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1 <tool id="plant_tribes_gene_family_scaffold_updater" name="Update PlantTribes scaffold" version="@WRAPPER_VERSION@.0.0">
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2 <description>with a new genome</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="2.7.1">blast</requirement>
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8 <requirement type="package" version="3.1b2">hmmer</requirement>
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9 <requirement type="package" version="7.313">mafft</requirement>
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10 <requirement type="package" version="5.22.0">perl</requirement>
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11 <requirement type="package" version="1.641">perl-dbi</requirement>
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12 <requirement type="package" version="3.5.3">perl-dbd-pg</requirement>
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13 </requirements>
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14 <command detect_errors="exit_code"><![CDATA[
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15 perl '$__tool_directory__/gene_family_scaffold_updater.pl'
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16 --database_connection_string '$__app__.config.plant_tribes_database_connection'
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17 --proteins '$input_proteins'
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18 --coding_sequences '$input_coding_sequences'
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19 --scaffold '$GALAXY_DATA_INDEX_DIR/plant_tribes/scaffolds/$scaffold'
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20 --species_name '$species_name'
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21 --species_code '$species_code'
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22 --species_family '$species_family'
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23 --species_order '$species_order'
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24 --species_group '$species_group'
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25 --species_clade '$species_clade'
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26 --rooting_order_species_code '$rooting_order_species_code'
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27 --num_threads \${GALAXY_SLOTS:-4}
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28 &>'$output']]></command>
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29 <inputs>
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30 <expand macro="param_scaffold"/>
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31 <param name="input_proteins" format="fasta" type="data" label="Proteins fasta file">
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32 <validator type="empty_field"/>
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33 </param>
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34 <param name="input_coding_sequences" format="fasta" type="data" label="Coding sequences fasta file">
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35 <validator type="empty_field"/>
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36 </param>
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37 <param name="species_name" type="text" value="" label="Species name">
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38 <validator type="empty_field"/>
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39 </param>
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40 <param name="species_code" type="text" value="" label="Species code">
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41 <validator type="empty_field"/>
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42 </param>
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43 <param name="species_family" type="text" value="" label="Species family">
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44 <validator type="empty_field"/>
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45 </param>
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46 <param name="species_order" type="text" value="" label="Species order">
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47 <validator type="empty_field"/>
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48 </param>
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49 <param name="species_group" type="text" value="" label="Species group">
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50 <validator type="empty_field"/>
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51 </param>
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52 <param name="species_clade" type="text" value="" label="Species clade">
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53 <validator type="empty_field"/>
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54 </param>
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55 <param name="rooting_order_species_code" type="text" label="Species code for rooting order" help="The new species above will be placed immediately after this species code in the rooting order configuration file">
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56 <validator type="empty_field"/>
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57 </param>
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58 </inputs>
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59 <outputs>
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60 <data name="output" format="txt"/>
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61 </outputs>
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62 <tests>
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63 <test>
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64 <!--Testing this tool is a bit difficult at the current time.-->
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65 </test>
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66 </tests>
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67 <help>
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68 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary
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69 analyses of genome-scale gene families and transcriptomes. This tool adds a new genome to a scaffold installed into Galaxy
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70 by the PlantTribes Scaffolds Downloader data manager tool.
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71
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72 -----
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73
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74 **Required options**
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75
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76 * **Proteins fasta file** - amino acids (proteins) sequences fasta file for new genome.
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77 * **Coding sequences fasta file** - corresponding coding sequences (CDS) fasta file for new genome.
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78 * **Gene family scaffold** - one of the PlantTribes gene family scaffolds, installed into Galaxy by the PlantTribes Scaffold Data Manager tool.
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79 </help>
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80 <citations>
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81 <citation type="bibtex">
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82 @unpublished{None,
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83 author = {Eric Wafula},
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84 title = {None},
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85 year = {None},
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86 eprint = {None},
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87 url = {https://github.com/dePamphilis/PlantTribes}}
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88 </citation>
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89 </citations>
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90 </tool>
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91
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