Mercurial > repos > iuc > taxonomy_filter_refseq

annotate taxonomy_filter_refseq.xml @ 0:28e95c6a944d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc commit 665d364fb51576608b0eb66a4f89d92159925ccc
author iuc
date Wed, 16 Jan 2019 08:30:47 -0500
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1 <tool id="taxonomy_filter_refseq" name="Filter RefSeq by taxonomy" version="@TOOL_VERSION@+galaxy0">
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2 <description>Only retain sequences that are descendants of a given taxonomic node.</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">0.1.4</token>
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5 </macros>
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6 <edam_topics>
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7 <edam_topic>topic_0091</edam_topic>
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8 </edam_topics>
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9 <edam_operations>
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10 <edam_operation>operation_3460</edam_operation>
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11 </edam_operations>
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12 <requirements>
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13 <requirement type="package" version="@TOOL_VERSION@">rust-ncbitaxonomy</requirement>
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14 </requirements>
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15 <!-- current using redirect to output rather than output to file due to bug in pre-0.1.4 rust-ncbitaxonomy -->
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16 <command detect_errors="aggressive"><![CDATA[
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17 #if str($refseq.refseq_source) == 'cached':
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18 #set $refseq_input = str( $refseq.cached_refseq.fields.path )
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19 #else:
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20 ln -s '$refseq.history_refseq' refseq.fasta &&
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21 #set $refseq_input = "refseq.fasta"
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22 #end if
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23 #if str($taxonomy.taxonomy_source) == 'cached':
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24 #set $taxonomy_dir = $taxonomy.taxonomy_table.fields.path
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25 #else:
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26 mkdir taxonomy && ln -s '$taxonomy.nodes' taxonomy/nodes.dmp && ln -s '$taxonomy.names' taxonomy/names.dmp &&
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27 #set $taxonomy_dir = 'taxonomy'
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28 #end if
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29 taxonomy_filter_refseq '$refseq_input' '$taxonomy_dir' '$ancestor_name' >'$refseq_output_fasta'
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30 ]]></command>
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31 <inputs>
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32 <conditional name="taxonomy">
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33 <param name="taxonomy_source" type="select" label="Choose source of NCBI Taxonomy">
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34 <option value="cached" selected="true">Use built-in NCBI Taxonomy database</option>
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35 <option value="history">Datasets from history</option>
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36 </param>
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37 <when value="cached">
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38 <param type="select" name="taxonomy_table" label="NCBI Taxonomy database">
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39 <options from_data_table="ncbi_taxonomy">
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40 <filter type="sort_by" column="name" />
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41 <validator type="no_options" message="No NCBI Taxonomy downloads are available" />
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42 </options>
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43 <validator type="no_options" message="No NCBI Taxonomy database download is available" />
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44 </param>
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45 </when>
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46 <when value="history">
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47 <param name="nodes" type="data" format="txt" label="NCBI Taxonomy nodes.dmp file" />
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48 <param name="names" type="data" format="txt" label="NCBI Taxonomy names.dmp file" />
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49 </when>
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50 </conditional>
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51 <conditional name="refseq">
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52 <param name="refseq_source" type="select" label="Choose source of RefSeq sequences">
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53 <option value="cached" selected="true">Use a built-in RefSeq FASTA file</option>
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54 <option value="history">History</option>
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55 </param>
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56 <when value="cached">
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57 <param type="select" name="cached_refseq" label="Select RefSeq FASTA file">
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58 <options from_data_table="all_fasta">
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59 <filter type="sort_by" column="name" />
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60 <validator type="no_options" message="No FASTA data is available" />
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61 </options>
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62 <validator type="no_options" message="No FASTA data is available" />
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63 </param>
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64 </when>
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65 <when value="history">
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66 <param type="data" name="history_refseq" format="fasta" label="RefSeq FASTA file" />
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67 </when>
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68 </conditional>
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69 <param name="ancestor_name" type="text" label="Ancestor taxon (scientific) name" />
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70 </inputs>
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71 <outputs>
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72 <data name="refseq_output_fasta" format="fasta" label="${tool.name} on ${on_string}" />
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73 </outputs>
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74 <tests>
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75 <test>
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76 <param name="taxonomy_source" value="history" />
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77 <param name="refseq_source" value="history" />
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78 <param name="nodes" ftype="txt" value="sample_tree_nodes.dmp" />
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79 <param name="names" ftype="txt" value="sample_tree_names.dmp" />
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80 <param name="history_refseq" ftype="fasta" value="sample_refseq.fasta" />
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81 <param name="ancestor_name" value="unclassified bacterial viruses" />
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82 <output name="refseq_output_fasta" value="output1.fasta" />
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83 </test>
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84 <test>
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85 <param name="taxonomy_source" value="cached" />
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86 <param name="taxonomy_table" value="2019-01-01" />
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87 <param name="refseq_source" value="cached" />
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88 <param name="cached_refseq" value="refseq_sample" />
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89 <param name="nodes" ftype="txt" value="sample_tree_nodes.dmp" />
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90 <param name="names" ftype="txt" value="sample_tree_names.dmp" />
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91 <param name="history_refseq" ftype="fasta" value="sample_refseq.fasta" />
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92 <param name="ancestor_name" value="unclassified bacterial viruses" />
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93 <output name="refseq_output_fasta" value="output1.fasta" />
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94 </test>
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95 </tests>
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96 <help><![CDATA[
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97 This tool allows NCBI RefSeq sequences to be filtered so that only those whose species name are
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98 descendants of a given taxon in the NCBI taxonomy are retained. For example, from the NCBI RefSeq
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99 "other vertebrate" file only ray finned fishes can be retained by filtering for "Actinopterygii".
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100
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101 The NCBI RefSeq FASTA files can either be provided by the Galaxy administrator or from the user
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102 history. The NCBI taxonomy should be provided by the Galaxy administrator but if that is not
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103 possible the nodes.dmp and names.dmp files from the NCBI taxonomy can be provided in the history.
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104 ]]></help>
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105 <citations>
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106 <citation type="bibtex">
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107 @misc{vanHeusden2019,
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108 author = {van Heusden, Peter},
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109 year = {2019},
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110 title = ncbitaxonomy Rust crate},
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111 publisher = {crates.io},
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112 journal = {Rust Package Registry},
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113 url = {https://crates.io/crates/ncbitaxonomy},
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114 }
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115 </citation>
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116 </citations>
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117 </tool>