Mercurial > repos > sanbi-uwc > data_manager_fetch_refseq

annotate data_manager/fetch_refseq.xml @ 7:efdead58e937 draft

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author sanbi-uwc
date Fri, 07 Sep 2018 19:47:52 -0400
parents 7226cda27b03
children 97bf61f2fdae
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1 <tool id="data_manager_fetch_refseq" name="RefSeq data manager" version="0.0.8" tool_type="manage_data">
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2 <description>Fetch FASTA data from NCBI RefSeq and update all_fasta data table</description>
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3 <requirements>
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4 <requirement type="package" version="3">python</requirement>
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5 </requirements>
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6 <command detect_errors="aggressive"><![CDATA[
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7 python3 $__tool_directory__/fetch_refseq.py
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8 #if str( $advanced.advanced_selector ) == 'advanced':
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9 '${advanced.compress}'
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10 #end if
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11 --galaxy_datamanager_filename '${output_file}'
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12 --division_names ${division_names}
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13 --mol_types ${mol_types}
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14 #if str( $pin_date ) != 'NO':
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15 --pin_date '${pin_date}'
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16 #end if
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17 ]]></command>
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18 <inputs>
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19 <param argument="division_names" type="select" label="RefSeq division" multiple="true">
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20 <option value="archea">Archea</option>
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21 <option value="bacteria">Bacteria</option>
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22 <option value="complete">Complete</option>
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23 <option value="fungi">Fungi</option>
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24 <option value="invertebrate">Invertebrate</option>
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25 <option value="mitochondrion">Mitochondrion</option>
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26 <option value="other">Other</option>
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27 <option value="plant">Plant</option>
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28 <option value="plasmid">Plasmid</option>
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29 <option value="plastid">Plastid</option>
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30 <option value="protozoa">Protozoa</option>
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31 <option value="vertebrate_mammalian">Mammalian Vertebrate</option>
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32 <option value="vertebrate_other">Other Vertebrate</option>
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33 <option value="viral">Viral</option>
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34 </param>
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35 <param argument="mol_types" type="select" label="Molecule type" help="Select at least one of genomic, protein or rna sequence">
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36 <option value="protein">Protein</option>
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37 <option value="genomic">Genomic (DNA)</option>
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38 <option value="rna">RNA</option>
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39 </param>
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40 <conditional name="advanced">
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41 <param name="advanced_selector" type="select" label="Advanced Options">
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42 <option value="basic" selected="True">Basic</option>
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43 <option value="advanced">Advanced</option>
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44 </param>
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45 <when value="basic">
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46 </when>
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47 <when value="advanced">
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48 <param type="boolean" argument="--compress" truevalue="--compress" falsevalue="" label="Compress FASTA files"
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49 help="Compress downloaded FASTA files (with gzip). Limits compatibility with tools expecting uncompressed FASTA."/>
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50 </when>
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51 </conditional>
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52 <param argument="--pin_date" type="hidden" value="NO" help="Used for testing"/>
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53 </inputs>
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54 <outputs>
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55 <data name="output_file" format="data_manager_json"/>
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56 </outputs>
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57 <tests>
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58 <test>
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59 <param name="division_names" value="plastid"/>
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60 <param name="mol_types" value="protein"/>
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61 <param name="pin_date" value="2018-03-14"/>
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62 <param name="advanced_selector" value="basic"/>
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63 <output name="output_file">
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64 <assert_contents>
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65 <has_text text="2018-03-14"/>
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66 </assert_contents>
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67 </output>
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68 </test>
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69 </tests>
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70 <help><![CDATA[
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71 This data manager fetches FASTA format collections of proteins, nucleotides (genomic DNA) and RNA
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72 from NCBI's RefSeq_ data collection.
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73
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74 RefSeq is released every two months and consists of a number of divisions. Some sequences are shared
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75 between multiple divisions. This data manager allows the Galaxy administrator to select which
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76 divisions and which molecule types within each division to download. Once downloaded the
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77 files are made accessible by adding an entry into the *all_fasta* data table.
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78
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79 .. _RefSeq: https://www.ncbi.nlm.nih.gov/refseq/
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80 ]]>
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81 </help>
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82 <citations>
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83 <citation type="doi">10.1093/nar/gkv1189</citation>
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84 </citations>
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85 </tool>