Mercurial > repos > gga > tripal_analysis_load_fasta

comparison 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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-1:000000000000 0:ca1eb54c95d6
1 <?xml version="1.0"?>
2 <tool id="analysis_load_fasta" profile="16.04" name="Load a Fasta 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 '${fasta}' "\${tmp_dir}/content.fasta"
16
17 &&
18
19 @AUTH@
20
21 tripaille analysis load_fasta
22
23 --organism_id '${organism}'
24
25 --analysis_id '${analysis}'
26
27 --sequence_type '${sequence_type}'
28
29 --method '${loading.method}'
30
31 --match_type '${loading.match_type}'
32
33 #if str($naming.re_name):
34 --re_name '${naming.re_name}'
35 #end if
36
37 #if str($naming.re_uniquename):
38 --re_uniquename '${naming.re_uniquename}'
39 #end if
40
41 #if str($relationships.rel_type) != "none":
42 --rel_type '${relationships.rel_type}'
43 --rel_subject_re '${relationships.rel_subject_re}'
44 --rel_subject_type '${relationships.rel_subject_type}'
45 #end if
46
47 #if str($ext_db.db_ext_id):
48 --db_ext_id '${ext_db.db_ext_id}'
49 #end if
50
51 #if str($ext_db.re_accession):
52 --re_accession '${ext_db.re_accession}'
53 #end if
54
55 "\${tmp_dir}/content.fasta"
56
57 &&
58
59 echo "Data loaded" > $results
60 ]]></command>
61 <inputs>
62 <param name="fasta"
63 type="data"
64 format="fasta"
65 label="Fasta file to load" />
66
67 <param argument="--organism"
68 type="select"
69 dynamic_options="list_organisms()"
70 label="Organism" />
71
72 <param argument="--analysis"
73 type="select"
74 dynamic_options="list_analyses()"
75 label="Analysis" />
76
77 <param name="sequence_type"
78 argument="--sequence_type"
79 type="text"
80 label="Sequence type"
81 value="contig"
82 help="this should be a Sequence Ontology term" />
83
84 <conditional name="loading">
85 <param name="method"
86 argument="--method"
87 type="select"
88 label="Loading method"
89 help="select wether you expect feature to be already existing or not">
90 <option value="insup" selected="true">Insert and update</option>
91 <option value="insert">Insert only</option>
92 <option value="update">Update only</option>
93 </param>
94 <when value="insup">
95 <expand macro="match_type" />
96 </when>
97 <when value="insert"/>
98 <when value="update">
99 <expand macro="match_type" />
100 </when>
101 </conditional>
102
103 <section name="naming" title="Feature naming">
104 <param name="re_name"
105 argument="--re_name"
106 type="text"
107 optional="true"
108 label="Regular expression to extract feature name"
109 help="this regex will be applied on the fasta definition line to generate the feature name">
110 <expand macro="sanitized"/>
111 </param>
112
113 <param name="re_uniquename"
114 argument="--re_uniquename"
115 type="text"
116 optional="true"
117 label="Regular expression to extract feature uniquename"
118 help="this regex will be applied on the fasta definition line to generate the feature uniquename">
119 <expand macro="sanitized"/>
120 </param>
121 </section>
122
123 <conditional name="relationships">
124 <param name="rel_type"
125 argument="--rel_type"
126 type="select"
127 label="Relationship type"
128 help="Use this when inserting features that should be associated to other already existing features">
129 <option value="none" selected="true">No relationship</option>
130 <option value="part_of">Part of (for CDS sequences)</option>
131 <option value="derives_from">Derives from (for peptide sequences)</option>
132 </param>
133 <when value="none"/>
134 <when value="part_of">
135 <expand macro="feature_rel" />
136 </when>
137 <when value="derives_from">
138 <expand macro="feature_rel" />
139 </when>
140 </conditional>
141
142 <section name="ext_db" title="Cross references to external database">
143 <param name="db_ext_id"
144 argument="--db_ext_id"
145 type="integer"
146 optional="true"
147 label="External Database ID"
148 help="Numeric ID from the Chado database" />
149
150 <param name="re_accession"
151 argument="--re_accession"
152 type="text"
153 optional="true"
154 label="Regular expression to extract the accession from external DB"
155 help="this regex will be applied on the fasta definition line to generate the accession from external DB" />
156 </section>
157 </inputs>
158 <outputs>
159 <data format="txt" name="results" label="Load Fasta into Tripal" />
160 </outputs>
161 <tests>
162 <test expect_failure="true" expect_exit_code="1">
163 <param name="fasta" value="citrus_genome.fasta" />
164 <param name="organism" value="Testus testus" />
165 <param name="analysis" value="Annotation xx" />
166 <param name="sequence_type" value="mRNA" />
167 <conditional name="loading">
168 <param name="method" value="insup" />
169 <param name="match_type" value="uniquename" />
170 </conditional>
171 <section name="naming">
172 <param name="re_name" value="([a-z]{4}[0-9]+)_suffix" />
173 <param name="re_uniquename" value="([a-z]{4}[0-9]+_suffix)" />
174 </section>
175
176 <expand macro="test_result" />
177 </test>
178 </tests>
179 <help><![CDATA[
180 @HELP_OVERVIEW@
181
182 **Load Fasta**
183
184 With this tool, you can load sequences from a Fasta file into the Tripal/Chado database.
185
186 Corresponding features can be created if needed.
187
188 @HELP@
189 ]]></help>
190 <expand macro="citation"/>
191 </tool>