Mercurial > repos > iuc > enasearch_search_data

annotate enasearch_search_data.xml @ 1:6e692d5a5599 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/enasearch commit 11ee7ac206d41894c0b6a11f2439aaea490824f0
author iuc
date Thu, 09 Nov 2017 13:08:41 -0500
parents fc42e7901a23
children 63b13eb2cb8a
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fc42e7901a23 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87
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1 <tool id="enasearch_search_data" name="Search ENA data" version="@WRAPPER_VERSION@.0">
fc42e7901a23 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87
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2 <description>given a query</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <import>search_macros.xml</import>
fc42e7901a23 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87
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6 </macros>
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7 <expand macro="requirements"/>
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8 <expand macro="version"/>
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9 <command detect_errors="aggressive"><![CDATA[
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10 enasearch
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11 search_data
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12 $query_type.free_text_search
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13 #if $query_type.free_text_search == '--free_text_search'
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14 --query '$query_type.query'
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15 --result '$query_type.res.result'
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16 @SEARCH_DATA_DISPLAY@
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17 #else
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18 --result '$query_type.res.result'
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19 #set $queries=''
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20 #set $sep=''
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21 #for $i, $s in enumerate( $query_type.res.queries )
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22 #if $sep == ''
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23 #set $sep = str($s.combination_operation)
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24 #else
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25 #set $sep = str($s.combination_operation)
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26 #set $queries += ' %s ' % ($sep)
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27 #end if
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28 #if $s.filter_field.field != 'location'
fc42e7901a23 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87
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29 #set $queries += '%s' % (str($s.filter_field.field))
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30 #if str($s.filter_field.operation) == "equal"
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31 #set $queries += '='
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32 #elif str($s.filter_field.operation) == "different"
fc42e7901a23 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87
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33 #set $queries += '!='
fc42e7901a23 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87
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34 #elif str($s.filter_field.operation) == "lower"
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35 #set $queries += '<'
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36 #elif str($s.filter_field.operation) == "equal or lower"
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37 #set $queries += '<='
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38 #elif str($s.filter_field.operation) == "higher"
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39 #set $queries += '>'
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40 #elif str($s.filter_field.operation) == "equal or higher"
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41 #set $queries += '>='
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42 #end if
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43 #set $queries += '"%s"' % (str($s.filter_field.value))
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44 #else
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45 #set $queries += '%s(%s)' % (str($s.filter_field.operation),str($s.filter_field.values))
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46 #end if
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47 #end for
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48 --query '$queries'
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49 @SEARCH_DATA_DISPLAY@
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50 #end if
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51 --file '$output'
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52 --download 'txt'
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53 ]]></command>
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54 <inputs>
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55 <conditional name="query_type">
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56 <param argument="--free_text_search" type="select" label="Use free text search?" help="If not, the ENA data warehouse is used">
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57 <option value="--free_text_search">Yes</option>
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58 <option value="">False</option>
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59 </param>
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60 <when value="--free_text_search">
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61 <param argument="--query" type="text" label="Query"/>
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62 <expand macro="free_text_search"/>
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63 </when>
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64 <when value="">
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65 <expand macro="conditional_text_search"/>
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66 </when>
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67 </conditional>
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68 </inputs>
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69 <outputs>
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70 <data name="output" format="tabular" label="${tool.name}">
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71 <change_format>
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72 <when input="query_type.res.display_opt.display" value="fasta" format="fasta" />
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73 <when input="query_type.res.display_opt.display" value="fastq" format="fastq" />
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74 <when input="query_type.res.display_opt.display" value="html" format="html" />
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75 <when input="query_type.res.display_opt.display" value="text" format="text" />
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76 <when input="query_type.res.display_opt.display" value="xml" format="xml" />
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77 </change_format>
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78 </data>
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79 </outputs>
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80 <tests>
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81 <test>
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82 <conditional name="query_type">
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83 <param name="free_text_search" value="--free_text_search"/>
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84 <param name="query" value="kinase+homo+sapiens"/>
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85 <conditional name="res">
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86 <param name="result" value="sequence_update"/>
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87 <conditional name="display_opt">
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88 <param name="display" value="fasta"/>
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89 </conditional>
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90 </conditional>
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91 </conditional>
1
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92 <output name="output" ftype="fasta">
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93 <assert_contents>
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94 <has_text text=">ENA|LY285295|LY285295" />
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95 <has_text text=">ENA|LY285296|LY285296" />
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96 </assert_contents>
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97 </output>
0
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98 </test>
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99 <test>
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100 <conditional name="query_type">
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101 <param name="free_text_search" value="--free_text_search"/>
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102 <param name="query" value="kinase+homo+sapiens"/>
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103 <conditional name="res">
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104 <param name="result" value="wgs_set"/>
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105 <conditional name="display_opt">
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106 <param name="display" value="report"/>
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107 <param name="fields" value="accession,environmental_sample"/>
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108 </conditional>
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109 </conditional>
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110 </conditional>
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111 <output name="output" ftype="tabular" md5="c1f91a8276f59c90ec53025e1a3d31d5"/>
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112 </test>
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113 <test>
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114 <conditional name="query_type">
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115 <param name="free_text_search" value=""/>
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116 <conditional name="res">
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117 <param name="result" value="coding_release"/>
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118 <repeat name="queries">
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119 <param name="combination_operation" value="AND"/>
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120 <conditional name="filter_field">
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121 <param name="field" value="dataclass"/>
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122 <param name="operation" value="equal"/>
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123 <param name="value" value="STD"/>
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124 </conditional>
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125 </repeat>
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126 <repeat name="queries">
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127 <param name="combination_operation" value="AND"/>
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128 <conditional name="filter_field">
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129 <param name="field" value="tissue_lib"/>
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130 <param name="operation" value="equal"/>
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131 <param name="value" value="lambda gt11"/>
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132 </conditional>
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133 </repeat>
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134 <conditional name="display_opt">
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135 <param name="display" value="xml"/>
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136 </conditional>
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137 </conditional>
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138 </conditional>
1
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139 <output name="output" ftype="xml">
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140 <assert_contents>
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141 <has_text text="entry accession=&quot;AAA02481&quot;" />
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142 <has_text text="entry accession=&quot;AAA02488&quot;" />
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143 </assert_contents>
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144 </output>
0
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145 </test>
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146 </tests>
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147 <help><![CDATA[
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148 **What it does**
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149
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150 This tool retrieve ENA taxon data
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151 ]]></help>
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152 <expand macro="citations"/>
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153 </tool>