Mercurial > repos > iuc > ncbi_datasets

annotate datasets_gene.xml @ 16:a6a475ed58cb draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 9a34ebfc4d6b987b71e545dcf5dbdd884cd8d88e
author iuc
date Fri, 07 Jun 2024 14:19:58 +0000
parents 198c75abbf55
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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
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78 && 7z x -y ncbi_dataset.zip > 7z.log
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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>
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117 <param argument="--include-flanks-bp" type="integer" optional="true" min="0" label="Length of flanking nucleotides" help="WP accessions only"/>
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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>
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199 <data name="rna_fasta" label="NCBI Gene Datasets: RNA fasta" format="fasta" from_work_dir="ncbi_dataset/data/rna.fna">
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200 <filter>file_choices['kingdom_cond']['include'] and "rna" in file_choices['kingdom_cond']['include']</filter>
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201 </data>
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202 <data name="protein_fasta" label="NCBI Gene Datasets: protein fasta" format="fasta" from_work_dir="ncbi_dataset/data/protein.faa">
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203 <filter>file_choices['kingdom_cond']['include'] and "protein" in file_choices['kingdom_cond']['include']</filter>
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204 </data>
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205 <data name="cds_fasta" label="NCBI Gene Datasets: CDS fasta" format="fasta" from_work_dir="ncbi_dataset/data/cds.fna">
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206 <filter>file_choices['kingdom_cond']['include'] and "cds" in file_choices['kingdom_cond']['include']</filter>
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207 </data>
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208 <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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209 <filter>file_choices['kingdom_cond']['include'] and "5p-utr" in file_choices['kingdom_cond']['include']</filter>
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210 </data>
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211 <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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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 </outputs>
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215 <tests>
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216 <!-- 1: datasets download gene gene-id 672 -->
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217 <test expect_num_outputs="3">
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218 <conditional name="query|subcommand">
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219 <param name="download_by" value="gene-id"/>
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220 <conditional name="text_or_file">
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221 <param name="text_or_file" value="text"/>
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222 <param name="accession" value="672"/>
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223 </conditional>
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224 </conditional>
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225 <output name="gene_data_report">
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226 <assert_contents>
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227 <has_text text="human"/>
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228 <has_text text="BRCA1"/>
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229 <has_n_lines n="2"/>
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230 <has_n_columns n="8"/>
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231 </assert_contents>
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232 </output>
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233 <output name="rna_fasta">
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234 <assert_contents>
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235 <has_text text=">"/>
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236 </assert_contents>
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237 </output>
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238 <output name="protein_fasta">
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239 <assert_contents>
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240 <has_text text=">"/>
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241 </assert_contents>
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242 </output>
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243 </test>
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244 <!-- 2: datasets download gene gene-id 2597 14433 -->
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245 <test expect_num_outputs="3">
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246 <conditional name="query|subcommand">
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247 <param name="download_by" value="gene-id"/>
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248 <conditional name="text_or_file">
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249 <param name="text_or_file" value="text"/>
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250 <param name="accession" value="2597,14433"/>
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251 </conditional>
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252 </conditional>
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253 <output name="gene_data_report">
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254 <assert_contents>
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255 <has_text text="house mouse"/>
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256 <has_text text="glyceraldehyde-3-phosphate dehydrogenase"/>
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257 <has_n_lines n="3"/>
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258 <has_n_columns n="8"/>
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259 </assert_contents>
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260 </output>
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261 <output name="rna_fasta">
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262 <assert_contents>
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263 <has_text text=">"/>
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264 </assert_contents>
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265 </output>
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266 <output name="protein_fasta">
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267 <assert_contents>
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268 <has_text text=">"/>
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269 </assert_contents>
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270 </output>
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271 </test>
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272 <!-- 3: same as above + give accessions by file, 2 different outputs and ortholog-->
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273 <test expect_num_outputs="3">
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274 <conditional name="query|subcommand">
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275 <param name="download_by" value="gene-id"/>
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276 <conditional name="text_or_file">
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277 <param name="text_or_file" value="file"/>
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278 <param name="inputfile" value="geneids.txt"/>
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279 </conditional>
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280 <param name="ortholog" value="Haplorrhini,Strepsirrhini"/>
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281 </conditional>
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282 <section name="file_choices">
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iuc
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283 <conditional name="kingdom_cond">
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iuc
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284 <param name="include" value="gene,cds"/>
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285 </conditional>
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286 </section>
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iuc
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287 <output name="gene_data_report">
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288 <assert_contents>
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iuc
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289 <has_text text="baboon"/>
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290 <has_text text="glyceraldehyde-3-phosphate dehydrogenase"/>
12
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iuc
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291 <has_n_lines min="30"/>
11
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292 <has_n_columns n="8"/>
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293 </assert_contents>
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294 </output>
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295 <output name="gene_fasta">
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296 <assert_contents>
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iuc
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297 <has_text text=">"/>
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298 </assert_contents>
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299 </output>
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iuc
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300 <output name="cds_fasta">
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iuc
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301 <assert_contents>
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iuc
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diff changeset
302 <has_text text=">"/>
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303 </assert_contents>
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304 </output>
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305 </test>
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iuc
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306 <!-- 4: datasets download gene symbol tp53 -->
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iuc
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diff changeset
307 <test expect_num_outputs="1">
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iuc
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308 <conditional name="query|subcommand">
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iuc
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309 <param name="download_by" value="symbol"/>
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iuc
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diff changeset
310 <conditional name="text_or_file">
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iuc
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311 <param name="text_or_file" value="text"/>
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iuc
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312 <param name="accession" value="tp53"/>
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313 </conditional>
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314 </conditional>
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iuc
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diff changeset
315 <section name="file_choices">
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iuc
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diff changeset
316 <conditional name="kingdom_cond">
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iuc
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317 <param name="include" value=""/>
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318 </conditional>
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319 </section>
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iuc
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diff changeset
320 <output name="gene_data_report">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
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diff changeset
321 <assert_contents>
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iuc
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322 <has_text text="human"/>
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iuc
parents:
diff changeset
323 <has_n_lines n="2"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
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diff changeset
324 <has_n_columns n="8"/>
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325 </assert_contents>
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326 </output>
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327 </test>
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iuc
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328 <!-- 5: datasets download gene symbol brca1 \-\-taxon mouse -->
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iuc
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329 <test expect_num_outputs="4">
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iuc
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diff changeset
330 <conditional name="query|subcommand">
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iuc
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331 <param name="download_by" value="symbol"/>
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iuc
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diff changeset
332 <conditional name="text_or_file">
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iuc
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333 <param name="text_or_file" value="text"/>
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334 <param name="accession" value="brca1"/>
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335 </conditional>
16
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diff changeset
336 <param name="taxon" value="house mouse"/>
11
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337 </conditional>
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338 <section name="file_choices">
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diff changeset
339 <conditional name="kingdom_cond">
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iuc
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diff changeset
340 <param name="include" value="3p-utr,5p-utr,product-report"/>
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341 </conditional>
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342 </section>
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iuc
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diff changeset
343 <output name="gene_data_report">
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iuc
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diff changeset
344 <assert_contents>
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iuc
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diff changeset
345 <has_text text="house mouse"/>
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iuc
parents:
diff changeset
346 <has_text text="Brca1"/>
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iuc
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347 <has_n_lines n="2"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
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diff changeset
348 <has_n_columns n="8"/>
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349 </assert_contents>
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350 </output>
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iuc
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diff changeset
351 <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
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 <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
354 <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
355 <has_n_lines min="130"/>
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
356 <has_n_columns n="38"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
357 </assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
358 </output>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
359 <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
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 <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
362 </assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
363 </output>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
364 <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
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 <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
367 </assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
368 </output>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
369 </test>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
370 <!-- 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
371 <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
372 <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
373 <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
374 <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
375 <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
376 <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
377 </conditional>
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="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
379 </conditional>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
380 <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
381 <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
382 <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
383 </conditional>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
384 </section>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
385 <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
386 <assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
387 <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
388 <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
389 <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
390 <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
391 </assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
392 </output>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
393 </test>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
394 <!-- 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
395 <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
396 <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
397 <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
398 <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
399 <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
400 <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
401 </conditional>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
402 </conditional>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
403 <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
404 <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
405 <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
406 </conditional>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
407 </section>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
408 <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
409 <assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
410 <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
411 <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
412 <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
413 </assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
414 </output>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
415 </test>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
416 <!-- 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
417 <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
418 <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
419 <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
420 <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
421 <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
422 <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
423 </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
424 <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
425 </conditional>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
426 <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
427 <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
428 <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
429 </conditional>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
430 </section>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
431 <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
432 <assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
433 <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
434 <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
435 <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
436 </assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
437 </output>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
438 </test>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
439
15
198c75abbf55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1b6341a0430757c07760af2115ae4d5e70f5903a
iuc
parents: 14
diff changeset
440 <!-- 9: datasets download gene accession WP_004675351.1 + include_flanks_bp
198c75abbf55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1b6341a0430757c07760af2115ae4d5e70f5903a
iuc
parents: 14
diff changeset
441 test broken at the moment https://github.com/ncbi/datasets/issues/328
198c75abbf55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1b6341a0430757c07760af2115ae4d5e70f5903a
iuc
parents: 14
diff changeset
442 -->
198c75abbf55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1b6341a0430757c07760af2115ae4d5e70f5903a
iuc
parents: 14
diff changeset
443 <test expect_failure="true"> <!-- expect_num_outputs="3" -->
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
444 <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
445 <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
446 <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
447 <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
448 <param name="accession" value="WP_004675351.1"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
449 </conditional>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
450 <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
451 </conditional>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
452 <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
453 <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
454 <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
455 <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
456 </conditional>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
457 </section>
15
198c75abbf55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1b6341a0430757c07760af2115ae4d5e70f5903a
iuc
parents: 14
diff changeset
458 <!-- <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
459 <assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
460 <has_text text="glcE"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
461 <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
462 <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
463 </assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
464 </output>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
465 <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
466 <assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
467 <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
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 </output>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
470 <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
471 <assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
472 <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
473 </assert_contents>
15
198c75abbf55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1b6341a0430757c07760af2115ae4d5e70f5903a
iuc
parents: 14
diff changeset
474 </output> -->
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
475 <assert_command>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
476 <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
477 </assert_command>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
478 </test>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
479
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
480 <!-- 10: datasets download gene taxon human -->
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
481 <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
482 <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
483 <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
484 <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
485 </conditional>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
486 <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
487 <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
488 <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
489 </conditional>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
490 </section>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
491 <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
492 <assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
493 <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
494 <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
495 <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
496 </assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
497 </output>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
498 </test>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
499 <!-- 11: datasets download gene taxon human + \-\-fasta-filter -->
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
500 <test expect_num_outputs="2">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
501 <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
502 <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
503 <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
504 </conditional>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
505 <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
506 <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
507 <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
508 </conditional>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
509 </section>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
510 <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
511 <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
512 <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
513 <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
514 </conditional>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
515 </section>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
516 <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
517 <assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
518 <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
519 <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
520 <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
521 </assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
522 </output>
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="protein_fasta">
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=">" n="1" />
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
526 </assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
527 </output></test>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
528 </tests>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
529 <help>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
530 <![CDATA[
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
531 **Download Gene Datasets from NCBI**
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
diff changeset
532
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents:
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533 Download a gene dataset (gene sequence, transcipt, amino acid sequences,
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
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534 nucleotide coding sequences, 5'-UTR, 3'-UTR) as well as gene and gene
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
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535 product reports. Genes can be referred by gene id, symbol, accession,
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
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536 or taxon.
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
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537 ]]>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
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538 </help>
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539 <expand macro="citations"/>
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ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
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540 </tool>