Mercurial > repos > iuc > ncbi_datasets

annotate datasets_gene.xml @ 19:40a5d68e929a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 2fd3d371f0fa9ede0c1b5f2676e31aa645ce8929
author iuc
date Tue, 11 Mar 2025 09:17:11 +0000
parents da8260eba74b
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1 <tool id="datasets_download_gene" name="NCBI Datasets Gene" profile="@PROFILE@" license="@LICENSE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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2 <description>download gene sequences and metadata</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="bio_tools"/>
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7 <expand macro="requirements"></expand>
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8 <expand macro="version_command"/>
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9 <command><![CDATA[
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10 #import re
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11 @SETUP_CERTIFICATES@
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12 datasets download gene $query.subcommand.download_by
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13 #if $query.subcommand.download_by == 'taxon':
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14 '$query.subcommand.taxon_positional'
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15 #else:
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16 #if $query.subcommand.text_or_file.text_or_file == 'text':
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17 #echo " ".join(f"'{x}'" for x in re.split(" |,", str($query.subcommand.text_or_file.accession)) if x)
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18 #else
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19 --inputfile '$query.subcommand.text_or_file.inputfile'
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20 #end if
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21 #end if
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23 #if $query.subcommand.download_by != 'taxon' and $query.subcommand.ortholog:
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24 --ortholog '$query.subcommand.ortholog'
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25 #end if
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27 #if $query.subcommand.download_by == 'symbol':
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28 #if $query.subcommand.taxon
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29 --taxon '$query.subcommand.taxon'
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30 #end if
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31 #end if
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33 #if $query.subcommand.download_by == 'accession':
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34 #if $query.subcommand.taxon_filter
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35 --taxon-filter '$query.subcommand.taxon_filter'
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36 #end if
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37 #if str($query.subcommand.include_flanks_bp)
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38 --include-flanks-bp $query.subcommand.include_flanks_bp
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39 #end if
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40 #end if
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42 #if $filters.fasta_filter_cond.fasta_filter_select
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43 #if $filters.fasta_filter_cond.fasta_filter_select == 'text'
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44 --fasta-filter #echo ",".join(f"'{x}'" for x in $filters.fasta_filter_cond.fasta_filter.split(',') if x)
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45 #else
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46 --fasta-filter-file '$filters.fasta_filter_cond.fasta_filter_file'
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47 #end if
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48 #end if
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49
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50 --include
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51 #if $file_choices.kingdom_cond.include
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52 #echo ",".join($file_choices.kingdom_cond.include)
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53 #else
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54 none
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55 #end if
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56
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57 --no-progressbar
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58
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59 ## produce TSV report file (either gene or prok-gene)
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60 &&
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61 dataformat
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62 tsv
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63 $file_choices.kingdom_cond.kingdom_sel
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64 --package ncbi_dataset.zip
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65 --fields #echo ",".join($file_choices.kingdom_cond.report_columns)
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66 > gene_data_report.tsv
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67 ## if ! dataformat tsv gene --package ncbi_dataset.zip > gene_data_report.tsv 2> dataformat.log; then
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68 ## dataformat tsv prok-gene --package ncbi_dataset.zip > gene_data_report.tsv 2>> dataformat.log;
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69 ## fi
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70
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71 #if $file_choices.kingdom_cond.include and "product-report" in $file_choices.kingdom_cond.include
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72 && dataformat tsv gene-product --package ncbi_dataset.zip > gene_product_report.tsv
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73 #end if
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74
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75 ## unzip and rehydrate if any data is to be downloaded (include is not None)
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76 #if $file_choices.kingdom_cond.include
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77 ## unzip
17
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78 && unzip ncbi_dataset.zip
11
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79 #end if
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80 ]]></command>
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81 <inputs>
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82 <section name="query" title="Query" expanded="true">
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83 <conditional name="subcommand">
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84 <param name="download_by" type="select" label="Choose how to find genes to download">
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85 <option value="gene-id">By NCBI Gene ID</option>
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86 <option value="symbol">By Gene symbol</option>
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87 <option value="accession">By RefSeq nucleotide or protein accession</option>
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88 <option value="taxon">By taxon (NCBI Taxonomy ID, scientific or common name at any tax rank)</option>
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89 </param>
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90 <when value="gene-id">
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91 <expand macro="text_or_file" what="Gene ID" what_extended="NCBI Gene ID" help=""/>
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92 <expand macro="ortholog"/>
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93 </when>
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94 <when value="symbol">
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95 <expand macro="text_or_file" what="Gene Symbol" what_extended="NCBI Gene Symbol" help=""/>
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96 <expand macro="ortholog"/>
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97 <param argument="--taxon" type="text" value="human" label="Species for gene symbol" help="NCBI taxid, common or scientific name">
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98 <sanitizer invalid_char="">
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99 <valid initial="string.letters">
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100 <add value=" " />
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101 <add value="-" />
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102 </valid>
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103 </sanitizer>
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104 </param>
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105 </when>
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106 <when value="accession">
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107 <expand macro="text_or_file" what="Gene Accession" what_extended="NCBI Gene Accession" help=""/>
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108 <expand macro="ortholog"/>
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109 <param argument="--taxon-filter" type="text" value="" label="Limit gene sequences and annotation report file to specified taxon" help="any rank, only available for WP accessions">
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110 <sanitizer invalid_char="">
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111 <valid initial="string.letters">
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112 <add value=" " />
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113 <add value="-" />
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114 </valid>
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115 </sanitizer>
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116 </param>
17
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diff changeset
117 <param argument="--include-flanks-bp" type="integer" optional="true" min="0" value="" label="Length of flanking nucleotides" help="WP accessions only"/>
11
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118 </when>
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119 <when value="taxon">
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120 <expand macro="taxon_positional"/>
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121 </when>
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122 </conditional>
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123 </section>
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124 <section name="filters" title="Filters and Limit">
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125 <conditional name="fasta_filter_cond" label="Filter protein and RNA sequences by RefSeq nucleotide and protein accessions">
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126 <param name="fasta_filter_select" type="select" label="Apply filter">
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127 <option value="">No</option>
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128 <option value="text">Enter accessions</option>
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129 <option value="file">Read a list of accessions from a dataset</option>
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130 </param>
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131 <when value=""/>
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132 <when value="text">
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133 <param argument="--fasta-filter" type="text" label="RefSeq nucleotide and protein accessions" help="Comma separated">
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134 <sanitizer invalid_char="">
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135 <valid initial="string.letters,string.digits">
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136 <add value="," />
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137 </valid>
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138 </sanitizer>
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139 </param>
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140 </when>
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141 <when value="file">
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142 <param argument="--fasta-filter-file" type="data" format="txt" label="Dataset with list of RefSeq nucleotide and protein accessions" help=""/>
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143 </when>
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144 </conditional>
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145 </section>
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146 <section name="file_choices" title="Output options" expanded="true">
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147 <conditional name="kingdom_cond">
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148 <param name="kingdom_sel" type="select" label="Kingdom" help="Prokaryotic: Accessions starting with WP_. Data report has a different format and the rna, cds, 3/5' UTR and gene-product report are not suported. ">
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149 <option value="gene">Eukaryote</option>
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150 <option value="prok-gene">Prokaryote</option>
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151 </param>
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152 <when value="gene">
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153 <expand macro="gene_tsv_report_columns">
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154 <option value="gene-id" selected="true">NCBI GeneID</option>
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155 <option value="gene-type" selected="true">Gene Type</option>
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156 <option value="common-name" selected="true">Common Name</option>
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157 <option value="description" selected="true">Description</option>
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158 <option value="symbol" selected="true">Symbol</option>
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159 <option value="synonyms" selected="true">Synonyms</option>
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160 <option value="tax-id" selected="true">Taxonomic ID</option>
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161 <option value="tax-name" selected="true">Taxonomic Name</option>
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162 </expand>
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163 <expand macro="include">
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164 <expand macro="gene_includes">
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165 <option value="rna" selected="true">transcript (rna)</option>
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166 <option value="cds">nucleotide coding sequences (cds)</option>
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167 <option value="5p-utr">5'-UTR (5p-utr)</option>
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168 <option value="3p-utr">3'-UTR (3p-utr)</option>
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169 <option value="product-report"> (product-report)</option>
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170 </expand>
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171 </expand>
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172 </when>
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173 <when value="prok-gene">
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174 <expand macro="prok_gene_tsv_report_columns">
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175 <option value="accession" selected="true">Accession</option>
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176 <option value="description" selected="true">Description</option>
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177 <option value="ec-number" selected="true">EC Number</option>
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178 <option value="gene-symbol" selected="true">Gene Symbol</option>
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179 <option value="mapping-count" selected="true">Number of Genome Mappings</option>
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180 <option value="protein-length" selected="true">Protein Length</option>
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181 <option value="protein-name" selected="true">Protein Name</option>
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182 </expand>
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183 <expand macro="include">
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184 <expand macro="gene_includes"/>
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185 </expand>
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186 </when>
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187 </conditional>
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188 <param name="decompress" type="boolean" label="Decompress FASTA" help="By default FASTA files are provided zipped (fasta.gz) if this is checked the data will be decompressed"/>
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189 </section>
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190 </inputs>
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191 <outputs>
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192 <data name="gene_data_report" format="tabular" label="NCBI Gene Datasets: Data Report" from_work_dir="gene_data_report.tsv"/>
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193 <data name="gene_product_report" format="tabular" label="NCBI Gene Datasets: Product Report" from_work_dir="gene_product_report.tsv">
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194 <filter>file_choices['kingdom_cond']['include'] and "product-report" in file_choices['kingdom_cond']['include']</filter>
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195 </data>
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196 <data name="gene_fasta" label="NCBI Gene Datasets: Gene fasta" format="fasta" from_work_dir="ncbi_dataset/data/gene.fna">
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197 <filter>file_choices['kingdom_cond']['include'] and "gene" in file_choices['kingdom_cond']['include']</filter>
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198 </data>
17
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199 <data name="gene_flanks" label="NCBI Gene Datasets: Flanking faste" format="fasta" from_work_dir="ncbi_dataset/data/gene_flank.fna">
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200 <filter>query['subcommand']['download_by'] == "accession" and query['subcommand']['include_flanks_bp'] != ""</filter>
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201 </data>
11
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202 <data name="rna_fasta" label="NCBI Gene Datasets: RNA fasta" format="fasta" from_work_dir="ncbi_dataset/data/rna.fna">
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203 <filter>file_choices['kingdom_cond']['include'] and "rna" in file_choices['kingdom_cond']['include']</filter>
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204 </data>
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205 <data name="protein_fasta" label="NCBI Gene Datasets: protein fasta" format="fasta" from_work_dir="ncbi_dataset/data/protein.faa">
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206 <filter>file_choices['kingdom_cond']['include'] and "protein" in file_choices['kingdom_cond']['include']</filter>
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207 </data>
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208 <data name="cds_fasta" label="NCBI Gene Datasets: CDS fasta" format="fasta" from_work_dir="ncbi_dataset/data/cds.fna">
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209 <filter>file_choices['kingdom_cond']['include'] and "cds" in file_choices['kingdom_cond']['include']</filter>
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210 </data>
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211 <data name="threep_utr_fasta" label="NCBI Gene Datasets: 3' UTR fasta" format="fasta" from_work_dir="ncbi_dataset/data/3p_utr.fna">
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212 <filter>file_choices['kingdom_cond']['include'] and "5p-utr" in file_choices['kingdom_cond']['include']</filter>
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213 </data>
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214 <data name="fivep_utr_fasta" label="NCBI Gene Datasets: 5' UTR fasta" format="fasta" from_work_dir="ncbi_dataset/data/5p_utr.fna">
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215 <filter>file_choices['kingdom_cond']['include'] and "5p-utr" in file_choices['kingdom_cond']['include']</filter>
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216 </data>
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217 </outputs>
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218 <tests>
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219 <!-- 1: datasets download gene gene-id 672 -->
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220 <test expect_num_outputs="3">
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221 <conditional name="query|subcommand">
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222 <param name="download_by" value="gene-id"/>
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223 <conditional name="text_or_file">
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224 <param name="text_or_file" value="text"/>
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225 <param name="accession" value="672"/>
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226 </conditional>
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227 </conditional>
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228 <output name="gene_data_report">
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229 <assert_contents>
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230 <has_text text="human"/>
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231 <has_text text="BRCA1"/>
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232 <has_n_lines n="2"/>
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233 <has_n_columns n="8"/>
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234 </assert_contents>
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235 </output>
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236 <output name="rna_fasta">
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237 <assert_contents>
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238 <has_text text=">"/>
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239 </assert_contents>
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240 </output>
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241 <output name="protein_fasta">
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242 <assert_contents>
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243 <has_text text=">"/>
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244 </assert_contents>
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245 </output>
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246 </test>
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247 <!-- 2: datasets download gene gene-id 2597 14433 -->
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248 <test expect_num_outputs="3">
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249 <conditional name="query|subcommand">
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250 <param name="download_by" value="gene-id"/>
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251 <conditional name="text_or_file">
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252 <param name="text_or_file" value="text"/>
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253 <param name="accession" value="2597,14433"/>
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254 </conditional>
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255 </conditional>
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256 <output name="gene_data_report">
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257 <assert_contents>
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258 <has_text text="house mouse"/>
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259 <has_text text="glyceraldehyde-3-phosphate dehydrogenase"/>
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260 <has_n_lines n="3"/>
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261 <has_n_columns n="8"/>
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262 </assert_contents>
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263 </output>
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264 <output name="rna_fasta">
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265 <assert_contents>
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266 <has_text text=">"/>
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267 </assert_contents>
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268 </output>
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269 <output name="protein_fasta">
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270 <assert_contents>
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271 <has_text text=">"/>
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272 </assert_contents>
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273 </output>
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274 </test>
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275 <!-- 3: same as above + give accessions by file, 2 different outputs and ortholog-->
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276 <test expect_num_outputs="3">
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277 <conditional name="query|subcommand">
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278 <param name="download_by" value="gene-id"/>
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279 <conditional name="text_or_file">
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280 <param name="text_or_file" value="file"/>
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281 <param name="inputfile" value="geneids.txt"/>
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282 </conditional>
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283 <param name="ortholog" value="Haplorrhini,Strepsirrhini"/>
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284 </conditional>
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285 <section name="file_choices">
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286 <conditional name="kingdom_cond">
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287 <param name="include" value="gene,cds"/>
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288 </conditional>
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289 </section>
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290 <output name="gene_data_report">
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291 <assert_contents>
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292 <has_text text="baboon"/>
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293 <has_text text="glyceraldehyde-3-phosphate dehydrogenase"/>
12
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294 <has_n_lines min="30"/>
11
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295 <has_n_columns n="8"/>
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296 </assert_contents>
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297 </output>
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298 <output name="gene_fasta">
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299 <assert_contents>
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iuc
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300 <has_text text=">"/>
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301 </assert_contents>
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302 </output>
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303 <output name="cds_fasta">
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304 <assert_contents>
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diff changeset
305 <has_text text=">"/>
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306 </assert_contents>
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307 </output>
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308 </test>
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309 <!-- 4: datasets download gene symbol tp53 -->
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diff changeset
310 <test expect_num_outputs="1">
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iuc
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311 <conditional name="query|subcommand">
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iuc
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312 <param name="download_by" value="symbol"/>
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iuc
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diff changeset
313 <conditional name="text_or_file">
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314 <param name="text_or_file" value="text"/>
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iuc
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diff changeset
315 <param name="accession" value="tp53"/>
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316 </conditional>
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317 </conditional>
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318 <section name="file_choices">
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319 <conditional name="kingdom_cond">
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iuc
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320 <param name="include" value=""/>
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321 </conditional>
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322 </section>
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iuc
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323 <output name="gene_data_report">
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324 <assert_contents>
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325 <has_text text="human"/>
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iuc
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326 <has_n_lines n="2"/>
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iuc
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diff changeset
327 <has_n_columns n="8"/>
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328 </assert_contents>
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329 </output>
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330 </test>
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331 <!-- 5: datasets download gene symbol brca1 \-\-taxon mouse -->
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332 <test expect_num_outputs="4">
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333 <conditional name="query|subcommand">
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334 <param name="download_by" value="symbol"/>
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iuc
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diff changeset
335 <conditional name="text_or_file">
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336 <param name="text_or_file" value="text"/>
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337 <param name="accession" value="brca1"/>
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338 </conditional>
16
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diff changeset
339 <param name="taxon" value="house mouse"/>
11
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340 </conditional>
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341 <section name="file_choices">
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342 <conditional name="kingdom_cond">
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diff changeset
343 <param name="include" value="3p-utr,5p-utr,product-report"/>
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344 </conditional>
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345 </section>
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346 <output name="gene_data_report">
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diff changeset
347 <assert_contents>
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iuc
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348 <has_text text="house mouse"/>
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iuc
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349 <has_text text="Brca1"/>
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diff changeset
350 <has_n_lines n="2"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
351 <has_n_columns n="8"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
352 </assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
353 </output>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
354 <output name="gene_product_report">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
355 <assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
356 <has_text text="house mouse"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
357 <has_text text="XR_004936704.1"/>
12
d78faac2c6ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit affffdbe7237a2c0ba5793c0e7dd11cebb8413a9
iuc
parents: 11
diff changeset
358 <has_n_lines min="130"/>
17
da8260eba74b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1c7abf3293422fb432b5acd2ef178e7536d65f0b
iuc
parents: 16
diff changeset
359 <has_n_columns n="39"/>
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
360 </assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
361 </output>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
362 <output name="threep_utr_fasta">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
363 <assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
364 <has_text text=">"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
365 </assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
366 </output>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
367 <output name="fivep_utr_fasta">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
368 <assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
369 <has_text text=">"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
370 </assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
371 </output>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
372 </test>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
373 <!-- 6: datasets download gene symbol brca1 \-\-ortholog -->
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
374 <test expect_num_outputs="1">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
375 <conditional name="query|subcommand">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
376 <param name="download_by" value="symbol"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
377 <conditional name="text_or_file">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
378 <param name="text_or_file" value="text"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
379 <param name="accession" value="brca1"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
380 </conditional>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
381 <param name="ortholog" value="rodentia"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
382 </conditional>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
383 <section name="file_choices">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
384 <conditional name="kingdom_cond">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
385 <param name="include" value=""/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
386 </conditional>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
387 </section>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
388 <output name="gene_data_report">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
389 <assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
390 <has_text text="rat"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
391 <has_text text="Brca1"/>
12
d78faac2c6ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit affffdbe7237a2c0ba5793c0e7dd11cebb8413a9
iuc
parents: 11
diff changeset
392 <has_n_lines min="30"/>
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
393 <has_n_columns n="8"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
394 </assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
395 </output>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
396 </test>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
397 <!-- 7: datasets download gene accession NP_000483.3 -->
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
398 <test expect_num_outputs="1">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
399 <conditional name="query|subcommand">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
400 <param name="download_by" value="accession"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
401 <conditional name="text_or_file">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
402 <param name="text_or_file" value="text"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
403 <param name="accession" value="NP_000483.3"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
404 </conditional>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
405 </conditional>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
406 <section name="file_choices">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
407 <conditional name="kingdom_cond">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
408 <param name="include" value=""/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
409 </conditional>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
410 </section>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
411 <output name="gene_data_report">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
412 <assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
413 <has_text text="human"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
414 <has_n_lines n="2"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
415 <has_n_columns n="8"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
416 </assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
417 </output>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
418 </test>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
419 <!-- 8: datasets download gene accession NM_000546.6 NM_000492.4 + ortholog-->
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
420 <test expect_num_outputs="1">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
421 <conditional name="query|subcommand">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
422 <param name="download_by" value="accession"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
423 <conditional name="text_or_file">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
424 <param name="text_or_file" value="text"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
425 <param name="accession" value="NM_000546.6 NM_000492.4"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
426 </conditional>
14
75acf92c8fd5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 390b8177036c256e7e870dfe67c6de7d6417ad39
iuc
parents: 13
diff changeset
427 <param name="ortholog" value="all"/>
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
428 </conditional>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
429 <section name="file_choices">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
430 <conditional name="kingdom_cond">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
431 <param name="include" value=""/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
432 </conditional>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
433 </section>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
434 <output name="gene_data_report">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
435 <assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
436 <has_text text="human"/>
12
d78faac2c6ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit affffdbe7237a2c0ba5793c0e7dd11cebb8413a9
iuc
parents: 11
diff changeset
437 <has_n_lines min="800"/>
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
438 <has_n_columns n="8"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
439 </assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
440 </output>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
441 </test>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
442
17
da8260eba74b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1c7abf3293422fb432b5acd2ef178e7536d65f0b
iuc
parents: 16
diff changeset
443 <!-- 9: datasets download gene accession WP_003249567.1 + include_flanks_bp -->
da8260eba74b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1c7abf3293422fb432b5acd2ef178e7536d65f0b
iuc
parents: 16
diff changeset
444 <test expect_num_outputs="4">
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
445 <conditional name="query|subcommand">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
446 <param name="download_by" value="accession"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
447 <conditional name="text_or_file">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
448 <param name="text_or_file" value="text"/>
17
da8260eba74b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1c7abf3293422fb432b5acd2ef178e7536d65f0b
iuc
parents: 16
diff changeset
449 <param name="accession" value="WP_003249567.1"/>
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
450 </conditional>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
451 <param name="include_flanks_bp" value="100"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
452 </conditional>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
453 <section name="file_choices">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
454 <conditional name="kingdom_cond">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
455 <param name="kingdom_sel" value="prok-gene"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
456 <param name="include" value="gene,protein"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
457 </conditional>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
458 </section>
17
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iuc
parents: 16
diff changeset
459 <output name="gene_data_report">
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
460 <assert_contents>
17
da8260eba74b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1c7abf3293422fb432b5acd2ef178e7536d65f0b
iuc
parents: 16
diff changeset
461 <has_text text="WP_003249567.1"/>
da8260eba74b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1c7abf3293422fb432b5acd2ef178e7536d65f0b
iuc
parents: 16
diff changeset
462 <has_text text="menG"/>
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
463 <has_n_lines n="2"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
464 <has_n_columns n="7"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
465 </assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
466 </output>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
467 <output name="gene_fasta">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
468 <assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
469 <has_text text=">"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
470 </assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
471 </output>
17
da8260eba74b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1c7abf3293422fb432b5acd2ef178e7536d65f0b
iuc
parents: 16
diff changeset
472 <output name="gene_flanks">
da8260eba74b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1c7abf3293422fb432b5acd2ef178e7536d65f0b
iuc
parents: 16
diff changeset
473 <assert_contents>
da8260eba74b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1c7abf3293422fb432b5acd2ef178e7536d65f0b
iuc
parents: 16
diff changeset
474 <has_text text=">"/>
da8260eba74b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1c7abf3293422fb432b5acd2ef178e7536d65f0b
iuc
parents: 16
diff changeset
475 </assert_contents>
da8260eba74b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1c7abf3293422fb432b5acd2ef178e7536d65f0b
iuc
parents: 16
diff changeset
476 </output>
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
477 <output name="protein_fasta">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
478 <assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
479 <has_text text=">"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
480 </assert_contents>
17
da8260eba74b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1c7abf3293422fb432b5acd2ef178e7536d65f0b
iuc
parents: 16
diff changeset
481 </output>
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
482 <assert_command>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
483 <has_text text="include-flanks-bp 100"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
484 </assert_command>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
485 </test>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
486
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
487 <!-- 10: datasets download gene taxon human -->
17
da8260eba74b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1c7abf3293422fb432b5acd2ef178e7536d65f0b
iuc
parents: 16
diff changeset
488 <!-- <test expect_num_outputs="1">
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
489 <conditional name="query|subcommand">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
490 <param name="download_by" value="taxon"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
491 <param name="taxon_positional" value="human"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
492 </conditional>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
493 <section name="file_choices">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
494 <conditional name="kingdom_cond">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
495 <param name="include" value=""/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
496 </conditional>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
497 </section>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
498 <output name="gene_data_report">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
499 <assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
500 <has_text text="human"/>
12
d78faac2c6ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit affffdbe7237a2c0ba5793c0e7dd11cebb8413a9
iuc
parents: 11
diff changeset
501 <has_n_lines min="72000"/>
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
502 <has_n_columns n="8"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
503 </assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
504 </output>
17
da8260eba74b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1c7abf3293422fb432b5acd2ef178e7536d65f0b
iuc
parents: 16
diff changeset
505 </test> -->
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
506 <!-- 11: datasets download gene taxon human + \-\-fasta-filter -->
17
da8260eba74b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1c7abf3293422fb432b5acd2ef178e7536d65f0b
iuc
parents: 16
diff changeset
507 <!-- <test expect_num_outputs="2">
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
508 <conditional name="query|subcommand">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
509 <param name="download_by" value="taxon"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
510 <param name="taxon_positional" value="human"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
511 </conditional>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
512 <section name="file_choices">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
513 <conditional name="kingdom_cond">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
514 <param name="include" value="protein"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
515 </conditional>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
516 </section>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
517 <section name="filters">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
518 <conditional name="fasta_filter_cond">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
519 <param name="fasta_filter_select" value="text"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
520 <param name="fasta_filter" value="NP_542432.2"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
521 </conditional>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
522 </section>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
523 <output name="gene_data_report">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
524 <assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
525 <has_text text="human"/>
12
d78faac2c6ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit affffdbe7237a2c0ba5793c0e7dd11cebb8413a9
iuc
parents: 11
diff changeset
526 <has_n_lines min="72000"/>
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
527 <has_n_columns n="8"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
528 </assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
529 </output>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
530 <output name="protein_fasta">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
531 <assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
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532 <has_text text=">" n="1" />
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533 </assert_contents>
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534 </output>
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535 </test> -->
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536 </tests>
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537 <help>
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538 <![CDATA[
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539 **Download Gene Datasets from NCBI**
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540
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541 Download a gene dataset (gene sequence, transcipt, amino acid sequences,
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542 nucleotide coding sequences, 5'-UTR, 3'-UTR) as well as gene and gene
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543 product reports. Genes can be referred by gene id, symbol, accession,
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544 or taxon.
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545 ]]>
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546 </help>
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547 <expand macro="citations"/>
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548 </tool>