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1 <tool id="get_species_taxids" name="NCBI get species taxids" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description></description>
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3 <macros>
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4 <import>ncbi_macros.xml</import>
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5 </macros>
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6 <expand macro="preamble"/>
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7 <command detect_errors="aggressive"><![CDATA[
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8 #if $type_cond.type_sel == 'names'
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9 #for name in $type_cond.names.split(',')
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10 taxid=\$(get_species_taxids.sh -n '$name' | grep Taxid | sed 's/Taxid\s*:\s*//') &&
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11 if [ -z "\$taxid" ]; then
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12 >&2 echo "could not find taxid for $name" && exit 1;
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13 else
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14 echo " $name -> \$taxid";
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15 fi &&
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16 get_species_taxids.sh -t "\$taxid" >> species_ids.txt &&
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17 #end for
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18 #else
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19 #for taxid in $type_cond.ids.split(',')
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20 get_species_taxids.sh -t "$taxid" >> species_ids.txt &&
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21 #end for
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22 #end if
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23 sort -n -u species_ids.txt > '$output'
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24 ]]></command>
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25 <inputs>
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26 <conditional name="type_cond">
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27 <param name="type_sel" type="select" label="Get taxids by">
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28 <option value="names">Taxon names</option>
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29 <option value="ids">Taxon ids</option>
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30 </param>
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31 <when value="names">
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32 <param name="names" type="text" label="Taxon names" help="comma separated">
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33 <validator type="regex" message="Enter a comma separated list of taxon names">[a-zA-Z ,]+$</validator>
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34 </param>
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35 </when>
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36 <when value="ids">
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37 <param name="ids" type="text" label="Taxon ids" help="comma separated">
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38 <validator type="regex" message="Enter a comma separated list of taxids">[0-9,]+$</validator>
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39 </param>
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40 </when>
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41 </conditional>
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42 </inputs>
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43 <outputs>
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44 <data format="txt" name="output"/>
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45 </outputs>
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46 <tests>
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47 <test>
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48 <param name="type_cond|type_sel" value="names"/>
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49 <param name="type_cond|names" value="Enterobacterales"/>
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50 <output name="output" ftype="txt">
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51 <assert_contents>
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52 <has_line line="9"/>
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53 <has_line line="2791989"/>
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54 </assert_contents>
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55 </output>
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56 </test>
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57 <test>
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58 <param name="type_cond|type_sel" value="ids"/>
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59 <param name="type_cond|ids" value="91347"/>
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60 <output name="output" ftype="txt">
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61 <assert_contents>
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62 <has_line line="9"/>
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63 <has_line line="2791989"/>
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64 </assert_contents>
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65 </output>
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66 </test>
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67 <test>
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68 <param name="type_cond|type_sel" value="names"/>
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69 <param name="type_cond|names" value="Enterobacterales,Hominidae"/>
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70 <output name="output" ftype="txt">
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71 <assert_contents>
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72 <has_line line="9"/>
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73 <has_line line="9606"/>
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74 <has_line line="2791989"/>
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75 </assert_contents>
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76 </output>
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77 </test>
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78 <test>
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79 <param name="type_cond|type_sel" value="ids"/>
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80 <param name="type_cond|ids" value="91347,9604"/>
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81 <output name="output" ftype="txt">
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82 <assert_contents>
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83 <has_line line="9"/>
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84 <has_line line="9606"/>
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85 <has_line line="2791989"/>
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86 </assert_contents>
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87 </output>
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88 </test>
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89 </tests>
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90 <help>
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91
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92 **What it does**
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93
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94 Returns a list of species taxids for a taxon. It relies on the get_species_taxids.sh script of the BLAST+ package https://www.ncbi.nlm.nih.gov/books/NBK546209/
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95
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96 -------
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97
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98 **References**
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99
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100 If you use this Galaxy tool in work leading to a scientific publication please
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101 cite the following papers:
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102
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103 @REFERENCES@
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104 </help>
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105 <expand macro="blast_citations"/>
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106 </tool>
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