacean, Hexamita Nuclear</option>
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57 <option value="7">7 Echinoderm and Flatworm Mitochondrial</option>
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58 <option value="8">8 Euplotid Nuclear</option>
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59 <option value="9">9 Bacterial, Archaeal and Plant Plastid</option>
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60 <option value="10">10 Alternative Yeast nuclear</option>
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61 <option value="11">11 Ascidian mitochondrial</option>
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62 <option value="12">12 Alternative Flatworm mitochondrial</option>
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63 <option value="13">13 Chlorophycean mitochondrial</option>
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64 <option value="14">14 Trematode mitochondrial</option>
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65 <option value="15">15 Scenedesmus obliquus mitochondrial</option>
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66 <option value="16">16 Thraustochytrium mitochondrial code</option>
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67 <option value="17">17 Pterobranchia mitochondrial</option>
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68 <option value="18">18 Candidate Division SR1 and Gracilibacteria</option>
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69 <option value="19">19 Pachysolen tannophilus Nuclear Code</option>
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70 <option value="20">20 Karyorelict nuclear</option>
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71 <option value="21">21 Condylostoma nuclear</option>
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72 <option value="22">22 Mesodinium nuclear</option>
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73 <option value="23">23 Peritrich nuclear</option>
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74 </param>
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75 <param name="out_files" argument="--bed,--bed12,--dna,--rna,--pep" type="select" multiple="true" display="checkboxes" label="Select outputs"
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76 help="DNA, RNA, and Peptide options will produce FASTA outputs">
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77 <option value="BED" selected="true">BED</option>
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78 <option value="BED12">BED12</option>
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79 <option value="DNA">DNA</option>
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80 <option value="RNA">RNA</option>
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81 <option value="PEP">Peptides</option>
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82 </param>
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83 <param argument="--strand" type="select" display="radio" label="Select strand" help="Identify ORFs on which strand">
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84 <option value="b" selected="true">Both</option>
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85 <option value="f">Forward</option>
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86 <option value="r">Reverse</option>
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87 </param>
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88 <param argument="--min" type="integer" min="0" optional="true" label="Minimum length of ORFs"
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89 help="No ORFs below this value will be reported. All ORFs will be reported if this parameter is not set. Default is 30"/>
1
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90 <param argument="--max" type="integer" min="0" optional="true" label="Maximum length of ORFs"
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91 help="This value doesn't take in account the STOP codon. No ORFs over this value will be reported. Default is 1.000.000.000."/>
0
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92 <param argument="--start" type="text" optional="true" label="Start codon(s) to use"
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93 help="A comma-separated list without spaces. Only ATCG and comma are allowed">
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94 <validator type="regex" message="Only 'ATCGatcg' and ',' are allowed in this field">^[ATGCatcg,]*$</validator>
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95 </param>
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96 <param argument="--stop" type="text" optional="true" label="Stop codon(s) to use"
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97 help="A commma separated list without spaces. Only ATCG and comma are allowed">
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98 <validator type="regex" message="Only 'ATCGatcg' and ',' are allowed in this field">^[ATGCatcg,]*$</validator>
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99 </param>
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100 <param argument="--ignore-case" type="boolean" truevalue="--ignore-case" falsevalue="" display="radio" label="Ignore case?"
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101 help="Ignore case and find ORFs in lower case sequences too. NO = do not ignore (use upper case only). YES = ignore"/>
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102 <param argument="--partial-3" type="boolean" truevalue="--partial-3" falsevalue="" display="radio" label="Output ORFs with Start but no Stop?"
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103 help="Output ORFs with a start codon but lacking an inframe stop codon. NO = do not output. YES = do output"/>
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104 <param argument="--partial-5" type="boolean" truevalue="--partial-5" falsevalue="" display="radio" label="Output ORFs with Stop but no Start?"
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105 help="Output ORFs with an inframe stop codon lacking an inframe start codon. NO = do not output. YES = do output"/>
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106 <param argument="--between-stops" type="boolean" display="radio" truevalue="--between-stops" falsevalue="" label="Output ORFs bound by Stop codons?"
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107 help="Output ORFs defined as regions between stop codons (regions free of stop codon). This will set --partial-3 and --partial-5 true"/>
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108 <param argument="--include-stop" type="boolean" truevalue="--include-stop" falsevalue="" display="radio" label="Include stop codon in the results?"
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109 help="Output ORFs with an inframe stop codon lacking an inframe start codon. NO = do not include. YES = include"/>
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110 </inputs>
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111 <outputs>
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112 <data name="out_bed" format="bed6" label="ORFs on ${on_string} (BED format)">
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113 <filter>"BED" in out_files</filter>
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114 </data>
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115 <data name="out_bed12" format="bed12" label="ORFs on ${on_string} (BED12 format)">
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116 <filter>"BED12" in out_files</filter>
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117 </data>
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118 <data name="out_dna" format="fasta" label="ORFs on ${on_string} (FASTA DNA)">
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119 <filter>"DNA" in out_files</filter>
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120 </data>
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121 <data name="out_rna" format="fasta" label="ORFs on ${on_string} (FASTA RNA)">
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122 <filter>"RNA" in out_files</filter>
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123 </data>
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124 <data name="out_pep" format="fasta" label="ORFs on ${on_string} (FASTA Protein)">
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125 <filter>"PEP" in out_files</filter>
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126 </data>
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127 </outputs>
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128 <tests>
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129 <test expect_num_outputs="1">
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130 <param name="input1" value="orfipy.fa"/>
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131 <param name="out_files" value="BED"/>
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132 <output name="out_bed" file="test1.bed"/>
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133 </test>
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134 <test expect_num_outputs="1">
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135 <param name="input1" value="orfipy.fa"/>
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136 <param name="out_files" value="DNA"/>
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137 <param name="min" value="100"/>
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138 <param name="partial_5" value="true"/>
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139 <output name="out_dna" file="test2.fa"/>
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140 </test>
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141 <test expect_num_outputs="1">
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142 <param name="input1" value="orfipy.fa.gz"/>
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143 <param name="out_files" value="DNA"/>
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144 <param name="min" value="100"/>
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145 <param name="partial_5" value="true"/>
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146 <output name="out_dna" file="test2.fa"/>
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147 </test>
1
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148 <test expect_num_outputs="1">
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149 <param name="input1" value="orfipy.fa.gz"/>
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150 <param name="out_files" value="DNA"/>
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151 <param name="max" value="100000000"/>
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152 <output name="out_dna" file="test3.fa"/>
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153 </test>
0
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154 </tests>
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155 <help><![CDATA[
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156 **What it does**
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157
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158 Orfipy is a tool for finding open reading frames (ORFs).
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159
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160 **Parameters**
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161
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162 Galaxy interface of Orfipy supports the following parameters (the following is taken from the tool help)::
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163
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164 --table TABLE The codon table number to use or path to .json file
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165 with codon table. Use --show-tables to see available
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166 tables compiled from: https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?chapter=cgencodes Default: 1
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167 --start START Comma-separated list of start-codons. This will
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
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168 override start codons described in translation table.
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169 E.g. "--start ATG,ATT" Default: Derived from the
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170 translation table selected
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171 --stop STOP Comma-separated list of stop codons. This will
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
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172 override stop codons described in translation table.
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
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173 E.g. "--start TAG,TTT" Default: Derived from the
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
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174 translation table selected
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
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175 --outdir OUTDIR Path to outdir default: orfipy_<infasta>_out
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
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176 --bed12 BED12 bed12 out file Default: None
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177 --bed BED bed out file Default: None
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178 --dna DNA fasta (DNA) out file Default: None
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179 --rna RNA fasta (RNA) out file Default: None
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180 --pep PEP fasta (peptide) out file Default: None
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181 --min MIN Minimum length of ORF, excluding stop codon
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
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182 (nucleotide) Default: 30
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
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183 --max MAX Maximum length of ORF, excluding stop codon
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184 (nucleotide) Default: 1,000,000,000
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185 --strand {f,r,b} Strands to find ORFs [(f)orward,(r)everse,(b)oth]
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186 Default: b
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187 --ignore-case Ignore case and find ORFs in lower case sequences too.
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188 Useful for soft-masked sequences. Default: False
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189 --partial-3 Output ORFs with a start codon but lacking an inframe
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190 stop codon. E.g. "ATG TTT AAA" Default: False
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191 --partial-5 Output ORFs with an inframe stop codon lacking an
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192 inframe start codon. E.g. "TTT AAA TAG" Default: False
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193 --between-stops Output ORFs defined as regions between stop codons
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194 (regions free of stop codon). This will set
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
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195 --partial-3 and --partial-5 true. Default: False
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196 --include-stop Include stop codon in the results, if a stop codon
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197 exists. This output format is compatible with
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
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198 TransDecoder's which includes stop codon coordinates
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199 Default: False
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200 ]]></help>
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201 <citations>
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202 <citation type="doi">10.1093/bioinformatics/btab090</citation>
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203 </citations>
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204 </tool>