annotate gstf_preparation.xml @ 5:b3ba0c84667c draft

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 95bab1105cf8a7b07c668f08f712399e8775a4ae
author earlhaminst
date Mon, 16 Apr 2018 14:05:09 -0400
parents 284f64ad9d43
children 56bbdbfe3eaa
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284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
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1 <tool id="gstf_preparation" name="GeneSeqToFamily preparation" version="0.4.0">
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2 <description>converts data for the workflow</description>
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3 <command detect_errors="exit_code">
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4 <![CDATA[
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5 python '$__tool_directory__/gstf_preparation.py'
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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6 #for $q in $queries
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7 --gff3 '${q.genome}:${q.gff3_input}'
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8 #end for
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9 #if str($json) != 'None'
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10 #for $v in $json
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11 --json '$v'
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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12 #end for
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13 #end if
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14 #for $fasta_input in $fasta_inputs
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15 --fasta '${fasta_input}'
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16 #end for
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17 #if $headers
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18 --headers
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19 #end if
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20 #if $longestCDS
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21 -l
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22 #end if
0
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23 -o '$output_db'
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24 --of '$output_fasta'
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25 ]]>
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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26 </command>
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27
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28 <inputs>
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29 <repeat name="queries" title="GFF3 dataset">
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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30 <param name="gff3_input" type="data" format="gff3" label="GFF3 dataset" />
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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31 <param name="genome" type="text" label="Genome name" help="Genome name without whitespaces or special characters">
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32 <validator type="empty_field" />
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33 </param>
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34 </repeat>
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35 <param name="json" type="data" format="json" multiple="true" optional="true" label="Gene features in JSON format generated by 'Get features by Ensembl ID' tool" />
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36 <param name="fasta_inputs" type="data" format="fasta" multiple="true" label="Corresponding FASTA datasets" help="Each FASTA header line should start with a transcript id" />
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37 <param name="longestCDS" type="boolean" checked="false" label="Keep only the longest CDS per gene" />
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38 <param name="headers" type="boolean" checked="true" label="Change the header line of the FASTA sequences to the &gt;TranscriptId_species format" help="As required by TreeBest, part of the GeneSeqToFamily workflow" />
0
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39 </inputs>
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40
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41 <outputs>
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42 <data name="output_db" format="sqlite" label="${tool.name} on ${on_string}: SQLite" />
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43 <data name="output_fasta" format="fasta" label="${tool.name} on ${on_string}: FASTA" />
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44 </outputs>
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45
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46 <tests>
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47 <test>
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48 <param name="fasta_inputs" ftype="fasta" value="Caenorhabditis_elegans.WBcel235.cds.all.shortened.fa" />
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49 <param name="gff3_input" ftype="gff3" value="Caenorhabditis_elegans.WBcel235.87.chromosome.I.shortened.gff3" />
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50 <param name="genome" value="caenorhabditis_elegans" />
4
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51 <param name="longestCDS" value="false" />
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52 <param name="headers" value="true" />
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53
0
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54 <output name="output_db" file="test1.sqlite" compare="sim_size" />
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55 <output name="output_fasta" file="test1.fasta" />
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56 </test>
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57 <test>
4
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58 <param name="fasta_inputs" ftype="fasta" value="Caenorhabditis_elegans.WBcel235.cds.all.shortened.fa" />
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59 <param name="gff3_input" ftype="gff3" value="Caenorhabditis_elegans.WBcel235.87.chromosome.I.shortened.gff3" />
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60 <param name="genome" value="caenorhabditis_elegans" />
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61 <param name="longestCDS" value="true" />
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62 <param name="headers" value="true" />
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63
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64 <output name="output_db" file="test1.sqlite" compare="sim_size" />
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65 <output name="output_fasta" file="test1_longest.fasta" />
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66 </test>
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67 <test>
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68 <param name="fasta_inputs" ftype="fasta" value="Caenorhabditis_elegans.WBcel235.cds.all.shortened.fa" />
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69 <param name="gff3_input" ftype="gff3" value="Caenorhabditis_elegans.WBcel235.87.chromosome.I.shortened.gff3" />
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70 <param name="genome" value="caenorhabditis_elegans" />
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71 <param name="longestCDS" value="false" />
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72 <param name="headers" value="false" />
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73
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74 <output name="output_db" file="test1.sqlite" compare="sim_size" />
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75 <output name="output_fasta" file="Caenorhabditis_elegans.WBcel235.cds.all.shortened.fa" />
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76 </test>
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77 <test>
0
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78 <param name="fasta_inputs" ftype="fasta" value="CDS.fasta" />
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79 <param name="json" ftype="json" value="gene.json" />
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80 <param name="longestCDS" value="false" />
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81 <param name="headers" value="true" />
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82
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83 <output name="output_db" file="test2.sqlite" compare="sim_size" />
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84 <output name="output_fasta" file="test2.fasta" />
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85 </test>
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86 </tests>
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87 <help>
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88 <![CDATA[
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89 **What it does**
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90
4
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91 This tool converts a set of GFF3 and/or JSON gene feature information datasets into SQLite format.
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92
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93 It also filters a CDS FASTA dataset to keep only the transcripts present in the gene feature information. Optionally it can also keep only the longest CDS per gene and/or change the header line of the FASTA sequences to the >TranscriptId_species format (as required by TreeBest, part of the GeneSeqToFamily workflow).
0
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94
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95 Example GFF3 file::
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96
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97 scaffold_0 MYZPE13164_Clone_G006_v1.0 gene 44968 69413 . - . ID=MYZPE13164_G006_v1.0_000000030;Name=MYZPE13164_G006_v1.0_000000030;biotype=protein_coding
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98 scaffold_0 MYZPE13164_Clone_G006_v1.0 mRNA 44968 69413 . - . ID=MYZPE13164_G006_v1.0_000000030.1;Parent=MYZPE13164_G006_v1.0_000000030;Name=MYZPE13164_G006_v1.0_000000030.1;biotype=protein_coding;_AED=0.31
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99 scaffold_0 MYZPE13164_Clone_G006_v1.0 three_prime_utr 44968 46637 . - . ID=MYZPE13164_G006_v1.0_000000030.1.3utr1;Parent=MYZPE13164_G006_v1.0_000000030.1
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100 scaffold_0 MYZPE13164_Clone_G006_v1.0 exon 44968 47432 . - . ID=MYZPE13164_G006_v1.0_000000030.1.exon1;Parent=MYZPE13164_G006_v1.0_000000030.1
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101 scaffold_0 MYZPE13164_Clone_G006_v1.0 CDS 46638 47432 . - 0 ID=MYZPE13164_G006_v1.0_000000030.1.cds1;Parent=MYZPE13164_G006_v1.0_000000030.1
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102 scaffold_0 MYZPE13164_Clone_G006_v1.0 exon 53325 53539 . - . ID=MYZPE13164_G006_v1.0_000000030.1.exon2;Parent=MYZPE13164_G006_v1.0_000000030.1
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103 scaffold_0 MYZPE13164_Clone_G006_v1.0 CDS 53325 53539 . - 2 ID=MYZPE13164_G006_v1.0_000000030.1.cds2;Parent=MYZPE13164_G006_v1.0_000000030.1
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104 scaffold_0 MYZPE13164_Clone_G006_v1.0 exon 54614 54719 . - . ID=MYZPE13164_G006_v1.0_000000030.1.exon3;Parent=MYZPE13164_G006_v1.0_000000030.1
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105 scaffold_0 MYZPE13164_Clone_G006_v1.0 CDS 54614 54719 . - 0 ID=MYZPE13164_G006_v1.0_000000030.1.cds3;Parent=MYZPE13164_G006_v1.0_000000030.1
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106 scaffold_0 MYZPE13164_Clone_G006_v1.0 CDS 54852 55106 . - 0 ID=MYZPE13164_G006_v1.0_000000030.1.cds4;Parent=MYZPE13164_G006_v1.0_000000030.1
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107 scaffold_0 MYZPE13164_Clone_G006_v1.0 exon 54852 55117 . - . ID=MYZPE13164_G006_v1.0_000000030.1.exon4;Parent=MYZPE13164_G006_v1.0_000000030.1
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108 scaffold_0 MYZPE13164_Clone_G006_v1.0 five_prime_utr 55107 55117 . - . ID=MYZPE13164_G006_v1.0_000000030.1.5utr1;Parent=MYZPE13164_G006_v1.0_000000030.1
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109 scaffold_0 MYZPE13164_Clone_G006_v1.0 five_prime_utr 68851 69413 . - . ID=MYZPE13164_G006_v1.0_000000030.1.5utr2;Parent=MYZPE13164_G006_v1.0_000000030.1
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110 scaffold_0 MYZPE13164_Clone_G006_v1.0 exon 68851 69413 . - . ID=MYZPE13164_G006_v1.0_000000030.1.exon5;Parent=MYZPE13164_G006_v1.0_000000030.1
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111
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112 The following features are parsed: **gene**, **mRNA**, **transcript**, **exon**, **five_prime_utr**, **three_prime_utr** and **CDS**, all other are ignored. Also, **ID** and **Parent** attributes in the 9th column are needed to create relations among features.
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113
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114 .. class:: warningmark
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115
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116 If a value in the **ID** and **Parent** attribute contains a colon, everything up to the first colon will be discarded.
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117 ]]>
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118 </help>
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119 <citations>
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120 </citations>
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121 </tool>