Mercurial > repos > earlhaminst > gstf_preparation

annotate gstf_preparation.xml @ 10:e8e75a79de59 draft

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"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 9c8611fee927883f50bc6955771aa69df1ce8457"
author earlhaminst
date Thu, 31 Oct 2019 08:16:51 -0400
parents 92f3966d5bc3
children dbe37a658cd2
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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"><![CDATA[
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4 python '$__tool_directory__/gstf_preparation.py'
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5 #for $q in $queries
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6 --gff3 '${q.genome}:${q.gff3_input}'
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7 #end for
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8 #if str($json) != 'None'
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9 #for $v in $json
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10 --json '$v'
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11 #end for
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12 #end if
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13 #for $fasta_input in $fasta_inputs
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14 --fasta '${fasta_input}'
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15 #end for
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16 #if $headers
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17 --headers
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18 #end if
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19 #if $longestCDS
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20 -l
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21 #end if
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22 #if $regions
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23 --regions '$regions'
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24 --ff '$filtered_fasta'
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25 #end if
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26 -o '$output_db'
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27 --of '$output_fasta'
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28 ]]></command>
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29
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30 <inputs>
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31 <repeat name="queries" title="GFF3 dataset">
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32 <param name="gff3_input" type="data" format="gff3" label="GFF3 dataset" />
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33 <param name="genome" type="text" label="Genome name" help="Genome name without whitespaces or special characters">
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34 <validator type="empty_field" />
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35 </param>
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36 </repeat>
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37 <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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38 <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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39 <param name="longestCDS" type="boolean" checked="false" label="Keep only the longest CDS per gene" />
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40 <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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41 <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 out" 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 out chromosomes with a non-standard genetic code, like mitochondria, to be analysed separately" />
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42 </inputs>
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43
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44 <outputs>
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45 <data name="output_db" format="sqlite" label="${tool.name} on ${on_string}: SQLite" />
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46 <data name="output_fasta" format="fasta" label="${tool.name} on ${on_string}: FASTA" />
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47 <data name="filtered_fasta" format="fasta" label="${tool.name} on ${on_string}: filtered sequences">
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48 <filter>regions</filter>
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49 </data>
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50 </outputs>
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51
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52 <tests>
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53 <test expect_num_outputs="2">
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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
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60 <output name="output_db" file="test1.sqlite" compare="sim_size" delta="30000" />
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61 <output name="output_fasta" file="test1.fasta" />
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62 </test>
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63 <test expect_num_outputs="2">
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64 <param name="fasta_inputs" ftype="fasta" value="Caenorhabditis_elegans.WBcel235.cds.all.shortened.fa" />
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65 <param name="gff3_input" ftype="gff3" value="Caenorhabditis_elegans.WBcel235.87.chromosome.I.shortened.gff3" />
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66 <param name="genome" value="caenorhabditis_elegans" />
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67 <param name="longestCDS" value="true" />
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68 <param name="headers" value="true" />
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69
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70 <output name="output_db" file="test1.sqlite" compare="sim_size" delta="30000" />
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71 <output name="output_fasta" file="test1_longest.fasta" />
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72 </test>
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73 <test expect_num_outputs="2">
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74 <param name="fasta_inputs" ftype="fasta" value="Caenorhabditis_elegans.WBcel235.cds.all.shortened.fa" />
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75 <param name="gff3_input" ftype="gff3" value="Caenorhabditis_elegans.WBcel235.87.chromosome.I.shortened.gff3" />
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
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76 <param name="genome" value="caenorhabditis_elegans" />
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77 <param name="longestCDS" value="false" />
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78 <param name="headers" value="false" />
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
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79
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80 <output name="output_db" file="test1.sqlite" compare="sim_size" delta="30000" />
4
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
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81 <output name="output_fasta" file="Caenorhabditis_elegans.WBcel235.cds.all.shortened.fa" />
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
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82 </test>
10
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83 <test expect_num_outputs="2">
0
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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84 <param name="fasta_inputs" ftype="fasta" value="CDS.fasta" />
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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85 <param name="json" ftype="json" value="gene.json" />
4
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
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86 <param name="longestCDS" value="false" />
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
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87 <param name="headers" value="true" />
0
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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88
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89 <output name="output_db" file="test4.sqlite" compare="sim_size" delta="30000" />
6
56bbdbfe3eaa planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit fa875eea77a9471acada2b7b8882a0467994c960
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90 <output name="output_fasta" file="test4.fasta" />
56bbdbfe3eaa planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit fa875eea77a9471acada2b7b8882a0467994c960
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91 </test>
56bbdbfe3eaa planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit fa875eea77a9471acada2b7b8882a0467994c960
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92 <test>
56bbdbfe3eaa planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit fa875eea77a9471acada2b7b8882a0467994c960
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93 <param name="fasta_inputs" ftype="fasta" value="CDS.fasta" />
56bbdbfe3eaa planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit fa875eea77a9471acada2b7b8882a0467994c960
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94 <param name="json" ftype="json" value="gene.json" />
56bbdbfe3eaa planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit fa875eea77a9471acada2b7b8882a0467994c960
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95 <param name="longestCDS" value="false" />
56bbdbfe3eaa planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit fa875eea77a9471acada2b7b8882a0467994c960
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96 <param name="headers" value="true" />
56bbdbfe3eaa planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit fa875eea77a9471acada2b7b8882a0467994c960
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97 <param name="regions" value="X" />
56bbdbfe3eaa planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit fa875eea77a9471acada2b7b8882a0467994c960
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98
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99 <output name="output_db" file="test4.sqlite" compare="sim_size" delta="30000" />
6
56bbdbfe3eaa planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit fa875eea77a9471acada2b7b8882a0467994c960
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100 <output name="output_fasta" file="test5_filtered.fasta" />
56bbdbfe3eaa planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit fa875eea77a9471acada2b7b8882a0467994c960
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101 <output name="filtered_fasta" file="test5.ns.fasta" />
0
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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102 </test>
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103 <test expect_num_outputs="2">
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104 <param name="fasta_inputs" ftype="fasta" value="Mus_pahari.PAHARI_EIJ_v1.1.cds.all.shortened.fa" />
e8e75a79de59 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 9c8611fee927883f50bc6955771aa69df1ce8457"
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105 <param name="gff3_input" ftype="gff3" value="MGP_PahariEiJ_G0008413.1.gff3" />
e8e75a79de59 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 9c8611fee927883f50bc6955771aa69df1ce8457"
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106 <param name="genome" value="mus_pahari" />
e8e75a79de59 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 9c8611fee927883f50bc6955771aa69df1ce8457"
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107 <param name="longestCDS" value="true" />
e8e75a79de59 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 9c8611fee927883f50bc6955771aa69df1ce8457"
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108 <param name="headers" value="true" />
e8e75a79de59 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 9c8611fee927883f50bc6955771aa69df1ce8457"
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109
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110 <output name="output_db" file="test6.sqlite" compare="sim_size" delta="30000" />
e8e75a79de59 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 9c8611fee927883f50bc6955771aa69df1ce8457"
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111 <output name="output_fasta" file="test6.fasta" />
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112 </test>
0
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113 </tests>
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114 <help><![CDATA[
0
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115 **What it does**
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116
4
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117 This tool converts a set of GFF3 and/or JSON gene feature information datasets into SQLite format.
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118
8
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119 It also filters the CDS FASTA datasets to:
92f3966d5bc3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 88ba62ae8c3d9587a0015c72209242ad0c1df0c2
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120
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121 - remove coding sequences whose length is not a multiple of 3
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122 - keep only the transcripts present in the gene feature information.
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123
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124 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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125
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126 Example GFF3 file::
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127
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128 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
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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129 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
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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130 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
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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131 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
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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132 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
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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133 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
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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134 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
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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135 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
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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136 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
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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137 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
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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138 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
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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139 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
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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140 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
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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141 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
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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142
2
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143 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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144
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145 .. class:: warningmark
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146
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147 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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148 ]]></help>
0
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149 <citations>
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
150 </citations>
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
151 </tool>