Mercurial > repos > gga > tripal_analysis_load_gff3

comparison analysis_load_gff3.xml @ 0:5ce8ae1288c1 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 05:51:14 -0400
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children 16acaa0aa58c
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-1:000000000000 0:5ce8ae1288c1
1 <?xml version="1.0"?>
2 <tool id="analysis_load_gff3" profile="16.04" name="Load a GFF3 annotation file" version="@WRAPPER_VERSION@.0">
3 <description>into Tripal</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <code file="tripal.py"/>
9 <expand macro="stdio"/>
10 <command><![CDATA[
11 tmp_dir=`mktemp -d -p "@DATA_DIR@"` && chmod a+rx "\${tmp_dir}"
12
13 &&
14
15 cp '${gff3}' "\${tmp_dir}/annotation.gff3"
16
17 &&
18
19 @AUTH@
20
21 tripaille analysis load_gff3
22
23 --organism_id '${organism}'
24
25 --analysis_id '${analysis}'
26
27 --import_mode '${import_mode}'
28
29 #if str($naming.mode) == 'manual':
30 --re_mrna '${naming.re_mrna}'
31 --re_protein '${naming.re_protein}'
32 #end if
33
34 #if str($advanced.landmark_type):
35 --landmark_type '${advanced.landmark_type}'
36 #end if
37
38 #if str($advanced.alt_id_attr):
39 --alt_id_attr '${advanced.alt_id_attr}'
40 #end if
41
42 ${advanced.create_organism}
43
44 #if str($target.target_organism):
45 --target_organism '${target.target_organism}'
46 #end if
47
48 #if str($target.target_type):
49 --target_type '${target.target_type}'
50 #end if
51
52 ${target.target_create}
53
54 "\${tmp_dir}/annotation.gff3"
55
56 &&
57
58 echo "Data loaded" > $results
59 ]]></command>
60 <inputs>
61 <param name="gff3"
62 type="data"
63 format="gff3"
64 label="Annotation file" />
65
66 <param argument="--organism"
67 type="select"
68 dynamic_options="list_organisms()"
69 label="Organism" />
70
71 <param argument="--analysis"
72 type="select"
73 dynamic_options="list_analyses()"
74 label="Analysis" />
75
76 <param name="import_mode"
77 argument="--import_mode"
78 type="select"
79 label="Loading method">
80 <option value="update" selected="true">Import everything, update when already existing</option>
81 <option value="add_only">Import only new features</option>
82 </param>
83
84 <conditional name="naming">
85 <param name="mode"
86 type="select"
87 label="Naming method for proteins"
88 help="in case your GFF file does not contain polypeptide features">
89 <option value="auto">Automatic</option>
90 <option value="manual">Manual</option>
91 </param>
92 <when value="auto"/>
93 <when value="manual">
94 <param name="re_mrna"
95 argument="--re_mrna"
96 type="text"
97 label="Regular expression for the mRNA name"
98 help="this regex will be used to extract parts of the mRNA feature name">
99 <expand macro="sanitized"/>
100 </param>
101
102 <param name="re_protein"
103 argument="--re_protein"
104 type="text"
105 label="Replacement string for the protein name"
106 help="will be used to generate the protein name based on the mRNA name">
107 <expand macro="sanitized"/>
108 </param>
109 </when>
110 </conditional>
111
112 <section name="advanced" title="Advanced options" expanded="False">
113 <param name="landmark_type"
114 argument="--landmark_type"
115 type="text"
116 optional="true"
117 label="Landmark type"
118 help="A Sequence Ontology type for the landmark sequences in the GFF fie (e.g. \'chromosome\'). Will be used to create them if they don't already exist." />
119
120 <param name="alt_id_attr"
121 argument="--alt_id_attr"
122 type="text"
123 optional="true"
124 label="ID attribute"
125 help="Name of the GFF attribute that contains a unique identifier for each feature. Leave empty to use the 'ID' attribute" />
126
127 <param name="create_organism"
128 argument="--create_organism"
129 type="boolean"
130 checked="false"
131 truevalue="--create_organism"
132 falsevalue=""
133 label="Create organisms specified in 'organism' attribute"
134 help="If not found, create features referenced in the target attribute." />
135 </section>
136
137 <section name="target" title="Target attribute handling" expanded="False">
138 <param name="target_organism"
139 argument="--target_organism"
140 type="text"
141 optional="true"
142 label="Target organism name"
143 help="Name of organism corresponding to target attribute. Abbreviation or common name as created with the 'Create Organism' tool." />
144 <param name="target_type"
145 argument="--target_type"
146 type="text"
147 optional="true"
148 label="Target feature type"
149 help="Type of features referenced in the target attribute. Should be a Sequence Ontology term." />
150 <param name="target_create"
151 argument="--target_create"
152 type="boolean"
153 checked="false"
154 truevalue="--target_create"
155 falsevalue=""
156 label="Create target features"
157 help="If not found, create features referenced in the target attribute." />
158 </section>
159 </inputs>
160 <outputs>
161 <data format="txt" name="results" label="Load GFF3 into Tripal" />
162 </outputs>
163 <tests>
164 <test expect_failure="true" expect_exit_code="1">
165 <param name="gff3" value="sample.gff3" />
166 <param name="organism" value="Testus testus" />
167 <param name="analysis" value="Annotation xx" />
168 <conditional name="naming">
169 <param name="mode" value="manual" />
170 <param name="re_mrna" value="([a-z]{4}[0-9]+)_rna" />
171 <param name="re_protein" value="([a-z]{4}[0-9]+)_prot" />
172 </conditional>
173
174 <expand macro="test_result" />
175 </test>
176 </tests>
177 <help><![CDATA[
178 @HELP_OVERVIEW@
179
180 **Load GFF3**
181
182 With this tool, you can load features from a GFF3 file into the Tripal/Chado database.
183
184 @HELP@
185 ]]></help>
186 <expand macro="citation"/>
187 </tool>