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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823
author iuc
date Wed, 24 Aug 2022 07:37:11 +0000
parents 0824abf509c1
children
comparison
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0:0824abf509c1 1:0cc8a1171465
1 <tool id="gubbins" name="Gubbins" version="0.1.0"> 1 <tool id="gubbins" name="Gubbins" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
2 <description>Recombination detection in Bacteria</description> 2 <description>Recombination detection in Bacteria</description>
3 <macros>
4 <token name="@TOOL_VERSION@">3.2.1</token>
5 <token name="@VERSION_SUFFIX@">0</token>
6 </macros>
7 <xrefs>
8 <xref type="bio.tools">gubbins</xref>
9 </xrefs>
3 <requirements> 10 <requirements>
4 <requirement type="package" version="2.2.1">gubbins</requirement> 11 <requirement type="package" version="@TOOL_VERSION@">gubbins</requirement>
5 </requirements> 12 </requirements>
6 13
7 <version_command>run_gubbins.py --version</version_command> 14 <version_command>run_gubbins.py --version</version_command>
8 15
9 <command detect_errors="exit_code"><![CDATA[ 16 <command detect_errors="exit_code"><![CDATA[
12 19
13 run_gubbins.py 20 run_gubbins.py
14 21
15 --threads \${GALAXY_SLOTS:-1} 22 --threads \${GALAXY_SLOTS:-1}
16 23
17 #if $adv.iters 24 -i '$adv.iterations'
18 -i '$adv.iters' 25 -z '$adv.converge_method'
19 #end if 26 $adv.extensive_search
20 27
21 #if $adv.conv_meth
22 -z '$adv.conv_meth'
23 #end if
24
25 #if $adv.outgroup 28 #if $adv.outgroup
26 -o '$adv.outgroup' 29 -o '$adv.outgroup'
27 #end if 30 #end if
28 31
29 #if $really_adv.tree_builder 32 -t '$really_adv.tree_builder'
30 -t '$really_adv.tree_builder' 33 -m '$really_adv.min_snps'
31 #end if 34 -f '$really_adv.filter_percentage'
32 35 -a '$really_adv.min_window_size'
33 #if $really_adv.min_snps 36 -b '$really_adv.max_window_size'
34 -m '$really_adv.min_snps' 37 -p '$really_adv.p_value'
35 #end if 38 --trimming-ratio '$really_adv.trimming_ratio'
36 39 $really_adv.remove_identical_sequences
37 #if $really_adv.filter_percentage 40
38 -f '$really_adv.filter_percentage'
39 #end if
40
41 #if $really_adv.min_window_size
42 -a '$really_adv.min_window_size'
43 #end if
44
45 #if $really_adv.max_window_size
46 -b '$really_adv.max_window_size'
47 #end if
48
49 $really_adv.remove_duplicates
50
51 foo.aln 41 foo.aln
52 42
43 ## Requited because the p-value is included as prefix
44
45 && mv *branch_base_reconstruction.embl branch_base_reconstruction.embl
46 && mv *filtered_polymorphic_sites.fasta filtered_polymorphic_sites.fasta
47 && mv *filtered_polymorphic_sites.phylip filtered_polymorphic_sites.phylip
48 && mv *node_labelled.final_tree.tre node_labelled.final_tree
49 && mv *final_tree.tre final_tree.tre
50 && mv *per_branch_statistics.csv per_branch_statistics.csv
51 && mv *recombination_predictions.embl recombination_predictions.embl
52 && mv *recombination_predictions.gff recombination_predictions.gff
53 && mv *summary_of_snp_distribution.vcf summary_of_snp_distribution.vcf
54
53 ]]></command> 55 ]]></command>
54 <inputs> 56 <inputs>
55 <!-- Just the data set.. --> 57 <!-- Just the data set.. -->
56 <param type="data" name="alignment_file" format="fasta" label="Whole genome alignment file" help="Whole genome alignment file in fasta format"/> 58 <param type="data" name="alignment_file" format="fasta" label="Whole genome alignment file" help="Whole genome alignment file in fasta format"/>
57 59
58 <!-- output file picker --> 60 <!-- output file picker -->
59 <param type="select" name="outfiles" multiple="true" display="checkboxes" label="Select the required output files" help="Default selections are the Final Tree in Newick format, the Recombination Predictions in gff3 format and the Summary of SNP Distribution"> 61 <param name="outfiles" type="select" multiple="true" display="checkboxes" label="Select the required output files" help="Default selections are the Final Tree in Newick format, the Recombination Predictions in gff3 format and the Summary of SNP Distribution">
60 <option value="ftree" selected="true">Final Tree in newick format</option> 62 <option value="ftree" selected="true">Final Tree in newick format</option>
61 <option value="gff" selected="true">Recombination Predictions in gff3 format</option> 63 <option value="gff" selected="true">Recombination Predictions in gff3 format</option>
62 <option value="vcf" selected="true">Summary of SNP Distribution in vcf format</option> 64 <option value="vcf" selected="true">Summary of SNP Distribution in vcf format</option>
63 <option value="recomb_embl">Recombination Predictions in embl format</option> 65 <option value="recomb_embl">Recombination Predictions in embl format</option>
64 <option value="fpoly">Filtered Polymorphic Sites in fasta format</option> 66 <option value="fpoly">Filtered Polymorphic Sites in fasta format</option>
67 <option value="baseb">Base Branch Reconstruction in embl format</option> 69 <option value="baseb">Base Branch Reconstruction in embl format</option>
68 </param> 70 </param>
69 71
70 <!-- A semi advanced section, really shouldn't have to change anything. --> 72 <!-- A semi advanced section, really shouldn't have to change anything. -->
71 <section name="adv" title="Advanced options" expanded="True"> 73 <section name="adv" title="Advanced options" expanded="True">
72 <param name="iters" type="integer" label="Iterations" value="5" help="Maximum No. of iterations, default is 5" /> 74 <param argument="--iterations" type="integer" label="Iterations" min="0" value="5" help="Maximum No. of iterations, default is 5" />
73 <param name="conv_meth" type="select" label="Model Conversion Options" help="Criteria to use to know when to halt iterations"> 75 <param argument="--converge-method" type="select" label="Model conversion Options" help="Criteria to use to know when to halt iterations">
74 <option value="weighted_robinson_foulds" selected="True">Weighted Robinson Foulds</option> 76 <option value="weighted_robinson_foulds" selected="True">Weighted Robinson Foulds</option>
75 <option value="robinson_foulds">Robinson Foulds</option> 77 <option value="robinson_foulds">Robinson Foulds</option>
76 <option value="recombination">Recombination</option> 78 <option value="recombination">Recombination</option>
77 </param> 79 </param>
78 <param name="outgroup" type="text" label="Outgroup" value="" help="Outgroup name for rerooting. A list of comma separated names can be used if they form a clade."/> 80 <param argument="--outgroup" type="text" label="Outgroup" value="" help="Outgroup name for rerooting. A list of comma separated names can be used if they form a clade.">
81 <sanitizer invalid_char="">
82 <valid initial="string.letters,string.digits">
83 <add value="+" />
84 <add value="-" />
85 <add value=" " />
86 <add value="_" />
87 </valid>
88 </sanitizer>
89 </param>
90 <param argument="--extensive-search" type="boolean" truevalue="--extensive-search" falsevalue="" checked="false" label="Extensive search " help="Default: False" />
79 </section> 91 </section>
80 92
81 <!-- a really advanced section, play with this at your peril! --> 93 <!-- a really advanced section, play with this at your peril! -->
82 <section name="really_adv" title="Really advanced options - change these if you really know what you are doing." expanded="false"> 94 <section name="really_adv" title="Really advanced options - change these if you really know what you are doing." expanded="false">
83 <param name="tree_builder" type="select" label="Tree builder" help="Application to use for tree building, default RAxML"> 95 <param argument="--tree-builder" type="select" label="Tree builder" help="Application to use for tree building, default RAxML">
84 <option value="raxml" selected="true">RAxML</option> 96 <option value="raxml" selected="true">RAxML</option>
97 <option value="raxmlng">RAxML-NG</option>
98 <option value="iqtree">IQ-TREE</option>
85 <option value="fasttree">FastTree</option> 99 <option value="fasttree">FastTree</option>
86 <option value="hybrid">Hybrid</option> 100 <option value="hybrid">Hybrid</option>
101 <option value="rapidnj">RapidNJ</option>
87 </param> 102 </param>
88 <param name="min_snps" type="integer" label="Minimum SNPS" value="3" help="Min SNPs to identify a recombination block, default is 3" /> 103 <param argument="--min-snps" type="integer" label="Minimum SNPs" min="0" value="3" help="Min SNPs to identify a recombination block. Default: 3" />
89 <param name="filter_percentage" type="integer" label="Filter Percentage" value="25" help="Filter out taxa with more than this percentage of gaps, default is 25" /> 104 <param argument="--filter-percentage" type="float" label="Filter percentage" min="0" value="25" help="Filter out taxa with more than this percentage of gaps. Default: 25" />
90 <param name="min_window_size" type="integer" label="Minimum Window Size" value="100" help="Minimum window size, default 100" /> 105 <param argument="--min-window-size" type="integer" label="Minimum window size" min="0" value="100" help="Minimum window size. Default: 100" />
91 <param name="max_window_size" type="integer" label="Maximum Window Size" value="10000" help="Maximum window size, default 10000" /> 106 <param argument="--max-window-size" type="integer" label="Maximum window size" min="0" value="10000" help="Maximum window size. Default: 10000" />
92 <param name="remove_duplicates" type="boolean" label="Remove identical sequences" falsevalue="" truevalue="-d" /> 107 <param argument="--remove-identical-sequences" type="boolean" label="Remove identical sequences" falsevalue="" truevalue="-d" />
108 <param argument="--p-value" type="float" min="0" max="1" value="0.05" label="p-Value" help="p-Value for detecting recombinations. Default: 0.05" />
109 <param argument="--trimming_ratio" type="float" min="0" value="1" label="Trimming ration" help="Ratio of log probabilities used to trim recombinations. Default: 1" />
110
93 </section> 111 </section>
94 112
95 </inputs> 113 </inputs>
96 114
97 <outputs> 115 <outputs>
98 <data format="txt" name="final_tree" label="${tool.name} on ${on_string} Final Tree" from_work_dir="foo.final_tree.tre" > 116 <data format="txt" name="final_tree" label="${tool.name} on ${on_string} Final Tree" from_work_dir="final_tree.tre" >
99 <filter>outfiles and 'ftree' in outfiles</filter> 117 <filter>outfiles and 'ftree' in outfiles</filter>
100 </data> 118 </data>
101 <data format="gff3" name="recomb_pred_gff" label="${tool.name} on ${on_string} Recombinations Prediction gff" from_work_dir="foo.recombination_predictions.gff" > 119 <data format="gff3" name="recomb_pred_gff" label="${tool.name} on ${on_string} Recombinations Prediction gff" from_work_dir="recombination_predictions.gff" >
102 <filter>outfiles and 'gff' in outfiles</filter> 120 <filter>outfiles and 'gff' in outfiles</filter>
103 </data> 121 </data>
104 <data format="embl" name="recomb_pred_embl" label="${tool.name} on ${on_string} Recombinations Prediction embl" from_work_dir="foo.recombination_predictions.embl" > 122 <data format="embl" name="recomb_pred_embl" label="${tool.name} on ${on_string} Recombinations Prediction embl" from_work_dir="recombination_predictions.embl" >
105 <filter>outfiles and 'recomb_embl' in outfiles</filter> 123 <filter>outfiles and 'recomb_embl' in outfiles</filter>
106 </data> 124 </data>
107 <data format="fasta" name="filt_polymorph_fna" label="${tool.name} on ${on_string} Filtered Polymorphic Sites fasta" from_work_dir="foo.filtered_polymorphic_sites.fasta" > 125 <data format="fasta" name="filt_polymorph_fna" label="${tool.name} on ${on_string} Filtered Polymorphic Sites fasta" from_work_dir="filtered_polymorphic_sites.fasta" >
108 <filter>outfiles and 'fpoly' in outfiles</filter> 126 <filter>outfiles and 'fpoly' in outfiles</filter>
109 </data> 127 </data>
110 <data format="phylip" name="filt_polymorph_phy" label="${tool.name} on ${on_string} Filtered Polymorphic Sites phylip" from_work_dir="foo.filtered_polymorphic_sites.phylip" > 128 <data format="phylip" name="filt_polymorph_phy" label="${tool.name} on ${on_string} Filtered Polymorphic Sites phylip" from_work_dir="filtered_polymorphic_sites.phylip" >
111 <filter>outfiles and 'ppoly' in outfiles</filter> 129 <filter>outfiles and 'ppoly' in outfiles</filter>
112 </data> 130 </data>
113 <data format="csv" name="per_b_stat_csv" label="${tool.name} on ${on_string} Per Branch Statistics csv" from_work_dir="foo.per_branch_statistics.csv" > 131 <data format="csv" name="per_b_stat_csv" label="${tool.name} on ${on_string} Per Branch Statistics csv" from_work_dir="per_branch_statistics.csv" >
114 <filter>outfiles and 'stats' in outfiles</filter> 132 <filter>outfiles and 'stats' in outfiles</filter>
115 </data> 133 </data>
116 <data format="vcf" name="sum_snp_vcf" label="${tool.name} on ${on_string} Summary of SNP Distribution vcf" from_work_dir="foo.summary_of_snp_distribution.vcf" > 134 <data format="vcf" name="sum_snp_vcf" label="${tool.name} on ${on_string} Summary of SNP Distribution vcf" from_work_dir="summary_of_snp_distribution.vcf" >
117 <filter>outfiles and 'vcf' in outfiles</filter> 135 <filter>outfiles and 'vcf' in outfiles</filter>
118 </data> 136 </data>
119 <data format="embl" name="base_branch_embl" label="${tool.name} on ${on_string} Branch Base Reconstruction embl" from_work_dir="foo.branch_base_reconstruction.embl" > 137 <data format="embl" name="base_branch_embl" label="${tool.name} on ${on_string} Branch Base Reconstruction embl" from_work_dir="branch_base_reconstruction.embl" >
120 <filter>outfiles and 'baseb' in outfiles</filter> 138 <filter>outfiles and 'baseb' in outfiles</filter>
121 </data> 139 </data>
122 </outputs> 140 </outputs>
123 141
124 142
125 <tests> 143 <tests>
126 <test> 144 <test expect_num_outputs="3">
127 <param name="alignment_file" value="multiple_recombinations.aln" ftype="fasta" /> 145 <param name="alignment_file" value="multiple_recombinations.aln" ftype="fasta" />
128 <output name="recomb_pred_gff"> 146 <output name="recomb_pred_gff">
129 <assert_contents> 147 <assert_contents>
130 <has_text text="##gff-version 3" /> 148 <has_text text="##gff-version 3" />
131 </assert_contents> 149 </assert_contents>
132 </output> 150 </output>
133 <output name="sum_snp_vcf"> 151 <output name="sum_snp_vcf">
134 <assert_contents> 152 <assert_contents>
135 <has_text text="##fileformat=VCFv4.2" /> 153 <has_text text="##fileformat=VCFv4.2" />
136 </assert_contents> 154 </assert_contents>
137 </output> 155 </output>
138 </test> 156 </test>
139 157
140 <test> 158 <test expect_num_outputs="3">
141 <param name="alignment_file" value="multiple_recombinations.aln" ftype="fasta" /> 159 <param name="alignment_file" value="multiple_recombinations.aln" ftype="fasta" />
142 <param name="iters" value="3"/> 160 <param name="iterations" value="3"/>
143 <output name="recomb_pred_gff"> 161 <output name="recomb_pred_gff">
144 <assert_contents> 162 <assert_contents>
145 <has_text text="##gff-version 3" /> 163 <has_text text="##gff-version 3" />
146 </assert_contents> 164 </assert_contents>
147 </output> 165 </output>
148 <output name="sum_snp_vcf"> 166 <output name="sum_snp_vcf">
149 <assert_contents> 167 <assert_contents>
150 <has_text text="##fileformat=VCFv4.2" /> 168 <has_text text="##fileformat=VCFv4.2" />
151 </assert_contents> 169 </assert_contents>
152 </output> 170 </output>
153 </test> 171 </test>
154 172
155 <test> 173 <test expect_num_outputs="3">
156 <param name="alignment_file" value="multiple_recombinations.aln" ftype="fasta" /> 174 <param name="alignment_file" value="multiple_recombinations.aln" ftype="fasta" />
157 <param name="conv_meth" value="recombination" /> 175 <param name="converge_method" value="recombination" />
158 <output name="recomb_pred_gff"> 176 <output name="recomb_pred_gff">
159 <assert_contents> 177 <assert_contents>
160 <has_text text="##gff-version 3" /> 178 <has_text text="##gff-version 3" />
161 </assert_contents> 179 </assert_contents>
162 </output> 180 </output>
163 <output name="sum_snp_vcf"> 181 <output name="sum_snp_vcf">
164 <assert_contents> 182 <assert_contents>
165 <has_text text="##fileformat=VCFv4.2" /> 183 <has_text text="##fileformat=VCFv4.2" />
166 </assert_contents> 184 </assert_contents>
167 </output> 185 </output>
168 </test> 186 </test>
169 187
170 <test> 188 <test expect_num_outputs="8">
171 <param name="alignment_file" value="multiple_recombinations.aln" ftype="fasta" /> 189 <param name="alignment_file" value="multiple_recombinations.aln" ftype="fasta" />
172 <param name="conv_meth" value="recombination" /> 190 <param name="converge_method" value="recombination" />
173 <param name="outfiles" value="gff,vcf,ftree,recomb_embl,fpoly,ppoly,stats,baseb"/> 191 <param name="outfiles" value="gff,vcf,ftree,recomb_embl,fpoly,ppoly,stats,baseb"/>
174 <output name="recomb_pred_gff"> 192 <output name="recomb_pred_gff">
175 <assert_contents> 193 <assert_contents>
176 <has_text text="##gff-version 3" /> 194 <has_text text="##gff-version 3" />
177 </assert_contents> 195 </assert_contents>
207 </assert_contents> 225 </assert_contents>
208 </output> 226 </output>
209 <output name="final_tree"> 227 <output name="final_tree">
210 <assert_contents> 228 <assert_contents>
211 <has_text text="((sequence_" /> 229 <has_text text="((sequence_" />
230 </assert_contents>
231 </output>
232 </test>
233 <!-- Test new options-->
234 <test expect_num_outputs="8" >
235 <param name="alignment_file" value="multiple_recombinations.aln" ftype="fasta" />
236 <param name="outfiles" value="ftree,gff,vcf,recomb_embl,fpoly,ppoly,stats,baseb"/>
237 <section name="adv">
238 <param name="expensive_research" value="true"/>
239 </section>
240 <section name="really_adv">
241 <param name="tree_builder" value="fasttree"/>
242 <param name="remove_identical_sequences" value="true"/>
243 </section>
244 <output name="recomb_pred_gff">
245 <assert_contents>
246 <has_text text="##gff-version 3" />
247 <has_text text="sequence_4" />
248 </assert_contents>
249 </output>
250 <output name="sum_snp_vcf">
251 <assert_contents>
252 <has_text text="##fileformat=VCFv4.2" />
253 </assert_contents>
254 </output>
255 <output name="base_branch_embl">
256 <assert_contents>
257 <has_n_lines n="1638"/>
258 <has_text text="sequence_8" />
259 </assert_contents>
260 </output>
261 <output name="final_tree">
262 <assert_contents>
263 <has_n_lines n="1"/>
264 <has_text text="sequence_10" />
265 </assert_contents>
266 </output>
267 <output name="recomb_pred_embl">
268 <assert_contents>
269 <has_n_lines n="24"/>
270 <has_text text="sequence_2" />
271 </assert_contents>
272 </output>
273 <output name="filt_polymorph_fna">
274 <assert_contents>
275 <has_n_lines n="18"/>
276 <has_text text="GAAAA" />
277 </assert_contents>
278 </output>
279 <output name="filt_polymorph_phy">
280 <assert_contents>
281 <has_n_lines n="10"/>
282 <has_text text="GAAAA" />
283 </assert_contents>
284 </output>
285 <output name="per_b_stat_csv">
286 <assert_contents>
287 <has_n_lines n="18"/>
288 <has_text text="Number of SNPs Inside Recombinations" />
289 </assert_contents>
290 </output>
291 <output name="sum_snp_vcf">
292 <assert_contents>
293 <has_text text="ID=1,length=242" />
212 </assert_contents> 294 </assert_contents>
213 </output> 295 </output>
214 </test> 296 </test>
215 </tests> 297 </tests>
216 298