Mercurial > repos > cpt > cpt_gbk_adjacent

annotate adjacent_features.xml @ 2:e2531f4dcdde draft default tip

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author cpt
date Fri, 05 Jan 2024 05:51:24 +0000
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1 <tool id="edu.tamu.cpt2.gbk.adjacent_features" name="Find adjacent Genbank features" version="RC4">
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2 <description>Searches a Genbank file for a given FASTA sequence, then outputs a file with adjacent upstream features, and another with adjacent downstream features.</description>
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3 <macros>
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4 <import>macros.xml</import>
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5
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6 </macros>
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7 <expand macro="requirements"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 python '$__tool_directory__/adjacent_features.py'
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10 #set repeat_var_1 = '" "'.join([ str('$var') for '$var' in '$gbkIn' ])
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11 #set repeat_var_2 = '" "'.join([ str('$var') for '$var' in '$fastaIn' ])
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12 -genbankFiles "$repeat_var_1"
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13 -fastaFiles "$repeat_var_2"
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14 -tTable '$tTable'
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15 -fTable '$fTable'
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16 -upOut '$upstreamOut'
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17 -downOut '$downstreamOut'
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18 '$translate'
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19 '$forceID'
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20 '$mode'
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21 --forward '$ahead'
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22 --behind '$back'
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23 ]]></command>
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24 <inputs>
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25 <param label="Genbank file" name="gbkIn" type="data" format="genbank" multiple="True"/>
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26 <param label="Fasta file" name="fastaIn" type="data" format="fasta" multiple="True"/>
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27 <param label="Translation table to use on Fasta input:" name="fTable" type="select">
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28 <option value="0" selected="true">[0] Do not translate/ Fasta already translated</option>
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29 <option value="1">[1] The Standard Code</option>
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30 <option value="2">[2] The Vertebrate Mitochondrial Code</option>
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31 <option value="3">[3] The Yeast Mitochondrial Code</option>
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32 <option value="4">[4] The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
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33 <option value="5">[5] The Invertebrate Mitochondrial Code </option>
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34 <option value="6">[6] The Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
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35 <option value="9">[9] The Echinoderm and Flatworm Mitochondrial Code</option>
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36 <option value="10">[10] The Euplotid Nuclear Code</option>
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37 <option value="11">[11] The Bacterial, Archaeal and Plant Plastid Code</option>
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38 <option value="12">[12] The Alternative Yeast Nuclear Code</option>
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39 <option value="13">[13] The Ascidian Mitochondrial Code</option>
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40 <option value="14">[14] The Alternative Flatworm Mitochondrial Code</option>
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41 <option value="15">[15] Blepharisma Nuclear Code</option>
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42 <option value="16">[16] Chlorophycean Mitochondrial Code</option>
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43 <option value="21">[21] Trematode Mitochondrial Code</option>
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44 <option value="22">[22] Scenedesmus Obliquus Mitochondrial Code</option>
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45 <option value="23">[23] Thraustochytrium Mitochondrial Code</option>
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46 <option value="24">[24] Pterobranchia Mitochondrial Code</option>
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47 <option value="25">[25] Candidate Division SR1 and Gracilibacteria Code</option>
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48 </param>
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49 <param label="Translation table to use on Genbank features:" name="tTable" type="select">
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50 <option value="0">[0] Do not translate (Use nucleotide sequence of features)</option>
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51 <option value="1">[1] The Standard Code</option>
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52 <option value="2">[2] The Vertebrate Mitochondrial Code</option>
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53 <option value="3">[3] The Yeast Mitochondrial Code</option>
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54 <option value="4">[4] The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
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55 <option value="5">[5] The Invertebrate Mitochondrial Code </option>
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56 <option value="6">[6] The Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
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57 <option value="9">[9] The Echinoderm and Flatworm Mitochondrial Code</option>
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58 <option value="10">[10] The Euplotid Nuclear Code</option>
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59 <option value="11" selected="true">[11] The Bacterial, Archaeal and Plant Plastid Code</option>
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60 <option value="12">[12] The Alternative Yeast Nuclear Code</option>
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61 <option value="13">[13] The Ascidian Mitochondrial Code</option>
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62 <option value="14">[14] The Alternative Flatworm Mitochondrial Code</option>
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63 <option value="15">[15] Blepharisma Nuclear Code</option>
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64 <option value="16">[16] Chlorophycean Mitochondrial Code</option>
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65 <option value="21">[21] Trematode Mitochondrial Code</option>
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66 <option value="22">[22] Scenedesmus Obliquus Mitochondrial Code</option>
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67 <option value="23">[23] Thraustochytrium Mitochondrial Code</option>
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68 <option value="24">[24] Pterobranchia Mitochondrial Code</option>
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69 <option value="25">[25] Candidate Division SR1 and Gracilibacteria Code</option>
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70 </param>
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71 <param label="Number of features upstream to return" name="ahead" type="integer" value="1"/>
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72 <param label="Number of features downstream to return" name="back" type="integer" value="1"/>
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73 <param label="Translate output to protein sequence" name="translate" type="boolean" truevalue="--outProt" falsevalue=""/>
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74 <param label="Genbank Protein's ID must also match Fasta Sequence's ID " name="forceID" type="boolean" truevalue="--forceSeqID" falsevalue="" checked="true"/>
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75 <param name="mode" type="select" label="Mode">
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76 <option value="--genesOnly">Search only Gene-type features</option>
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77 <option value="--cdsOnly">Search only CDS-type features</option>
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78 <option value="">Search all features (Will most likely cause duplicate results, as this will include sub-features)</option>
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79 </param>
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80 </inputs>
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81 <outputs>
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82 <data name="upstreamOut" format="fasta" label="upOut"/>
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83 <data name="downstreamOut" format="fasta" label="downOut"/>
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84 </outputs>
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85 <help><![CDATA[
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86 Currently Experimental: Uploaded for review purposes
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87
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88 **What it does**
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89
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90 For a given Fasta file, this tool searches through the features of a Genbank file for one that matches the sequence in the Fasta. If found, it will then output a specified number of features upstream from the hit and a specified number of features downstream as a multifasta file.
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91
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92 The drop down menus provide a selection of translation tables for the Fasta and Genbank inputs. If "translate output to protein sequence"
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93 is selected, the output will be translated using the table selected for the Genbank translation.
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94
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95 It is currently recommended to select either the Gene only or CDS only options for mode, as searching all features will include sub-features of neighbors (ie, selecting 2 for upstream will give you the neighboring gene and then its CDS sub feature, rather than 2 proper neighbors) as well as the sub-features of the search hit itself.
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96
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97
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98 ]]></help>
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99 <citations>
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100 <citation type="doi">10.1371/journal.pcbi.1008214</citation>
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101 <citation type="bibtex">
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102 @unpublished{galaxyTools,
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103 author = {A. Criscione},
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104 title = {CPT Galaxy Tools},
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105 year = {2019-2021},
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106 note = {https://github.com/tamu-cpt/galaxy-tools/}
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107 }
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108 </citation>
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109 </citations>
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110 </tool>