Mercurial > repos > gga > tripal_analysis_load_fasta

annotate analysis_load_fasta.xml @ 3:f6c2ca9dd23f draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1
author gga
date Mon, 06 Aug 2018 04:44:16 -0400
parents 0fbe72b81b9e
children 9e38e70f02f6
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1 <?xml version="1.0"?>
2
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2 <tool id="analysis_load_fasta" profile="16.04" name="Load a Fasta file" version="@WRAPPER_VERSION@.2">
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3 <description>into Tripal</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <code file="tripal.py"/>
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9 <expand macro="stdio"/>
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10 <command><![CDATA[
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11 tmp_dir=`mktemp -d -p "@DATA_DIR@"` && chmod a+rx "\${tmp_dir}"
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12
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13 &&
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15 cp '${fasta}' "\${tmp_dir}/content.fasta"
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17 &&
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19 @AUTH@
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21 tripaille analysis load_fasta
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23 --organism_id '${organism}'
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25 --analysis_id '${analysis}'
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27 --sequence_type '${sequence_type}'
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29 --method '${loading.method}'
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30
1
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31 #if str($loading.method) != "insert":
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32 --match_type '${loading.match_type}'
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33 #end if
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35 #if str($naming.re_name):
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36 --re_name '${naming.re_name}'
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37 #end if
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39 #if str($naming.re_uniquename):
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40 --re_uniquename '${naming.re_uniquename}'
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41 #end if
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43 #if str($relationships.rel_type) != "none":
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44 --rel_type '${relationships.rel_type}'
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45 --rel_subject_re '${relationships.rel_subject_re}'
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46 --rel_subject_type '${relationships.rel_subject_type}'
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47 #end if
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49 #if str($ext_db.db_ext_id):
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50 --db_ext_id '${ext_db.db_ext_id}'
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51 #end if
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52
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53 #if str($ext_db.re_accession):
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54 --re_accession '${ext_db.re_accession}'
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55 #end if
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56
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57 "\${tmp_dir}/content.fasta"
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58
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59 &&
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60
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61 echo "Data loaded" > $results
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62 ]]></command>
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63 <inputs>
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64 <param name="fasta"
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65 type="data"
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66 format="fasta"
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67 label="Fasta file to load" />
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68
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69 <param argument="--organism"
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70 type="select"
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71 dynamic_options="list_organisms()"
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72 label="Organism" />
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73
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74 <param argument="--analysis"
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75 type="select"
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76 dynamic_options="list_analyses()"
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77 label="Analysis" />
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78
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79 <param name="sequence_type"
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80 argument="--sequence_type"
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81 type="text"
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82 label="Sequence type"
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83 value="contig"
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84 help="this should be a Sequence Ontology term" />
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85
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86 <conditional name="loading">
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87 <param name="method"
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88 argument="--method"
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89 type="select"
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90 label="Loading method"
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91 help="select wether you expect feature to be already existing or not">
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92 <option value="insup" selected="true">Insert and update</option>
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93 <option value="insert">Insert only</option>
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94 <option value="update">Update only</option>
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95 </param>
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96 <when value="insup">
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97 <expand macro="match_type" />
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98 </when>
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99 <when value="insert"/>
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100 <when value="update">
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101 <expand macro="match_type" />
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102 </when>
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103 </conditional>
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104
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105 <section name="naming" title="Feature naming">
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106 <param name="re_name"
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107 argument="--re_name"
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108 type="text"
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109 optional="true"
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110 label="Regular expression to extract feature name"
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111 help="this regex will be applied on the fasta definition line to generate the feature name">
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112 <expand macro="sanitized"/>
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113 </param>
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114
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115 <param name="re_uniquename"
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116 argument="--re_uniquename"
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117 type="text"
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118 optional="true"
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119 label="Regular expression to extract feature uniquename"
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120 help="this regex will be applied on the fasta definition line to generate the feature uniquename">
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121 <expand macro="sanitized"/>
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122 </param>
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123 </section>
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124
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125 <conditional name="relationships">
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126 <param name="rel_type"
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127 argument="--rel_type"
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128 type="select"
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129 label="Relationship type"
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130 help="Use this when inserting features that should be associated to other already existing features">
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131 <option value="none" selected="true">No relationship</option>
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132 <option value="part_of">Part of (for CDS sequences)</option>
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133 <option value="derives_from">Derives from (for peptide sequences)</option>
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134 </param>
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135 <when value="none"/>
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136 <when value="part_of">
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137 <expand macro="feature_rel" />
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138 </when>
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139 <when value="derives_from">
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140 <expand macro="feature_rel" />
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141 </when>
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142 </conditional>
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143
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144 <section name="ext_db" title="Cross references to external database">
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145 <param name="db_ext_id"
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146 argument="--db_ext_id"
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147 type="integer"
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148 optional="true"
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149 label="External Database ID"
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150 help="Numeric ID from the Chado database" />
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151
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152 <param name="re_accession"
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153 argument="--re_accession"
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154 type="text"
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155 optional="true"
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156 label="Regular expression to extract the accession from external DB"
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157 help="this regex will be applied on the fasta definition line to generate the accession from external DB" />
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158 </section>
2
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159 <expand macro="wait_for"/>
0
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160 </inputs>
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161 <outputs>
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162 <data format="txt" name="results" label="Load Fasta into Tripal" />
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163 </outputs>
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164 <tests>
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165 <test expect_failure="true" expect_exit_code="1">
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166 <param name="fasta" value="citrus_genome.fasta" />
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167 <param name="organism" value="Testus testus" />
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168 <param name="analysis" value="Annotation xx" />
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169 <param name="sequence_type" value="mRNA" />
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170 <conditional name="loading">
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171 <param name="method" value="insup" />
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172 <param name="match_type" value="uniquename" />
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173 </conditional>
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174 <section name="naming">
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175 <param name="re_name" value="([a-z]{4}[0-9]+)_suffix" />
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176 <param name="re_uniquename" value="([a-z]{4}[0-9]+_suffix)" />
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177 </section>
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178
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179 <expand macro="test_result" />
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180 </test>
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181 </tests>
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182 <help><![CDATA[
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183 @HELP_OVERVIEW@
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184
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185 **Load Fasta**
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186
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187 With this tool, you can load sequences from a Fasta file into the Tripal/Chado database.
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188
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189 Corresponding features can be created if needed.
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190
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191 @HELP@
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192 ]]></help>
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193 <expand macro="citation"/>
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194 </tool>