Mercurial > repos > gga > tripal_analysis_load_fasta

annotate analysis_load_fasta.xml @ 0:ca1eb54c95d6 draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
author gga
date Mon, 11 Sep 2017 05:50:45 -0400
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children 43bb9308b52d
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ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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1 <?xml version="1.0"?>
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2 <tool id="analysis_load_fasta" profile="16.04" name="Load a Fasta file" version="@WRAPPER_VERSION@.0">
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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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28
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29 --method '${loading.method}'
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30
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31 --match_type '${loading.match_type}'
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32
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33 #if str($naming.re_name):
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34 --re_name '${naming.re_name}'
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35 #end if
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36
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37 #if str($naming.re_uniquename):
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38 --re_uniquename '${naming.re_uniquename}'
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39 #end if
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40
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41 #if str($relationships.rel_type) != "none":
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42 --rel_type '${relationships.rel_type}'
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43 --rel_subject_re '${relationships.rel_subject_re}'
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44 --rel_subject_type '${relationships.rel_subject_type}'
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45 #end if
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46
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47 #if str($ext_db.db_ext_id):
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48 --db_ext_id '${ext_db.db_ext_id}'
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49 #end if
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51 #if str($ext_db.re_accession):
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52 --re_accession '${ext_db.re_accession}'
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53 #end if
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54
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55 "\${tmp_dir}/content.fasta"
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56
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57 &&
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58
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59 echo "Data loaded" > $results
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60 ]]></command>
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61 <inputs>
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62 <param name="fasta"
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63 type="data"
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64 format="fasta"
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65 label="Fasta file to load" />
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66
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67 <param argument="--organism"
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68 type="select"
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69 dynamic_options="list_organisms()"
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70 label="Organism" />
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71
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72 <param argument="--analysis"
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73 type="select"
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74 dynamic_options="list_analyses()"
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75 label="Analysis" />
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76
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77 <param name="sequence_type"
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78 argument="--sequence_type"
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79 type="text"
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80 label="Sequence type"
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81 value="contig"
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82 help="this should be a Sequence Ontology term" />
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83
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84 <conditional name="loading">
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85 <param name="method"
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86 argument="--method"
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87 type="select"
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88 label="Loading method"
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89 help="select wether you expect feature to be already existing or not">
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90 <option value="insup" selected="true">Insert and update</option>
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91 <option value="insert">Insert only</option>
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92 <option value="update">Update only</option>
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93 </param>
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94 <when value="insup">
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95 <expand macro="match_type" />
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96 </when>
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97 <when value="insert"/>
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98 <when value="update">
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99 <expand macro="match_type" />
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100 </when>
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101 </conditional>
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102
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103 <section name="naming" title="Feature naming">
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104 <param name="re_name"
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105 argument="--re_name"
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106 type="text"
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107 optional="true"
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108 label="Regular expression to extract feature name"
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109 help="this regex will be applied on the fasta definition line to generate the feature name">
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110 <expand macro="sanitized"/>
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111 </param>
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112
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113 <param name="re_uniquename"
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114 argument="--re_uniquename"
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115 type="text"
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116 optional="true"
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117 label="Regular expression to extract feature uniquename"
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118 help="this regex will be applied on the fasta definition line to generate the feature uniquename">
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119 <expand macro="sanitized"/>
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120 </param>
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121 </section>
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122
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123 <conditional name="relationships">
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124 <param name="rel_type"
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125 argument="--rel_type"
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126 type="select"
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127 label="Relationship type"
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128 help="Use this when inserting features that should be associated to other already existing features">
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129 <option value="none" selected="true">No relationship</option>
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130 <option value="part_of">Part of (for CDS sequences)</option>
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131 <option value="derives_from">Derives from (for peptide sequences)</option>
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132 </param>
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133 <when value="none"/>
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134 <when value="part_of">
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135 <expand macro="feature_rel" />
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136 </when>
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137 <when value="derives_from">
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138 <expand macro="feature_rel" />
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139 </when>
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140 </conditional>
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141
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142 <section name="ext_db" title="Cross references to external database">
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143 <param name="db_ext_id"
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144 argument="--db_ext_id"
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145 type="integer"
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146 optional="true"
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147 label="External Database ID"
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148 help="Numeric ID from the Chado database" />
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149
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150 <param name="re_accession"
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151 argument="--re_accession"
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152 type="text"
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153 optional="true"
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154 label="Regular expression to extract the accession from external DB"
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155 help="this regex will be applied on the fasta definition line to generate the accession from external DB" />
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156 </section>
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157 </inputs>
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158 <outputs>
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159 <data format="txt" name="results" label="Load Fasta into Tripal" />
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160 </outputs>
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161 <tests>
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162 <test expect_failure="true" expect_exit_code="1">
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163 <param name="fasta" value="citrus_genome.fasta" />
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164 <param name="organism" value="Testus testus" />
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165 <param name="analysis" value="Annotation xx" />
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166 <param name="sequence_type" value="mRNA" />
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167 <conditional name="loading">
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168 <param name="method" value="insup" />
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169 <param name="match_type" value="uniquename" />
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170 </conditional>
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171 <section name="naming">
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172 <param name="re_name" value="([a-z]{4}[0-9]+)_suffix" />
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173 <param name="re_uniquename" value="([a-z]{4}[0-9]+_suffix)" />
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174 </section>
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175
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176 <expand macro="test_result" />
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177 </test>
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178 </tests>
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179 <help><![CDATA[
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180 @HELP_OVERVIEW@
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181
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182 **Load Fasta**
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183
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184 With this tool, you can load sequences from a Fasta file into the Tripal/Chado database.
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185
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186 Corresponding features can be created if needed.
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187
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188 @HELP@
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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189 ]]></help>
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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190 <expand macro="citation"/>
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191 </tool>