Mercurial > repos > iuc > seqkit_translate

annotate seqkit_translate.xml @ 2:6366952ddfd3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 99c10c3df0424268179b3f54f89e01a34b9e120e
author iuc
date Sat, 18 May 2024 23:11:22 +0000
parents 18f755f51204
children 0c011189b47e
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a589a34457ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 235285be5ca6e2320545b16d017e1795b1d345ad
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1 <tool id="seqkit_translate" name="SeqKit translate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
1
18f755f51204 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 4e3719a2c09e11afd9069bb520de11e3a0f02c72
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2 <description>nucleotid to protein sequence</description>
0
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3 <macros>
a589a34457ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 235285be5ca6e2320545b16d017e1795b1d345ad
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4 <import>macros.xml</import>
a589a34457ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 235285be5ca6e2320545b16d017e1795b1d345ad
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5 </macros>
a589a34457ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 235285be5ca6e2320545b16d017e1795b1d345ad
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6 <expand macro="bio_tools"/>
a589a34457ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 235285be5ca6e2320545b16d017e1795b1d345ad
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7 <expand macro="requirements"/>
a589a34457ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 235285be5ca6e2320545b16d017e1795b1d345ad
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8 <command detect_errors="exit_code"><![CDATA[
a589a34457ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 235285be5ca6e2320545b16d017e1795b1d345ad
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9 seqkit translate
a589a34457ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 235285be5ca6e2320545b16d017e1795b1d345ad
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10 '$input'
a589a34457ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 235285be5ca6e2320545b16d017e1795b1d345ad
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11 -o '$output'
a589a34457ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 235285be5ca6e2320545b16d017e1795b1d345ad
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12 #if $translate_or_remove_unknown.selector == 'trimming':
a589a34457ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 235285be5ca6e2320545b16d017e1795b1d345ad
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13 $translate_or_remove_unknown.trim
a589a34457ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 235285be5ca6e2320545b16d017e1795b1d345ad
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14 #elif $translate_or_remove_unknown.selector == 'translate':
a589a34457ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 235285be5ca6e2320545b16d017e1795b1d345ad
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15 $translate_or_remove_unknown.allow_unknown_codon
a589a34457ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 235285be5ca6e2320545b16d017e1795b1d345ad
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16 #end if
a589a34457ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 235285be5ca6e2320545b16d017e1795b1d345ad
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17 $append_frame
a589a34457ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 235285be5ca6e2320545b16d017e1795b1d345ad
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18 $clean
a589a34457ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 235285be5ca6e2320545b16d017e1795b1d345ad
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19 #if $frame
a589a34457ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 235285be5ca6e2320545b16d017e1795b1d345ad
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20 -f '$frame'
a589a34457ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 235285be5ca6e2320545b16d017e1795b1d345ad
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21 #end if
a589a34457ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 235285be5ca6e2320545b16d017e1795b1d345ad
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22 $init_codon_as_M
a589a34457ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 235285be5ca6e2320545b16d017e1795b1d345ad
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23 #if $transl_table
a589a34457ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 235285be5ca6e2320545b16d017e1795b1d345ad
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24 -T '$transl_table'
a589a34457ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 235285be5ca6e2320545b16d017e1795b1d345ad
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25 #end if
a589a34457ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 235285be5ca6e2320545b16d017e1795b1d345ad
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26
a589a34457ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 235285be5ca6e2320545b16d017e1795b1d345ad
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27 ]]></command>
a589a34457ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 235285be5ca6e2320545b16d017e1795b1d345ad
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28 <inputs>
a589a34457ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 235285be5ca6e2320545b16d017e1795b1d345ad
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29 <param name="input" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" label="Input file"/>
a589a34457ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 235285be5ca6e2320545b16d017e1795b1d345ad
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30 <param argument="--frame" type="select" multiple="true" label="Frame(s) to translate" >
a589a34457ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 235285be5ca6e2320545b16d017e1795b1d345ad
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31 <option value="1" selected="true">1 (default)</option>
a589a34457ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 235285be5ca6e2320545b16d017e1795b1d345ad
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32 <option value="2" selected="false">2</option>
a589a34457ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 235285be5ca6e2320545b16d017e1795b1d345ad
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33 <option value="3" selected="false">3</option>
a589a34457ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 235285be5ca6e2320545b16d017e1795b1d345ad
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34 <option value="-1" selected="false">-1</option>
a589a34457ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 235285be5ca6e2320545b16d017e1795b1d345ad
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35 <option value="-2" selected="false">-2</option>
a589a34457ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 235285be5ca6e2320545b16d017e1795b1d345ad
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36 <option value="-3" selected="false">-3</option>
a589a34457ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 235285be5ca6e2320545b16d017e1795b1d345ad
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37 <option value="6" selected="false">All 6 frames</option>
a589a34457ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 235285be5ca6e2320545b16d017e1795b1d345ad
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38 </param>
a589a34457ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 235285be5ca6e2320545b16d017e1795b1d345ad
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39 <param argument="--append-frame" type="boolean" truevalue="--append-frame" falsevalue="" checked="false" label="Append frame information to sequence ID ?" />
a589a34457ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 235285be5ca6e2320545b16d017e1795b1d345ad
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40 <param argument="--transl-table" type="select" label="Translate table / genetic code to use" >
a589a34457ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 235285be5ca6e2320545b16d017e1795b1d345ad
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41 <option value="1" selected="true">1: The Standard Code (default)</option>
a589a34457ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 235285be5ca6e2320545b16d017e1795b1d345ad
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42 <option value="2" selected="false">2: The Vertebrate Mitochondrial Code</option>
a589a34457ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 235285be5ca6e2320545b16d017e1795b1d345ad
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43 <option value="3" selected="false">3: The Yeast Mitochondrial Code</option>
a589a34457ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 235285be5ca6e2320545b16d017e1795b1d345ad
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44 <option value="4" selected="false">4: The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
a589a34457ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 235285be5ca6e2320545b16d017e1795b1d345ad
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45 <option value="5" selected="false">5: The Invertebrate Mitochondrial Code</option>
a589a34457ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 235285be5ca6e2320545b16d017e1795b1d345ad
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46 <option value="6" selected="false">6: The Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
a589a34457ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 235285be5ca6e2320545b16d017e1795b1d345ad
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47 <option value="9" selected="false">9: The Echinoderm and Flatworm Mitochondrial Code</option>
a589a34457ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 235285be5ca6e2320545b16d017e1795b1d345ad
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48 <option value="10" selected="false">10: The Euplotid Nuclear Code</option>
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49 <option value="11" selected="false">11: The Bacterial, Archaeal and Plant Plastid Code</option>
a589a34457ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 235285be5ca6e2320545b16d017e1795b1d345ad
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50 <option value="12" selected="false">12: The Alternative Yeast Nuclear Code</option>
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51 <option value="13" selected="false">13: The Ascidian Mitochondrial Code</option>
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52 <option value="14" selected="false">14: The Alternative Flatworm Mitochondrial Code</option>
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53 <option value="16" selected="false">16: Chlorophycean Mitochondrial Code</option>
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54 <option value="21" selected="false">21: Trematode Mitochondrial Code</option>
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55 <option value="22" selected="false">22: Scenedesmus obliquus Mitochondrial Code</option>
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56 <option value="23" selected="false">23: Thraustochytrium Mitochondrial Code</option>
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57 <option value="24" selected="false">24: Pterobranchia Mitochondrial Code</option>
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58 <option value="25" selected="false">25: Candidate Division SR1 and Gracilibacteria Code</option>
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59 <option value="26" selected="false">26: Pachysolen tannophilus Nuclear Code</option>
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60 <option value="27" selected="false">27: Karyorelict Nuclear</option>
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61 <option value="28" selected="false">28: Condylostoma Nuclear</option>
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62 <option value="29" selected="false">29: Mesodinium Nuclear</option>
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63 <option value="30" selected="false">30: Peritrich Nuclear</option>
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64 <option value="31" selected="false">31: Blastocrithidia Nuclear</option>
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65 </param>
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66 <param argument="--clean" type="boolean" truevalue="--clean" falsevalue="" checked="false" label="Change all STOP codon positions from the '*' character to 'X' (an unknown residue) ?" />
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67 <conditional name="translate_or_remove_unknown" >
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68 <param name="selector" type="select" label="Translate or remove unknown code ?" >
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69 <option value="trimming">Remove all 'X' and '*' characters</option>
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70 <option value="translate">Translate unknown code to 'X'</option>
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71 </param>
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72 <when value="trimming">
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73 <param argument="--trim" type="boolean" truevalue="--trim" falsevalue="" checked="false" label="Remove all 'X' and '*' characters from the right end of the translation" />
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74 </when>
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75 <when value="translate">
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76 <param argument="--allow-unknown-codon" type="boolean" truevalue="--allow-unknown-codon" falsevalue="" checked="false" label="Translate unknown code to 'X' ?" />
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77 </when>
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78 </conditional>
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79 <param argument="--init-codon-as-M" type="boolean" truevalue="--init-codon-as-M" falsevalue="" checked="false" label="Translate initial codon at beginning to 'M'" />
a589a34457ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 235285be5ca6e2320545b16d017e1795b1d345ad
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80 </inputs>
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81 <outputs>
1
18f755f51204 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 4e3719a2c09e11afd9069bb520de11e3a0f02c72
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82 <data name="output" format_source="input" label="${tool.name} on ${on_string}"/>
0
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83 </outputs>
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84 <tests>
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85 <!-- 1. fastq -->
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86 <test expect_num_outputs="1">
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87 <param name="input" value="input1.fastq.gz" ftype="fastqsanger.gz"/>
a589a34457ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 235285be5ca6e2320545b16d017e1795b1d345ad
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88 <output decompress="true" name="output" file="translate_output3.fastq.gz" ftype="fastqsanger.gz"/>
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89 </test>
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90 <!-- 2. fasta -->
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91 <test expect_num_outputs="1">
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92 <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>
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93 <conditional name="translate_or_remove_unknown">
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94 <param name="allow_unknown_codon" value="true"/>
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95 </conditional>
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96 <param name="append_frame" value="true"/>
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97 <param name="clean" value="true"/>
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98 <param name="frame" value="2,3" />
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99 <param name="init_codon_as_M" value="true" />
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100 <param name="transl_table" value="3" />
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101 <output decompress="true" name="output" file="translate_output1.fasta.gz" ftype="fasta.gz"/>
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102 </test>
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103 <!-- 3. fastq + trim -->
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104 <test expect_num_outputs="1">
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105 <param name="input" value="input1.fastq.gz" ftype="fastqsanger.gz"/>
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106 <conditional name="translate_or_remove_unknown">
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107 <param name="trim" value="true" />
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108 </conditional>
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109 <output decompress="true" name="output" file="translate_output2.fastq.gz" ftype="fastqsanger.gz"/>
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110 </test>
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111 </tests>
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112 <help>
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113 **What it does**
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114
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115 Translate DNA/RNA to protein sequence (supporting ambiguous bases)
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116
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117 </help>
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118 <expand macro="citations"/>
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119 </tool>