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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit 669dd4d406e86aee7d83e7420dced981c180d805
author iuc
date Sun, 11 Feb 2024 11:29:44 +0000
parents c4ac24510b55
children
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0:c4ac24510b55 1:1fdc517743e6
1 <tool id='aegean_locuspocus' name='AEGeAn LocusPocus' version='@TOOL_VERSION@' profile='20.01'> 1 <tool id="aegean_locuspocus" name="AEGeAn LocusPocus" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
2 <description> calculate locus coordinates for the given gene annotation</description> 2 <description> calculate locus coordinates for the given gene annotation</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro='xrefs'/> 6 <expand macro="edam_ontology"/>
7 <expand macro='edam_ontology'/> 7 <expand macro="xrefs"/>
8 <expand macro='requirements'/> 8 <expand macro="requirements"/>
9 <version_command>locuspocus --version</version_command> 9 <version_command>locuspocus --version</version_command>
10 <command detect_errors='exit_code'> 10 <command detect_errors="exit_code">
11 <![CDATA[ 11 <![CDATA[
12 locuspocus '$genesgff3' 12 locuspocus "$genesgff3"
13 -l $ilocus_parsing.delta 13 -l $ilocus_parsing.delta
14 $ilocus_parsing.mode 14 $ilocus_parsing.mode
15 $ilocus_parsing.skipiloci 15 $ilocus_parsing.skipiloci
16 #if $refine_options.refine_parameters.refine 16 #if $refine_options.refine_parameters.refine
17 $refine_options.refine_parameters.cds 17 $refine_options.refine_parameters.cds
18 #end if 18 #end if
19 -m $refine_options.minoverlap 19 -m $refine_options.minoverlap
20 -f '$input_options.filter' 20 -f "$input_options.filter"
21 #if $input_options.parent 21 #if $input_options.parent
22 -p '$input_options.parent' 22 -p "$input_options.parent"
23 #end if 23 #end if
24 $input_options.pseudo 24 $input_options.pseudo
25 #if $output_options.outputfiles 25 #if $output_options.outputfiles
26 #if "ilens" in $output_options.outputfiles 26 #if "ilens" in $output_options.outputfiles
27 --ilens '$output_ilens' 27 --ilens "$output_ilens"
28 #end if 28 #end if
29 #if "genemap" in $output_options.outputfiles 29 #if "genemap" in $output_options.outputfiles
30 --genemap '$output_genemap' 30 --genemap "$output_genemap"
31 #end if 31 #end if
32 #if "transmap" in $output_options.outputfiles 32 #if "transmap" in $output_options.outputfiles
33 --transmap '$output_transmap' 33 --transmap "$output_transmap"
34 #end if 34 #end if
35 #end if 35 #end if
36 #if $output_options.namefmt 36 #if $output_options.namefmt
37 -n '$output_options.namefmt' 37 -n "$output_options.namefmt"
38 #end if 38 #end if
39 $output_options.retainids 39 $output_options.retainids
40 -o '$output' 40 -o "$output"
41 ]]> 41 ]]>
42 </command> 42 </command>
43 <inputs> 43 <inputs>
44 <param name='genesgff3' type='data' format='gff3' label="GFF3 File" /> 44 <param name="genesgff3" type="data" format="gff3" label="GFF3 File" />
45 <section name='ilocus_parsing' title='iLocus parsing options' expanded='True'> 45 <section name="ilocus_parsing" title="iLocus parsing options" expanded="True">
46 <param argument='--delta' type='integer' 46 <param argument="--delta" type="integer"
47 min='0' max='1000' value='500' 47 min="0" max="1000" value="500"
48 label='Gene loci extension' 48 label="Gene loci extension"
49 help='When parsing interval loci, use the following delta to extend gene loci and include potential regulatory regions' /> 49 help="When parsing interval loci, use the following delta to extend gene loci and include potential regulatory regions" />
50 <param name='mode' type='select' label='Annotation mode'> 50 <param name="mode" type="select" label="Annotation mode">
51 <option value='' selected='true'>Default mode</option> 51 <option value="" selected="true">Default mode</option>
52 <option value='--skipends'> Exclude unannotated iLoci at either end of the sequence</option> 52 <option value="--skipends"> Exclude unannotated iLoci at either end of the sequence</option>
53 <option value='--endsonly'> Report only incomplete iLocus fragments at the unannotated ends of sequences</option> 53 <option value="--endsonly"> Report only incomplete iLocus fragments at the unannotated ends of sequences</option>
54 </param> 54 </param>
55 <param argument="--skipiloci" type='boolean' 55 <param argument="--skipiloci" type="boolean"
56 truevalue='--skipiiloci' falsevalue='' 56 truevalue="--skipiiloci" falsevalue=""
57 label='Do not report intergenic iLoci' /> 57 label="Do not report intergenic iLoci" />
58 </section> 58 </section>
59 <section name='refine_options' title='Refine options' expanded='false'> 59 <section name="refine_options" title="Refine options" expanded="false">
60 <conditional name='refine_parameters'> 60 <conditional name="refine_parameters">
61 <param name='refine' type='select' 61 <param name="refine" type="select"
62 label='Mode for handling of overlpping genes' 62 label="Mode for handling of overlpping genes"
63 help='Refine mode allows for a more nuanced handling of overlapping genes.'> 63 help="Refine mode allows for a more nuanced handling of overlapping genes.">
64 <option value=''>Default</option> 64 <option value="">Default</option>
65 <option value='--refine'>Refine mode</option> 65 <option value="--refine">Refine mode</option>
66 </param> 66 </param>
67 <when value=''/> 67 <when value=""/>
68 <when value='--refine'> 68 <when value="--refine">
69 <param argument='--cds' type='boolean' 69 <param argument="--cds" type="boolean"
70 truevalue='--cds' falsevalue='' 70 truevalue="--cds" falsevalue=""
71 label='Use CDS rather than UTRs' 71 label="Use CDS rather than UTRs"
72 help='(-c)' /> 72 help="(-c)" />
73 </when> 73 </when>
74 </conditional> 74 </conditional>
75 <param argument='--minoverlap' type='integer' 75 <param argument="--minoverlap" type="integer"
76 max='20' min='1' value='1' 76 max="20" min="1" value="1"
77 label='Minimum number of overlapping nucleotides' 77 label="Minimum number of overlapping nucleotides"
78 help='The minimum number of nucleotides two genes must overlap to be grouped in the same iLocus' /> 78 help="The minimum number of nucleotides two genes must overlap to be grouped in the same iLocus" />
79 </section> 79 </section>
80 <section name='input_options' title='Input options' expanded='false'> 80 <section name="input_options" title="Input options" expanded="false">
81 <param argument='--filter' type='text' 81 <param argument="--filter" type="text"
82 value='gene' 82 value="gene"
83 label='Comma-separated list of feature types to use' 83 label="Comma-separated list of feature types to use"
84 help="Select the featured used to annotate intervals on a genome (e.g. gene, intron, exon)." /> 84 help="Select the featured used to annotate intervals on a genome (e.g. gene, intron, exon)." />
85 <param argument='--parent' type='text' 85 <param argument="--parent" type="text"
86 value='' optional='true' 86 value="" optional="true"
87 label='Create a parent for features that lack a parent feature' 87 label="Create a parent for features that lack a parent feature"
88 help='If a feature of type $CT exists without a parent, create a parent for this feature with type $PT; for example, mRNA:gene will create a gene feature as a parent for any top-level mRNA feature.'/> 88 help="If a feature of type $CT exists without a parent, create a parent for this feature with type $PT; for example, mRNA:gene will create a gene feature as a parent for any top-level mRNA feature."/>
89 <param argument='--pseudo' type='boolean' 89 <param argument="--pseudo" type="boolean"
90 truevalue='--pseudo' falsevalue='' 90 truevalue="--pseudo" falsevalue=""
91 label='Correct erroneously labeled pseudogenes'/> 91 label="Correct erroneously labeled pseudogenes"/>
92 </section> 92 </section>
93 <section name='output_options' title='Output options' expanded='false'> 93 <section name="output_options" title="Output options" expanded="false">
94 <param argument='--retainids' type='boolean' 94 <param argument="--retainids" type="boolean"
95 truevalue='--retainids' falsevalue='' 95 truevalue="--retainids" falsevalue=""
96 label='Retain original feature IDs' 96 label="Retain original feature IDs"
97 help='Retain original feature IDs from input files; conflicts will arise if input contains duplicated ID values'/> 97 help="Retain original feature IDs from input files; conflicts will arise if input contains duplicated ID values"/>
98 <param argument='--namefmt' type='text' 98 <param argument="--namefmt" type="text"
99 value='' optional='true' 99 value="" optional="true"
100 label='ID format for newly created locy' 100 label="ID format for newly created locy"
101 help='Provide a format string to override the default ID format for newly created loci; default is "locus%lu" (locus1, locus2, etc) for loci and "iLocus%lu" (iLocus1, iLocus2, etc) for interval loci; note the format string should include a single %lu specifier to be filled in with a long unsigned integer value.'/> 101 help="Provide a format string to override the default ID format for newly created loci; default is &quot;locus%lu&quot; (locus1, locus2, etc) for loci and &quot;iLocus%lu&quot; (iLocus1, iLocus2, etc) for interval loci; note the format string should include a single %lu specifier to be filled in with a long unsigned integer value."/>
102 <param name="outputfiles" type="select" display="checkboxes" label="Output files" 102 <param name="outputfiles" type="select" display="checkboxes" label="Output files"
103 multiple="true" optional="true" > 103 multiple="true" optional="true" >
104 <option value="ilens">Create file with the lenghts of each intergenic iLocus</option> 104 <option value="ilens">Create file with the lenghts of each intergenic iLocus</option>
105 <option value="genemap">Create a mapping from each gene annotation to its correspondig locus</option> 105 <option value="genemap">Create a mapping from each gene annotation to its correspondig locus</option>
106 <option value="transmap">Create a mapping from each transcript annotation to its correspondent locus</option> 106 <option value="transmap">Create a mapping from each transcript annotation to its correspondent locus</option>
107 </param> 107 </param>
108 </section> 108 </section>
109 109
110 </inputs> 110 </inputs>
111 <outputs> 111 <outputs>
112 <data name='output' format='tabular' /> 112 <data name="output" format="tabular" />
113 <data name='output_ilens' format='tabular'> 113 <data name="output_ilens" format="tabular" label="${tool.name} on ${on_string}: Intergenic regions lengths">
114 <filter>output_options['outputfiles'] and "ilens" in output_options['outputfiles']</filter> 114 <filter>output_options["outputfiles"] and "ilens" in output_options["outputfiles"]</filter>
115 </data> 115 </data>
116 <data name='output_genemap' format='tabular'> 116 <data name="output_genemap" format="tabular" label="${tool.name} on ${on_string}: Annotation locus mapping">
117 <filter>output_options['outputfiles'] and "genemap" in output_options['outputfiles']</filter> 117 <filter>output_options["outputfiles"] and "genemap" in output_options["outputfiles"]</filter>
118 </data> 118 </data>
119 <data name='output_transmap' format='tabular'> 119 <data name="output_transmap" format="tabular" label="${tool.name} on ${on_string}: Transcript locus mapping">
120 <filter>output_options['outputfiles'] and "transmap" in output_options['outputfiles']</filter> 120 <filter>output_options["outputfiles"] and "transmap" in output_options["outputfiles"]</filter>
121 </data> 121 </data>
122 </outputs> 122 </outputs>
123 <tests> 123 <tests>
124 <test expect_num_outputs="1"> 124 <test expect_num_outputs="1">
125 <param name='genesgff3' value='TAIR10_GFF3_genes.gff'/> 125 <param name="genesgff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>
126 <output name='output' file='locuspocus_output_test1.txt'/> 126 <output name="output" file="locuspocus_output_test1.txt"/>
127 </test> 127 </test>
128 <test expect_num_outputs="1"> 128 <test expect_num_outputs="1">
129 <param name='genesgff3' value='TAIR10_GFF3_genes.gff'/> 129 <param name="genesgff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>
130 <section name='ilocus_parsing'> 130 <section name="ilocus_parsing">
131 <param name='delta' value='400'/> 131 <param name="delta" value="400"/>
132 <param name='mode' value='--skipends'/> 132 <param name="mode" value="--skipends"/>
133 </section> 133 </section>
134 <output name='output' file='locuspocus_output_test2.txt'/> 134 <output name="output" file="locuspocus_output_test2.txt"/>
135 </test> 135 </test>
136 <test expect_num_outputs="1"> 136 <test expect_num_outputs="1">
137 <param name='genesgff3' value='TAIR10_GFF3_genes.gff'/> 137 <param name="genesgff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>
138 <section name='ilocus_parsing'> 138 <section name="ilocus_parsing">
139 <param name='skipiloci' value='true'/> 139 <param name="skipiloci" value="true"/>
140 <param name='mode' value='--endsonly'/> 140 <param name="mode" value="--endsonly"/>
141 </section> 141 </section>
142 <output name='output' file='locuspocus_output_test3.txt'/> 142 <output name="output" file="locuspocus_output_test3.txt"/>
143 </test> 143 </test>
144 <test expect_num_outputs="1"> 144 <test expect_num_outputs="1">
145 <param name='genesgff3' value='TAIR10_GFF3_genes.gff'/> 145 <param name="genesgff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>
146 <section name='refine_options'> 146 <section name="refine_options">
147 <param name='refine_parameters|refine' value='--refine'/> 147 <param name="refine_parameters|refine" value="--refine"/>
148 <param name='minoverlap' value='5'/> 148 <param name="minoverlap" value="5"/>
149 </section> 149 </section>
150 <output name='output' file='locuspocus_output_test4.txt'/> 150 <output name="output" file="locuspocus_output_test4.txt"/>
151 </test> 151 </test>
152 <test expect_num_outputs="1"> 152 <test expect_num_outputs="1">
153 <param name='genesgff3' value='TAIR10_GFF3_genes.gff'/> 153 <param name="genesgff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>
154 <section name='input_options'> 154 <section name="input_options">
155 <param name='filter' value='gene,intron'/> 155 <param name="filter" value="gene,intron"/>
156 <param name='parent' value='mRNA:gene'/> 156 <param name="parent" value="mRNA:gene"/>
157 </section> 157 </section>
158 <output name='output' file='locuspocus_output_test5.txt'/> 158 <output name="output" file="locuspocus_output_test5.txt"/>
159 </test> 159 </test>
160 <test expect_num_outputs="1"> 160 <test expect_num_outputs="1">
161 <param name='genesgff3' value='TAIR10_GFF3_genes.gff'/> 161 <param name="genesgff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>
162 <section name='input_options'> 162 <section name="input_options">
163 <param name='filter' value='gene,intron'/> 163 <param name="filter" value="gene,intron"/>
164 <param name='parent' value='mRNA:gene'/> 164 <param name="parent" value="mRNA:gene"/>
165 <param name='pseudo' value='true'/> 165 <param name="pseudo" value="true"/>
166 </section> 166 </section>
167 <output name='output' file='locuspocus_output_test6.txt'/> 167 <output name="output" file="locuspocus_output_test6.txt"/>
168 </test> 168 </test>
169 <test expect_num_outputs="4"> 169 <test expect_num_outputs="4">
170 <param name='genesgff3' value='TAIR10_GFF3_genes.gff'/> 170 <param name="genesgff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>
171 <section name='output_options'> 171 <section name="output_options">
172 <param name='retainids' value='true'/> 172 <param name="retainids" value="true"/>
173 <param name='namefmt' value='test%lu'/> 173 <param name="namefmt" value="test%lu"/>
174 <param name='outputfiles' value='ilens,genemap,transmap'/> 174 <param name="outputfiles" value="ilens,genemap,transmap"/>
175 </section> 175 </section>
176 <output name='output' file='locuspocus_output_test7.txt'/> 176 <output name="output" file="locuspocus_output_test7.txt"/>
177 <output name='output_ilens' file='locuspocus_lenght_test7.txt'/> 177 <output name="output_ilens" file="locuspocus_lenght_test7.txt"/>
178 <output name='output_genemap' file='locuspocus_genemap_test7.txt'/> 178 <output name="output_genemap" file="locuspocus_genemap_test7.txt"/>
179 <output name='output_transmap' file='locuspocus_transmap_test7.txt'/> 179 <output name="output_transmap" file="locuspocus_transmap_test7.txt"/>
180 </test> 180 </test>
181 <test expect_num_outputs="4"> 181 <test expect_num_outputs="4">
182 <param name='genesgff3' value='TAIR10_GFF3_genes.gff'/> 182 <param name="genesgff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>
183 <section name='refine_options'> 183 <section name="refine_options">
184 <param name='refine_parameters|refine' value='--refine'/> 184 <param name="refine_parameters|refine" value="--refine"/>
185 <param name='refine_options|minoverlap' value='5'/> 185 <param name="refine_options|minoverlap" value="5"/>
186 </section> 186 </section>
187 <section name='ilocus_parsing'> 187 <section name="ilocus_parsing">
188 <param name='delta' value='400'/> 188 <param name="delta" value="400"/>
189 <param name='mode' value='--skipends'/> 189 <param name="mode" value="--skipends"/>
190 </section> 190 </section>
191 <section name='input_options'> 191 <section name="input_options">
192 <param name='filter' value='gene,intron'/> 192 <param name="filter" value="gene,intron"/>
193 <param name='parent' value='mRNA:gene'/> 193 <param name="parent" value="mRNA:gene"/>
194 </section> 194 </section>
195 <section name='output_options'> 195 <section name="output_options">
196 <param name='retainids' value='true'/> 196 <param name="retainids" value="true"/>
197 <param name='outputfiles' value='ilens,genemap,transmap'/> 197 <param name="outputfiles" value="ilens,genemap,transmap"/>
198 </section> 198 </section>
199 <output name='output' file='locuspocus_output_test8.txt'/> 199 <output name="output" file="locuspocus_output_test8.txt"/>
200 <output name='output_ilens' file='locuspocus_lenght_test8.txt'/> 200 <output name="output_ilens" file="locuspocus_lenght_test8.txt"/>
201 <output name='output_genemap' file='locuspocus_genemap_test8.txt'/> 201 <output name="output_genemap" file="locuspocus_genemap_test8.txt"/>
202 <output name='output_transmap' file='locuspocus_transmap_test8.txt'/> 202 <output name="output_transmap" file="locuspocus_transmap_test8.txt"/>
203 </test> 203 </test>
204 </tests> 204 </tests>
205 <help> 205 <help>
206 <![CDATA[ 206 <![CDATA[
207 .. class:: infomark 207 .. class:: infomark
230 230
231 LocusPocus computes the location of the iLoci from the given gene features and reports the iLocus locations in GFF3 format. By default, only the iLocus features themselves are reported, with attributes indicating the number of genes and transcripts in the locus. 231 LocusPocus computes the location of the iLoci from the given gene features and reports the iLocus locations in GFF3 format. By default, only the iLocus features themselves are reported, with attributes indicating the number of genes and transcripts in the locus.
232 232
233 ]]> 233 ]]>
234 </help> 234 </help>
235 <expand macro='citations'/> 235 <expand macro="citations"/>
236 </tool> 236 </tool>