Mercurial > repos > iuc > ncbi_datasets

annotate datasets_gene.xml @ 0:c6009f4d7261 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
author iuc
date Thu, 15 Jul 2021 13:31:56 +0000
parents
children 48e0814f250a
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c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
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1 <tool id="datasets-download-gene" name="NCBI datasets download gene" profile="@PROFILE@" license="@LICENSE" version="@TOOL_VERSION@">
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2 <description>Download genes from NCBI</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 <expand macro="requirements"></expand>
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7 <command><![CDATA[
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8 @SETUP_CERTIFICATES@
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9 datasets download gene $subcommand.download_by
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10 #if $subcommand.download_by != 'taxon':
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11 #if $subcommand.text_or_file.text_or_file == 'text':
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12 #if $subcommand.download_by == 'gene-id':
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13 $subcommand.text_or_file.accession
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14 #else if $subcommand.download_by == 'taxon':
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15 '$subcommand.taxon'
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16 #else
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17 #echo " ".join(f"'{x}'" for x in $subcommand.text_or_file.accession.split(' ') if x)
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18 #end if
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19 #if $subcommand.download_by == 'accession' and $subcommand.text_or_file.taxon_filter:
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20 --taxon-filter '$subcommand.taxon_filter'
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21 #end if
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22 #else
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23 --inputfile '$subcommand.text_or_file.inputfile'
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24 #end if
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25 #else:
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26 '$subcommand.taxon'
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27 #end if
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28 @EXCLUDES_GENE@
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29 #if $subcommand.download_by == 'accession' and $subcommand.include_flanks_bp:
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30 --include-flanks-bp $subcommand.include_flanks_bp
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31 #end if
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32 && 7z x ncbi_dataset.zip
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33 ]]></command>
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34 <inputs>
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35 <conditional name="subcommand">
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36 <param name="download_by" type="select" label="Choose how to find genomes to download">
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37 <option value="gene-id">Download a gene dataset by NCBI Gene ID</option>
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38 <option value="symbol">Download a gene dataset by gene symbol</option>
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39 <option value="accession">Download a gene dataset by RefSeq nucleotide or protein accession</option>
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40 <option value="taxon">Download a gene dataset by taxon</option>
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41 </param>
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42 <when value="gene-id">
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43 <expand macro="text_or_file" what="gene-id" what_extended="NCBI Gene ID" help="Should be valid NCBI Gene ID">
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44 <sanitizer invalid_char="">
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45 <valid initial="string.digits">
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46 <add value=" " />
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47 </valid>
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48 </sanitizer>
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49 </expand>
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50 </when>
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51 <when value="symbol">
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52 <expand macro="text_or_file" what="symbol" what_extended="gene symbol" help="Should be valid gene symbol"/>
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53 <param argument="--taxon" type="text" value="human" label="Specify a species name" help="Species name can be common or scientific name or species-level NCBI Taxonomy ID"/>
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54 </when>
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55 <when value="accession">
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56 <expand macro="text_or_file" what="accession" what_extended="RefSeq nucleotide or protein accession" help="Should be RefSeq nucleotide or protein accession"/>
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57 <param argument="--include-flanks-bp" type="integer" optional="true" min="0" label="Include gene flanking sequence, limited to prokaryotic genes" help="If not specified flanking gene sequences will not be downloaded. Accession must start with WP"/>
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58 <param argument="--taxon-filter" type="text" optional="true" label="limit genes to a specified taxon" help="any rank"/>
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59 </when>
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60 <when value="taxon">
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61 <param name="taxon" type="text" label="Enter taxon" help="e.g. human, mouse, bos taurs, etc."></param>
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62 </when>
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63 </conditional>
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64 <expand macro="excludes_gene"></expand>
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65 <conditional name="limit_fasta" label="Limit fasta by accession?">
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66 <param name="limit" type="select" label="Select limit method">
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67 <option value="none">None</option>
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68 <option value="text">Enter list of accessions</option>
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69 <option value="file">Read list of accessions from file</option>
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70 </param>
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71 <when value="none">
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72 </when>
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73 <when value="text">
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74 <param argument="--fasta-filter" type="text" label="Limit gene fasta download to these accessions"/>
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75 </when>
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76 <when value="file">
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77 <param argument="--fasta-filter-file" type="data" format="txt" label="File of accessions to limit gene fasta download"/>
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78 </when>
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79 </conditional>
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80 </inputs>
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81 <outputs>
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82 <data name="gene_fasta" format="fasta" label="NCBI datasets gene: gene fasta" from_work_dir="ncbi_dataset/data/gene.fna">
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83 <filter>not exclude_gene</filter>
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84 </data>
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85 <data name="protein_fasta" format="fasta" label="NCBI datasets gene: protein fasta" from_work_dir="ncbi_dataset/data/protein.faa">
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86 <filter>not exclude_protein</filter>
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87 </data>
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88 <data name="rna_fasta" format="fasta" label="NCBI datasets gene: rna fasta" from_work_dir="ncbi_dataset/data/rna.fna">
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
89 <filter>not exclude_rna</filter>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
90 </data>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
91 <data name="gene_flanks" format="fasta" label="NCBI datasets gene: flanking sequence fasta" from_work_dir="ncbi_dataset/data/gene_flank.fna">
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
92 <filter><![CDATA[subcommand['include_flanks_bp']]]></filter>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
93 </data>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
94 </outputs>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
95 <tests>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
96 <test title="test download by gene-id">
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
97 <conditional name="subcommand">
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
98 <param name="download_by" value="gene-id"></param>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
99 <conditional name="text_or_file">
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
100 <param name="text_or_file" value="text"></param>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
101 <param name="accession" value="472 672"></param>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
102 </conditional>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
103 </conditional>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
104 <output name="gene_fasta">
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
105 <assert_contents>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
106 <has_line line="CCGCGTCCGCGCTTACCCAATACAAGCCGGGCTACGTCCGAGGGTAACAACATGATCAAAACCACAGCAG"/>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
107 <has_line line="GCTGAGACTTCCTGGACGGGGGACAGGCTGTGGGGTTTCTCAGATAACTGGGCCCCTGCGCTCAGGAGGC"/>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
108 </assert_contents>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
109 </output>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
110 </test>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
111 <test title="test download by gene-id, test sanitizer">
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
112 <conditional name="subcommand">
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
113 <param name="download_by" value="gene-id"></param>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
114 <conditional name="text_or_file">
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
115 <param name="text_or_file" value="text"></param>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
116 <param name="accession" value="472 672"></param>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
117 </conditional>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
118 </conditional>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
119 <output name="gene_fasta">
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
120 <assert_contents>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
121 <has_line line="CCGCGTCCGCGCTTACCCAATACAAGCCGGGCTACGTCCGAGGGTAACAACATGATCAAAACCACAGCAG"/>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
122 <has_line line="GCTGAGACTTCCTGGACGGGGGACAGGCTGTGGGGTTTCTCAGATAACTGGGCCCCTGCGCTCAGGAGGC"/>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
123 </assert_contents>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
124 </output>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
125 <assert_command>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
126 <not_has_text text="exit"/>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
127 </assert_command>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
128 </test>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
129 <test title="test download by gene symbol">
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
130 <conditional name="subcommand">
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
131 <param name="download_by" value="symbol"></param>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
132 <conditional name="text_or_file">
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
133 <param name="text_or_file" value="text"></param>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
134 <param name="accession" value="BRCA1 ATM"></param>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
135 </conditional>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
136 </conditional>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
137 <output name="gene_fasta">
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
138 <assert_contents>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
139 <has_line line="CCGCGTCCGCGCTTACCCAATACAAGCCGGGCTACGTCCGAGGGTAACAACATGATCAAAACCACAGCAG"/>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
140 <has_line line="GCTGAGACTTCCTGGACGGGGGACAGGCTGTGGGGTTTCTCAGATAACTGGGCCCCTGCGCTCAGGAGGC"/>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
141 </assert_contents>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
142 </output>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
143 </test>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
144 <test title="test download by accession">
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
145 <conditional name="subcommand">
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
146 <param name="download_by" value="accession"></param>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
147 <conditional name="text_or_file">
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
148 <param name="text_or_file" value="text"></param>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
149 <param name="accession" value="NM_000546.6 NM_000492.4"></param>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
150 </conditional>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
151 </conditional>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
152 <output name="gene_fasta">
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
153 <assert_contents>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
154 <has_line line="GTAGTAGGTCTTTGGCATTAGGAGCTTGAGCCCAGACGGCCCTAGCAGGGACCCCAGCGCCCGAGAGACC"/>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
155 <has_line line="CTCAAAAGTCTAGAGCCACCGTCCAGGGAGCAGGTAGCTGCTGGGCTCCGGGGACACTTTGCGTTCGGGC"/>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
156 </assert_contents>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
157 </output>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
158 <assert_command>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
159 <has_text text="'NM_000546.6' 'NM_000492.4'"/>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
160 </assert_command>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
161 </test>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
162 <test title="test download by accession with flanking sequence">
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
163 <conditional name="subcommand">
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
164 <param name="download_by" value="accession"></param>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
165 <conditional name="text_or_file">
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
166 <param name="text_or_file" value="text"></param>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
167 <param name="accession" value="WP_004675351.1"></param>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
168 </conditional>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
169 <param name="include_flanks_bp" value="10"/>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
170 </conditional>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
171 <output name="gene_flanks">
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
172 <assert_contents>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
173 <has_line line="gccctgccgcATGATCGATCTGATGCCGACGAGCGAGGAACAGGCGGCGGCGATCGTCCGCACCCATGCG"/>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
174 </assert_contents>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
175 </output>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
176 <assert_command>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
diff changeset
177 <has_text text="--include-flanks-bp 10"/>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
iuc
parents:
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178 </assert_command>
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179 </test>
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180 <test title="test download by taxon">
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181 <conditional name="subcommand">
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182 <param name="download_by" value="taxon"></param>
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183 <param name="taxon" value="Mycobacterium tuberculosis H37Rv"></param>
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184 </conditional>
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185 <param name="exclude_rna" value="true"/>
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186 <param name="exclude_protein" value="true"/>
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187 <output name="gene_fasta">
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188 <assert_contents>
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189 <has_line line="GTGGCGCTGAATATCAAAGACCCTGAGGTAGACCGACTAGCCGCCGAACTCGCTGACCGGCTGCACACCA"/>
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190 </assert_contents>
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191 </output>
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192 </test>
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193 </tests>
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194 <help>
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195 Download a gene dataset including gene, transcript and protein sequence, a data table and a data report. Gene datasets can be specified by NCBI Gene ID, symbol or RefSeq accession. Datasets are downloaded as a zip file.
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196
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197 The default gene dataset includes the following files:
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198 * gene.fna (gene sequences)
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199 * rna.fna (transcript sequences)
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200 * protein.faa (protein sequences)
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201 * data_report.jsonl (data report with gene metadata)
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202 * data_table.tsv (data table with gene metadata, one transcript per row)
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203 * dataset_catalog.json (a list of files and file types included in the dataset)
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204 </help>
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205
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206 </tool>