Mercurial > repos > iuc > progressivemauve

comparison progressivemauve.xml @ 5:ce795616bd9c draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit fcddceef74e33d544e239d1036467f65ef11767f"
author iuc
date Sat, 27 Nov 2021 12:13:25 +0000
parents 4d869208bd52
children
comparison
equal deleted inserted replaced
4:4d869208bd52 5:ce795616bd9c
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="progressivemauve" name="progressiveMauve" version="@WRAPPER_VERSION@.0"> 2 <tool id="progressivemauve" name="progressiveMauve" version="@WRAPPER_VERSION@.1">
3 <description>constructs multiple genome alignments</description> 3 <description>constructs multiple genome alignments</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
33 #if $match_input: 33 #if $match_input:
34 --match-input=$match_input 34 --match-input=$match_input
35 #end if 35 #end if
36 36
37 $collinear 37 $collinear
38 #if $input_guide_tree
39 --input-guide-tree='$input_guide_tree'
40 #end if
38 --scoring-scheme=$scoring_scheme 41 --scoring-scheme=$scoring_scheme
39 $no_weight_scaling 42 $no_weight_scaling
40 43
41 --max-breakpoint-distance-scale=$max_breakpoint_distance_scale 44 --max-breakpoint-distance-scale=$max_breakpoint_distance_scale
42 --conservation-distance-scale=$conservation_distance_scale 45 --conservation-distance-scale=$conservation_distance_scale
48 #end if 51 #end if
49 52
50 #if $gap_open: 53 #if $gap_open:
51 --gap-open=$gap_open 54 --gap-open=$gap_open
52 #end if 55 #end if
53 56 --repeat-penalty=$repeat_penalty
54 #if $gap_extend: 57 #if $gap_extend:
55 --gap-extend=$gap_extend 58 --gap-extend=$gap_extend
56 #end if 59 #end if
57 60
58 #if $weight: 61 #if $weight:
77 --output=$output 80 --output=$output
78 #if $output_guide_tree: 81 #if $output_guide_tree:
79 --output-guide-tree=$output_guide_tree_file 82 --output-guide-tree=$output_guide_tree_file
80 #end if 83 #end if
81 84
82 #if $output_backbone: 85 #if $backbone_output:
83 --backbone-output=$output_backbone_file 86 --backbone-output=$output_backbone_file
84 #end if 87 #end if
85 88
86 ## Sequences 89 ## Sequences
87 #for file in $sequences: 90 #for file in $sequences:
88 `basename "${file}"` 91 `basename "${file}"`
89 #end for 92 #end for
90 93
91 ]]></command> 94 ]]></command>
92 <inputs> 95 <inputs>
93 <param type="data" format="fasta" name="sequences" multiple="True" 96 <param type="data" format="fasta" name="sequences" multiple="true"
94 label="Select sequences to align" help="in fasta format" /> 97 label="Select sequences to align" help="in fasta format" />
95 <param type="data" format="xmfa" label="Apply Backbone" name="apply_backbone" optional="True" 98 <param type="data" format="xmfa" label="Apply Backbone" name="apply_backbone" optional="true"
96 help="Read an existing sequence alignment in XMFA format and apply backbone statistics to it (--apply-backbone)" /> 99 help="Read an existing sequence alignment in XMFA format and apply backbone statistics to it (--apply-backbone)" />
97 100
98 <param type="integer" label="Island gap size" value="20" name="island_gap_size" 101 <param type="integer" label="Island gap size" value="20" argument="--island-gap-size"
99 help="Alignment gaps above this size in nucleotides are considered to be islands (--island-gap-size)"/> 102 help="Alignment gaps above this size in nucleotides are considered to be islands"/>
100 103
101 <param type="boolean" truevalue="--disable-backbone" falsevalue="" name="disable_backbone" 104 <param type="boolean" truevalue="--disable-backbone" falsevalue="" argument="--disable-backbone"
102 label="Disable backbone" help="Disable backbone detection (--disable-backbone)" /> 105 label="Disable backbone" help="Disable backbone detection" />
103 106
104 <param type="boolean" truevalue="True" falsevalue="" name="output_guide_tree" 107 <param type="boolean" truevalue="true" falsevalue="" argument="--output-guide-tree"
105 label="Output Guide Tree" help="Write out the guide tree used for alignment to a file (--output-guide-tree)" /> 108 label="Output Guide Tree" help="Write out the guide tree used for alignment to a file" />
106 109
107 <param type="boolean" truevalue="True" falsevalue="" name="output_backbone" 110 <param type="boolean" truevalue="true" falsevalue="" argument="--backbone-output"
108 label="Output Backbone" help="Write out the backbone to a file (--backbone-output)" /> 111 label="Output Backbone" help="Write out the backbone to a file" />
109 112
110 <param type="boolean" truevalue="--mums" falsevalue="" label="MUMs" name="mums" 113 <param type="boolean" truevalue="--mums" falsevalue="" label="MUMs" argument="--mums"
111 help="Find MUMs only, do not attempt to determine locally collinear blocks (LCBs) (--mums)" /> 114 help="Find MUMs only, do not attempt to determine locally collinear blocks (LCBs)" />
112 115
113 <param type="integer" label="Seed weight" name="seed_weight" value="0" optional="True" 116 <param type="integer" label="Seed weight" argument="--seed-weight" value="0" optional="true"
114 help="Use the specified seed weight for calculating initial anchors (--seed-weight)" /> 117 help="Use the specified seed weight for calculating initial anchors" />
115 118
116 <param type="data" format="tabular" label="Match Input" name="match_input" optional="True" 119 <param type="data" format="tabular" label="Match Input" argument="--match-input" optional="true"
117 help="Use specified match file instead of searching for matches (--match-input)" /> 120 help="Use specified match file instead of searching for matches" />
118 121
119 <!--<param type="file" label="input-id-matrix" help="An identity matrix describing similarity among all pairs of input sequences/alignments (- -input-id-matrix)" />--> 122 <!--<param type="file" label="input-id-matrix" help="An identity matrix describing similarity among all pairs of input sequences/alignments (- -input-id-matrix)" />-->
120 <param type="integer" label="Max gapped aligner length" value="0" optional="True" name="max_gapped_aligner_length" 123 <param type="integer" label="Max gapped aligner length" value="0" optional="true" argument="--max-gapped-aligner-length"
121 help="Maximum number of base pairs to attempt aligning with the gapped aligner (--max-gapped-aligner-length)" /> 124 help="Maximum number of base pairs to attempt aligning with the gapped aligner" />
122 125
123 <param type="data" format="nhx" label="input-guide-tree" optional="True" name="input_guide_tree" 126 <param type="data" format="nhx" label="input-guide-tree" optional="true" argument="--input-guide-tree"
124 help="A phylogenetic guide tree in Newick format that describes the order in which sequences will be aligned (--input-guide-tree)" /> 127 help="A phylogenetic guide tree in Newick format that describes the order in which sequences will be aligned" />
125 128
126 <param type="boolean" truevalue="--collinear" falsevalue="" label="Collinear inputs" name="collinear" 129 <param type="boolean" truevalue="--collinear" falsevalue="" label="Collinear inputs" argument="--collinear"
127 help="Assume that input sequences are collinear--they have no rearrangements (--collinear)" /> 130 help="Assume that input sequences are collinear--they have no rearrangements" />
128 131
129 <param type="select" label="Scoring scheme" name="scoring_scheme" help="Selects the anchoring score function. (--scoring-scheme)" > 132 <param type="select" label="Scoring scheme" argument="--scoring-scheme" help="Selects the anchoring score function" >
130 <option value="sp" selected="True">Extant sum-of-pairs (sp)</option> 133 <option value="sp" selected="true">Extant sum-of-pairs (sp)</option>
131 <option value="ancestral_sp">Sum-of-pairs + Ancestral (ancestral_sp)</option> 134 <option value="ancestral_sp">Sum-of-pairs + Ancestral (ancestral_sp)</option>
132 <option value="ancestral">Ancestral (ancestral)</option> 135 <option value="ancestral">Ancestral (ancestral)</option>
133 </param> 136 </param>
134 137
135 <param type="boolean" truevalue="--no-weight-scaling" falsevalue="" label="No weight scaling" name="no_weight_scaling" 138 <param type="boolean" truevalue="--no-weight-scaling" falsevalue="" label="No weight scaling" argument="--no-weight-scaling"
136 help="Don't scale LCB weights by conservation distance and breakpoint distance (--no-weight-scaling)" /> 139 help="Don't scale LCB weights by conservation distance and breakpoint distance" />
137 140
138 <param type="float" min="0" max="1" label="max-breakpoint-distance-scale" value="0.5" name="max_breakpoint_distance_scale" 141 <param type="float" min="0" max="1" label="max-breakpoint-distance-scale" value="0.5" argument="--max-breakpoint-distance-scale"
139 help="Set the maximum weight scaling by breakpoint distance. (--max-breakpoint-distance-scale)" /> 142 help="Set the maximum weight scaling by breakpoint distance" />
140 143
141 <param type="float" min="0" max="1" label="conservation-distance-scale" value="0.5" name="conservation_distance_scale" 144 <param type="float" min="0" max="1" label="conservation-distance-scale" value="0.5" argument="--conservation-distance-scale"
142 help="Scale conservation distances by this amount. (--conservation-distance-scale)" /> 145 help="Scale conservation distances by this amount" />
143 146
144 <param type="boolean" truevalue="--skip-refinement" falsevalue="" label="Skip refinement" name="skip_refinement" 147 <param type="boolean" truevalue="--skip-refinement" falsevalue="" label="Skip refinement" argument="--skip-refinement"
145 help="Do not perform iterative refinement (--skip-refinement)" /> 148 help="Do not perform iterative refinement" />
146 <param type="boolean" truevalue="--skip-gapped-alignment" falsevalue="" label="Skip gapped alignment" name="skip_gapped_alignment" 149 <param type="boolean" truevalue="--skip-gapped-alignment" falsevalue="" label="Skip gapped alignment" argument="--skip-gapped-alignment"
147 help="Do not perform gapped alignment (--skip-gapped-alignment)" /> 150 help="Do not perform gapped alignment" />
148 <param type="integer" label="BP dist estimate min score" name="bp_dist_estimate_min_score" value="0" optional="True" 151 <param type="integer" label="BP dist estimate min score" argument="--bp-dist-estimate-min-score" value="0" optional="true"
149 help="Minimum LCB score for estimating pairwise breakpoint distance (--bp-dist-estimate-min-score)" /> 152 help="Minimum LCB score for estimating pairwise breakpoint distance" />
150 153
151 <param type="integer" label="Gap open" name="gap_open" value="0" optional="True" 154 <param type="integer" label="Gap open" argument="--gap-open" value="0" optional="true"
152 help="Gap open penalty (--gap-open)" /> 155 help="Gap open penalty" />
153 156
154 <param type="select" label="Repeat penalty" name="repeat_penalty" 157 <param type="select" label="Repeat penalty" argument="--repeat-penalty"
155 help="Sets whether the repeat scores go negative or go to zero for highly repetitive sequences. (--repeat-penalty)"> 158 help="Sets whether the repeat scores go negative or go to zero for highly repetitive sequences">
156 <option value="negative" selected="True">Negative</option> 159 <option value="negative" selected="true">Negative</option>
157 <option value="zero">Zero</option> 160 <option value="zero">Zero</option>
158 </param> 161 </param>
159 162
160 <param type="integer" label="Gap extend" name="gap_extend" value="0" optional="True" 163 <param type="integer" label="Gap extend" argument="--gap-extend" value="0" optional="true"
161 help="Gap extend penalty (--gap-extend)" /> 164 help="Gap extend penalty" />
162 165
163 <!--<param type="data" label="Substitution matrix" --> 166 <!--<param type="data" label="Substitution matrix" -->
164 <!--help="Nucleotide substitution matrix in NCBI format (- -substitution-matrix)" />--> 167 <!--help="Nucleotide substitution matrix in NCBI format (- -substitution-matrix)" />-->
165 168
166 <param type="integer" label="Weight" name="weight" value="0" optional="True" 169 <param type="integer" label="Weight" argument="--weight" value="0" optional="true"
167 help="Minimum pairwise LCB score (--weight)" /> 170 help="Minimum pairwise LCB score" />
168 <param type="integer" label="Min scaled penalty" name="min_scaled_penalty" value="0" optional="True" 171 <param type="integer" label="Min scaled penalty" argument="--min-scaled-penalty" value="0" optional="true"
169 help="Minimum breakpoint penalty after scaling the penalty by expected divergence (--min-scaled-penalty)" /> 172 help="Minimum breakpoint penalty after scaling the penalty by expected divergence" />
170 173
171 <param type="float" label="HMM p go homologous" name="hmm_p_go_homologous" min="0" max="1" value="0.00001" 174 <param type="float" label="HMM p go homologous" argument="--hmm-p-go-homologous" min="0" max="1" value="0.00001"
172 help="Probability of transitioning from the unrelated to the homologous state (--hmm-p-go-homologous)" /> 175 help="Probability of transitioning from the unrelated to the homologous state" />
173 <param type="float" label="HMM p go unrelated" name="hmm_p_go_unrelated" min="0" max="1" value="0.000000001" 176 <param type="float" label="HMM p go unrelated" argument="--hmm-p-go-unrelated" min="0" max="1" value="0.000000001"
174 help="Probability of transitioning from the homologous to the unrelated state (--hmm-p-go-unrelated)" /> 177 help="Probability of transitioning from the homologous to the unrelated state" />
175 <param type="float" label="HMM identity" name="hmm_identity" min="0" max="1" value="0.7" 178 <param type="float" label="HMM identity" argument="--hmm-identity" min="0" max="1" value="0.7"
176 help="Expected level of sequence identity among pairs of sequences(--hmm-identity)" /> 179 help="Expected level of sequence identity among pairs of sequences" />
177 180
178 <param type="boolean" truevalue="--seed-family" falsevalue="" label="Seed family" name="seed_family" 181 <param type="boolean" truevalue="--seed-family" falsevalue="" label="Seed family" argument="--seed-family"
179 help="Use a family of spaced seeds to improve sensitivity (--seed-family)" /> 182 help="Use a family of spaced seeds to improve sensitivity" />
180 <param type="boolean" truevalue="--solid-seeds" falsevalue="" label="Solid seeds" name="solid_seeds" 183 <param type="boolean" truevalue="--solid-seeds" falsevalue="" label="Solid seeds" argument="--solid-seeds"
181 help="Use solid seeds. Do not permit substitutions in anchor matches. (--solid-seeds)" /> 184 help="Use solid seeds. Do not permit substitutions in anchor matches" />
182 <param type="boolean" truevalue="--coding-seeds" falsevalue="" label="Coding seeds" name="coding_seeds" 185 <param type="boolean" truevalue="--coding-seeds" falsevalue="" label="Coding seeds" argument="--coding-seeds"
183 help="Use coding pattern seeds. Useful to generate matches coding regions with 3rd codon position degeneracy. (--coding-seeds)" /> 186 help="Use coding pattern seeds. Useful to generate matches coding regions with 3rd codon position degeneracy" />
184 <param type="boolean" truevalue="--no-recursion" falsevalue="" label="No recursion" name="no_recursion" 187 <param type="boolean" truevalue="--no-recursion" falsevalue="" label="No recursion" argument="--no-recursion"
185 help="Disable recursive anchor search (--no-recursion)" /> 188 help="Disable recursive anchor search" />
186 </inputs> 189 </inputs>
187 <outputs> 190 <outputs>
188 <data format="xmfa" name="output" label="${tool.name} alignment of ${on_string}"> 191 <data format="xmfa" name="output" label="${tool.name} alignment of ${on_string}">
189 <change_format> 192 <change_format>
190 <when input="mums" value="--mums" format="tabular" /> 193 <when input="mums" value="--mums" format="tabular" />
191 </change_format> 194 </change_format>
192 </data> 195 </data>
193 <data format="nhx" name="output_guide_tree_file" label="${tool.name} alignment of ${on_string}: Guide tree"> 196 <data format="nhx" name="output_guide_tree_file" label="${tool.name} alignment of ${on_string}: Guide tree">
194 <filter>output_guide_tree</filter> 197 <filter>output_guide_tree and not mums</filter>
195 </data> 198 </data>
196 <data format="tabular" name="output_backbone_file" label="${tool.name} alignment of ${on_string}: Backbone"> 199 <data format="tabular" name="output_backbone_file" label="${tool.name} alignment of ${on_string}: Backbone">
197 <filter>output_backbone</filter> 200 <filter>backbone_output and not mums</filter>
198 </data> 201 </data>
199 </outputs> 202 </outputs>
200 <tests> 203 <tests>
201 <test> 204 <test expect_num_outputs="1">
202 <param name="sequences" value="phagey.fa,karma.fa" /> 205 <param name="sequences" value="phagey.fa,karma.fa" />
203 <output name="output" file="1.xmfa" lines_diff="20"/> 206 <output name="output" file="1.xmfa" lines_diff="20" ftype="xmfa"/>
204 </test> 207 </test>
205 <test> 208 <test expect_num_outputs="1">
206 <param name="sequences" value="merged.fa" /> 209 <param name="sequences" value="merged.fa" />
207 <output name="output" file="2.xmfa" lines_diff="20"/> 210 <output name="output" file="2.xmfa" lines_diff="20" ftype="xmfa"/>
208 </test> 211 </test>
209 <test> 212 <test expect_num_outputs="3">
210 <param name="sequences" value="merged.fa" /> 213 <param name="sequences" value="merged.fa" />
211 <param name="output_guide_tree" value="True" /> 214 <param name="output_guide_tree" value="true" />
212 <output name="output" file="2.xmfa" lines_diff="20"/> 215 <param name="backbone_output" value="true" />
213 <output name="output_guide_tree_file" file="1.nhx" /> 216 <output name="output" file="2.xmfa" lines_diff="20" ftype="xmfa"/>
214 </test> 217 <output name="output_guide_tree_file" file="1.nhx" />
215 <test> 218 <output name="output_backbone_file" file="1.backbone" />
216 <param name="sequences" value="merged.fa" /> 219 </test>
217 <param name="mums" value="True" /> 220 <test expect_num_outputs="1">
218 <output name="output" file="1.mums" compare="sim_size" delta="1000"/> 221 <param name="sequences" value="merged.fa" />
219 </test> 222 <param name="output_guide_tree" value="true" />
220 <test> 223 <param name="mums" value="true" />
221 <param name="sequences" value="merged.fa" /> 224 <output name="output" file="1.mums" compare="sim_size" delta="1000" ftype="tabular"/>
222 <param name="match_input" value="1.mums" ftype="tabular"/> 225 </test>
223 <output name="output" file="2.xmfa" lines_diff="24"/> 226 <test expect_num_outputs="1">
224 </test> 227 <param name="sequences" value="merged.fa" />
225 </tests> 228 <param name="match_input" value="1.mums" ftype="tabular"/>
226 <help><![CDATA[ 229 <output name="output" file="2.xmfa" lines_diff="24" ftype="xmfa"/>
230 </test>
231 </tests>
232 <help><![CDATA[
227 What it does 233 What it does
228 ============ 234 ============
229 235
230 Mauve is a system for efficiently constructing multiple genome alignments in 236 Mauve is a system for efficiently constructing multiple genome alignments in
231 the presence of large-scale evolutionary events such as rearrangement and 237 the presence of large-scale evolutionary events such as rearrangement and
432 are passed to the tool, compared to when those options are not passed. This 438 are passed to the tool, compared to when those options are not passed. This
433 means that if you wish to precisely replicate the results you see in Galaxy at 439 means that if you wish to precisely replicate the results you see in Galaxy at
434 the command line, you'll need to pass these flags with their "default" values. 440 the command line, you'll need to pass these flags with their "default" values.
435 441
436 @ATTRIBUTION@ 442 @ATTRIBUTION@
437 ]]></help> 443 ]]></help>
438 <expand macro="citation" /> 444 <expand macro="citation" />
439 </tool> 445 </tool>