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annotate gstf_preparation.xml @ 8:92f3966d5bc3 draft

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 88ba62ae8c3d9587a0015c72209242ad0c1df0c2
author earlhaminst
date Wed, 16 May 2018 20:03:57 -0400
parents 9ef7661e8e9c
children e8e75a79de59
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1 <tool id="gstf_preparation" name="GeneSeqToFamily preparation" version="0.4.1">
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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'
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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'
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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
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23 #if $regions
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24 --regions '$regions'
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25 #end if
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26 -o '$output_db'
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27 --of '$output_fasta'
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28 --ff '$filtered_fasta'
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29 ]]>
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30 </command>
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31
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32 <inputs>
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33 <repeat name="queries" title="GFF3 dataset">
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34 <param name="gff3_input" type="data" format="gff3" label="GFF3 dataset" />
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35 <param name="genome" type="text" label="Genome name" help="Genome name without whitespaces or special characters">
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36 <validator type="empty_field" />
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37 </param>
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38 </repeat>
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39 <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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40 <param name="fasta_inputs" type="data" format="fasta" multiple="true" label="Corresponding CDS datasets in FASTA format" help="Each FASTA header line should start with a transcript id" />
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41 <param name="longestCDS" type="boolean" checked="false" label="Keep only the longest CDS per gene" />
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42 <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" />
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43 <param name="regions" type="text" optional="true" label="Comma-separated list of region IDs (e.g. chromosomes or scaffolds) for which FASTA sequences should be filtered" help="Region IDs are in the `seqid` column for GFF3 and in the `seq_region_name` field in JSON. This is typically used to filter chromosomes with a non-standard genetic code, like mitochondria, to be analysed separately" />
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44 </inputs>
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45
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46 <outputs>
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47 <data name="output_db" format="sqlite" label="${tool.name} on ${on_string}: SQLite" />
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48 <data name="output_fasta" format="fasta" label="${tool.name} on ${on_string}: FASTA" />
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49 <data name="filtered_fasta" format="fasta" label="${tool.name} on ${on_string}: filtered sequences" />
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50 </outputs>
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51
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52 <tests>
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53 <test>
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54 <param name="fasta_inputs" ftype="fasta" value="Caenorhabditis_elegans.WBcel235.cds.all.shortened.fa" />
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55 <param name="gff3_input" ftype="gff3" value="Caenorhabditis_elegans.WBcel235.87.chromosome.I.shortened.gff3" />
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56 <param name="genome" value="caenorhabditis_elegans" />
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57 <param name="longestCDS" value="false" />
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58 <param name="headers" value="true" />
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59
0
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60 <output name="output_db" file="test1.sqlite" compare="sim_size" />
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61 <output name="output_fasta" file="test1.fasta" />
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62 <output name="filtered_fasta" file="test1.ns.fasta" />
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63 </test>
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64 <test>
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65 <param name="fasta_inputs" ftype="fasta" value="Caenorhabditis_elegans.WBcel235.cds.all.shortened.fa" />
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66 <param name="gff3_input" ftype="gff3" value="Caenorhabditis_elegans.WBcel235.87.chromosome.I.shortened.gff3" />
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67 <param name="genome" value="caenorhabditis_elegans" />
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68 <param name="longestCDS" value="true" />
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69 <param name="headers" value="true" />
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71 <output name="output_db" file="test1.sqlite" compare="sim_size" />
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72 <output name="output_fasta" file="test1_longest.fasta" />
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73 <output name="filtered_fasta" file="test1.ns.fasta" />
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74 </test>
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75 <test>
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76 <param name="fasta_inputs" ftype="fasta" value="Caenorhabditis_elegans.WBcel235.cds.all.shortened.fa" />
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77 <param name="gff3_input" ftype="gff3" value="Caenorhabditis_elegans.WBcel235.87.chromosome.I.shortened.gff3" />
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78 <param name="genome" value="caenorhabditis_elegans" />
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79 <param name="longestCDS" value="false" />
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80 <param name="headers" value="false" />
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81
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82 <output name="output_db" file="test1.sqlite" compare="sim_size" />
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83 <output name="output_fasta" file="Caenorhabditis_elegans.WBcel235.cds.all.shortened.fa" />
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84 <output name="filtered_fasta" file="test1.ns.fasta" />
4
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85 </test>
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86 <test>
0
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87 <param name="fasta_inputs" ftype="fasta" value="CDS.fasta" />
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88 <param name="json" ftype="json" value="gene.json" />
4
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89 <param name="longestCDS" value="false" />
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90 <param name="headers" value="true" />
0
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91
6
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92 <output name="output_db" file="test4.sqlite" compare="sim_size" />
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93 <output name="output_fasta" file="test4.fasta" />
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94 <output name="filtered_fasta" file="test4.ns.fasta" />
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95 </test>
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96 <test>
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97 <param name="fasta_inputs" ftype="fasta" value="CDS.fasta" />
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98 <param name="json" ftype="json" value="gene.json" />
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99 <param name="longestCDS" value="false" />
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100 <param name="headers" value="true" />
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101 <param name="regions" value="X" />
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102
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103 <output name="output_db" file="test5.sqlite" compare="sim_size" />
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104 <output name="output_fasta" file="test5_filtered.fasta" />
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105 <output name="filtered_fasta" file="test5.ns.fasta" />
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106 </test>
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107 </tests>
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108 <help>
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109 <![CDATA[
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110 **What it does**
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111
4
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112 This tool converts a set of GFF3 and/or JSON gene feature information datasets into SQLite format.
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113
8
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114 It also filters the CDS FASTA datasets to:
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115
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116 - remove coding sequences whose length is not a multiple of 3
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117 - keep only the transcripts present in the gene feature information.
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118
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119 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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120
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121 Example GFF3 file::
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122
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123 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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124 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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125 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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126 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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127 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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128 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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129 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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130 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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131 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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132 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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133 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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134 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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135 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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136 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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137
2
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138 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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139
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140 .. class:: warningmark
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141
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142 If a value in the **ID** and **Parent** attribute contains a colon, everything up to the first colon will be discarded.
0
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143 ]]>
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144 </help>
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145 <citations>
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146 </citations>
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147 </tool>