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comparison helixer.xml @ 5:c2fc4ac35199 draft default tip

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planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/helixer commit 54445b041f46b8b3a8e25e90e84f034cdddd2ab1
author genouest
date Tue, 09 Jul 2024 13:09:23 +0000
parents e3846dc36c4d
children
comparison
equal deleted inserted replaced
4:ec1a90b97047 5:c2fc4ac35199
10 <requirements> 10 <requirements>
11 <expand macro="requirements"/> 11 <expand macro="requirements"/>
12 </requirements> 12 </requirements>
13 13
14 <command detect_errors="exit_code"><![CDATA[ 14 <command detect_errors="exit_code"><![CDATA[
15
16 /usr/local/bin/fetch_helixer_models.py && 15 /usr/local/bin/fetch_helixer_models.py &&
17 Helixer.py 16 Helixer.py
18 --fasta-path '$input' 17 --fasta-path '$input'
19 --species '$species' 18 --species '$species'
20 --lineage '$lineages'
21 --gff-output-path '$output' 19 --gff-output-path '$output'
22
23 --temporary-dir ./ 20 --temporary-dir ./
24 21
25 #set default_subsequence_length = {"fungi": 21384, "land_plant": 106920, "invertebrate": 213840, "vertebrate": 213840} 22 #set default_subsequence_length = {"fungi": 21384, "land_plant": 106920, "invertebrate": 213840, "vertebrate": 213840}
26 #set subsequence_len = default_subsequence_length.get(str($lineages)) 23 #set subsequence_len = default_subsequence_length.get(str($lineages))
27 #set default_overlap_offset = {"fungi": 10692, "land_plant": 53460, "invertebrate": 106920, "vertebrate": 106920} 24 #set default_overlap_offset = {"fungi": 10692, "land_plant": 53460, "invertebrate": 106920, "vertebrate": 106920}
28 #set overlap_off = default_overlap_offset.get(str($lineages)) 25 #set overlap_off = default_overlap_offset.get(str($lineages))
29 #set default_overlap_core_length = {"fungi": 16038, "land_plant": 80190, "invertebrate": 160380, "vertebrate": 160380} 26 #set default_overlap_core_length = {"fungi": 16038, "land_plant": 80190, "invertebrate": 160380, "vertebrate": 160380}
30 #set overlap_core_len = default_overlap_core_length.get(str($lineages)) 27 #set overlap_core_len = default_overlap_core_length.get(str($lineages))
31 28
32 #if str($subsequence_length) == "": 29 #if str($input_model) != "" and str($input_model) != "None":
33 --subsequence-length '$subsequence_len' 30 --model-filepath '$input_model'
31 --subsequence-length '$subsequence_length'
32
34 #else: 33 #else:
35 --subsequence-length '$subsequence_length' 34 --lineage '$lineages'
36 #end if 35 #if str($subsequence_length) == "":
37 36 --subsequence-length '$subsequence_len'
38 #if str($option_overlap.use_overlap) == "true":
39 #if str($option_overlap.overlap_offset) == "":
40 --overlap-offset '$overlap_off'
41 #else: 37 #else:
42 --overlap-offset '$overlap_offset' 38 --subsequence-length '$subsequence_length'
43 #end if 39 #end if
44 40
45 #if str($option_overlap.overlap_core_length) == "": 41 #if str($option_overlap.use_overlap) == "true":
46 --overlap-core-length '$overlap_core_len' 42 #if str($option_overlap.overlap_offset) == "":
47 #else: 43 --overlap-offset '$overlap_off'
48 --overlap-core-length '$overlap_core_length' 44 #else:
45 --overlap-offset '$overlap_offset'
46 #end if
47
48 #if str($option_overlap.overlap_core_length) == "":
49 --overlap-core-length '$overlap_core_len'
50 #else:
51 --overlap-core-length '$overlap_core_length'
52 #end if
49 #end if 53 #end if
50 #end if 54 #end if
51 55
52 --batch-size $size 56 --batch-size $size
53 --window-size $post_processing.window_size 57 --window-size $post_processing.window_size
57 61
58 ]]></command> 62 ]]></command>
59 63
60 <inputs> 64 <inputs>
61 <param argument="--fasta-path" name="input" type="data" format="fasta,fasta.gz" label="Genomic sequence"></param> 65 <param argument="--fasta-path" name="input" type="data" format="fasta,fasta.gz" label="Genomic sequence"></param>
62 66 <param argument="--model-filepath" optional="true" name="input_model" type="data" format="h5" label="Lineage model" help="Import your lineage model to replace the default lineage. Please enter a value for the --subsequence_length parameter."></param>
63 <param argument="--lineage" name="lineages" type="select" label="Available lineages" help="Choose the model to use for the annotation"> 67 <param argument="--lineage" name="lineages" type="select" label="Available lineages" help="Choose the model to use for the annotation">
64 <option value="land_plant">land plant</option> 68 <option value="land_plant">land plant</option>
65 <option value="vertebrate">vertebrate</option> 69 <option value="vertebrate">vertebrate</option>
66 <option value="invertebrate">invertebrate</option> 70 <option value="invertebrate">invertebrate</option>
67 <option value="fungi">fungi</option> 71 <option value="fungi">fungi</option>
123 </conditional> 127 </conditional>
124 <output name="output" value="ouput_species.gff3" ftype="gff3" compare="sim_size" delta="100"/> 128 <output name="output" value="ouput_species.gff3" ftype="gff3" compare="sim_size" delta="100"/>
125 </test> 129 </test>
126 130
127 <test expect_num_outputs="1"> 131 <test expect_num_outputs="1">
128 <!-- Test for vertebrates--> 132 <!-- Test for vertebrates -->
129 <param name="input" value="sequence.fasta"/> 133 <param name="input" value="sequence.fasta"/>
130 <param name="lineages" value="vertebrate"/> 134 <param name="lineages" value="vertebrate"/>
131 <param name="size" value="8"/> 135 <param name="size" value="8"/>
132 <param name="size" value="8"/> 136 <param name="size" value="8"/>
133 <param name="subsequence_length" value=""/> 137 <param name="subsequence_length" value=""/>
142 <param name="overlap_offset" value=""/> 146 <param name="overlap_offset" value=""/>
143 <param name="overlap_core_length" value=""/> 147 <param name="overlap_core_length" value=""/>
144 </conditional> 148 </conditional>
145 <output name="output" value="vertebrate.gff3" ftype="gff3" lines_diff="2"/> 149 <output name="output" value="vertebrate.gff3" ftype="gff3" lines_diff="2"/>
146 </test> 150 </test>
151
152 <test expect_failure="true">
153 <!-- Test for model-filepath -->
154 <param name="input" value="sequence.fasta"/>
155 <param name="input_model" value="test.h5"/>
156 <param name="size" value="8"/>
157 <param name="size" value="8"/>
158 <param name="subsequence_length" value="1000"/>
159 <section name="post_processing">
160 <param name="window_size" value="100"/>
161 <param name="edge_threshold" value="0.1"/>
162 <param name="peak_threshold" value="0.8"/>
163 <param name="min_coding_length" value="100"/>
164 </section>
165 <conditional name="option_overlap">
166 <param name="use_overlap" value="true"/>
167 <param name="overlap_offset" value=""/>
168 <param name="overlap_core_length" value=""/>
169 </conditional>
170 </test>
147 </tests> 171 </tests>
148 172
149 <help><![CDATA[ 173 <help><![CDATA[
150 Helixer_: Gene calling with Deep Neural Networks. 174 Helixer_: Gene calling with Deep Neural Networks.
151 175