Mercurial > repos > iuc > gubbins
comparison gubbins.xml @ 1:96e6283e4745 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823
author | iuc |
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date | Wed, 24 Aug 2022 07:37:39 +0000 |
parents | 637ec5d5368c |
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0:637ec5d5368c | 1:96e6283e4745 |
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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 |