Mercurial > repos > devteam > clustalw

comparison rgClustalw.xml @ 3:fac9d3c091cb draft

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-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
author devteam
date Thu, 15 Sep 2022 12:12:19 +0000
parents bed27b5c0f63
children
comparison
equal deleted inserted replaced
2:bed27b5c0f63 3:fac9d3c091cb
1 <tool id="clustalw" name="ClustalW" version="2.1"> 1 <tool id="clustalw" name="ClustalW" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
2 <description>multiple sequence alignment program for DNA or proteins</description> 2 <description>multiple sequence alignment program for DNA or proteins</description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="2.1">clustalw</requirement> 4 <import>macros.xml</import>
5 </requirements> 5 </macros>
6 <expand macro="requirements"/>
6 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
7 ln -s '$input' input.fasta && 8 ln -s '$input' input.fasta &&
8 clustalw2 -INFILE=input.fasta -OUTFILE='$output' -OUTORDER=$out_order -TYPE=$dnarna 9 clustalw2 -INFILE=input.fasta -OUTFILE='$output' -OUTORDER=$out_order -TYPE=$type_conditional.dnarna
9 #if $outcontrol.outform == "clustal" 10 #if $outcontrol.outform == "clustal"
10 -OUTPUT=CLUSTAL 11 -OUTPUT=CLUSTAL
11 #if $outcontrol.out_seqnos == "ON" 12 #if $outcontrol.out_seqnos == "ON"
12 -SEQNOS=ON 13 -SEQNOS=ON
13 #end if 14 #end if
19 -OUTPUT=FASTA 20 -OUTPUT=FASTA
20 #end if 21 #end if
21 #if $range.mode == "part" 22 #if $range.mode == "part"
22 -RANGE=${range.seq_range_start},${range.seq_range_end} 23 -RANGE=${range.seq_range_start},${range.seq_range_end}
23 #end if 24 #end if
25 #if $type_conditional.dnarna == 'PROTEIN'
26 #if $type_conditional.algorithm_conditional.selector == ''
27 -PWMATRIX=$type_conditional.algorithm_conditional.slow_pairwise_alignments.PWMATRIX
28 @SLOW_PAIRWISE_ALIGNMENTS@
29 #else
30 @FAST_PAIRWISE_ALIGNMENTS@
31 #end if
32 -MATRIX=$type_conditional.multiple_alignments.MATRIX
33 @MULTIPLE_ALIGNMENTS@
34 #else
35 #if $type_conditional.algorithm_conditional.selector == ''
36 -PWDNAMATRIX=$type_conditional.algorithm_conditional.slow_pairwise_alignments.PWDNAMATRIX
37 @SLOW_PAIRWISE_ALIGNMENTS@
38 #else
39 @FAST_PAIRWISE_ALIGNMENTS@
40 #end if
41 -DNAMATRIX=$type_conditional.multiple_alignments.DNAMATRIX
42 @MULTIPLE_ALIGNMENTS@
43 #end if
44 -OUTPUTTREE=$tree_calculation.OUTPUTTREE
45 $tree_calculation.KIMURA
46 $tree_calculation.TOSSGAPS
24 ]]></command> 47 ]]></command>
25 <inputs> 48 <inputs>
26 <param name="input" type="data" format="fasta" label="FASTA file" /> 49 <param name="input" type="data" format="fasta" label="FASTA file" />
27 <param name="dnarna" type="select" label="Data type"> 50 <conditional name="type_conditional">
28 <option value="DNA" selected="True">DNA nucleotide sequences</option> 51 <param name="dnarna" type="select" label="Data type">
29 <option value="PROTEIN">Protein sequences</option> 52 <option value="DNA" selected="True">DNA nucleotide sequences</option>
30 </param> 53 <option value="PROTEIN">Protein sequences</option>
54 </param>
55 <when value="DNA">
56 <expand macro="macro_options" algorithm="PWDNAMATRIX" multiple="DNAMATRIX" label="DNA" default="IUB">
57 <option value="IUB" selected="true">IUB</option>
58 <option value="CLUSTALW">CLUSTALW</option>
59 </expand>
60 </when>
61 <when value="PROTEIN">
62 <expand macro="macro_options" algorithm="PWMATRIX" multiple="MATRIX" label="Protein" default="GONNET">
63 <option value="BLOSUM">BLOSUM</option>
64 <option value="PAM">PAM</option>
65 <option value="GONNET" selected="true">GONNET</option>
66 <option value="ID">ID</option>
67 </expand>
68 </when>
69 </conditional>
70 <section name="tree_calculation" title="Tree calculation/BOOTSTRAP options">
71 <param argument="-OUTPUTTREE" type="select" label="Output tree/distance forma" help="Specify the output format. Default: phylip">
72 <option value="PHYLIP">PHYLIP</option>
73 <option value="DIST">DIST</option>
74 <option value="NJ">NJ</option>
75 <option value="NEXUS">NEXUS</option>
76 </param>
77 <param argument="-KIMURA" type="boolean" truevalue="-KIMURA" falsevalue="" checked="false" label="Use Kimura correction"
78 help="For small divergence (say inferior 10%) this option makes no difference. For greater divergence, this option corrects for the fact that observed distances underestimate actual evolutionary distances." />
79 <param argument="-TOSSGAPS" type="boolean" truevalue="-TOSSGAPS" falsevalue="" checked="false" label="Ignore positions with gaps" help="Default: No" />
80 </section>
31 <conditional name="outcontrol"> 81 <conditional name="outcontrol">
32 <param name="outform" type="select" label="Output alignment format"> 82 <param name="outform" type="select" label="Output alignment format">
33 <option value="clustal" selected="True">Native Clustal output format</option> 83 <option value="clustal" selected="True">Native Clustal output format</option>
34 <option value="phylip">PHYLIP format</option> 84 <option value="phylip">PHYLIP format</option>
35 <option value="fasta">FASTA format</option> 85 <option value="fasta">FASTA format</option>
67 </outputs> 117 </outputs>
68 <tests> 118 <tests>
69 <test> 119 <test>
70 <param name="input" value="rgClustal_testin.fasta" /> 120 <param name="input" value="rgClustal_testin.fasta" />
71 <param name="outform" value="fasta" /> 121 <param name="outform" value="fasta" />
72 <param name="dnarna" value="DNA" /> 122 <conditional name="type_conditional">
123 <param name="dnarna" value="DNA"/>
124 </conditional>
73 <param name="mode" value="complete" /> 125 <param name="mode" value="complete" />
74 <param name="out_order" value="ALIGNED" /> 126 <param name="out_order" value="ALIGNED" />
75 <output name="output" file="rgClustal_testout.fasta" ftype="fasta" /> 127 <output name="output" file="rgClustal_testout.fasta" ftype="fasta" />
76 <output name="dnd" file="rgClustal_testin.dnd" ftype="nhx" /> 128 <output name="dnd" file="rgClustal_testin.dnd" ftype="nhx" />
77 </test> 129 </test>
130 <!-- Test DNA options-->
131 <test expect_num_outputs="2">
132 <param name="input" value="rgClustal_testin.fasta"/>
133 <param name="out_order" value="ALIGNED"/>
134 <section name="tree_calculation">
135 <param name="OUTPUTTREE" value="PHYLIP"/>
136 <param name="KIMURA" value="true"/>
137 <param name="TOSSGAPS" value="true"/>
138 </section>
139 <conditional name="type_conditional">
140 <param name="dnarna" value="DNA"/>
141 <section name="multiple_alignments">
142 <param name="DNAMATRIX" value="IUB"/>
143 <param name="GAPOPEN" value="2"/>
144 <param name="GAPEXT" value="1"/>
145 <param name="ENDGAPS" value="true"/>
146 <param name="GAPDIST" value="1"/>
147 <param name="NOPGAP" value="true"/>
148 <param name="NOHGAP" value="true"/>
149 <param name="MAXDIV" value="1"/>
150 <param name="NEGATIVE" value="true"/>
151 <param name="TRANSWEIGHT" value="1"/>
152 </section>
153 <conditional name="algorithm_conditional">
154 <param name="selector" value=""/>
155 <section name="slow_pairwise_alignments">
156 <param name="PWGAPOPEN" value="2"/>
157 <param name="PWGAPEXT" value="1"/>
158 </section>
159 </conditional>
160 </conditional>
161 <output name="output" file="rgClustal_testout02.aln" ftype="clustal"/>
162 <output name="dnd" file="rgClustal_testout02.dnd" ftype="nhx"/>
163 </test>
164 <!-- Test protein options and fast algorithm-->
165 <test expect_num_outputs="2">
166 <param name="input" value="rgClustal_testin_prot.fasta"/>
167 <param name="out_order" value="ALIGNED"/>
168 <section name="tree_calculation">
169 <param name="OUTPUTTREE" value="PHYLIP"/>
170 <param name="KIMURA" value="false"/>
171 <param name="TOSSGAPS" value="false"/>
172 </section>
173 <conditional name="type_conditional">
174 <param name="dnarna" value="PROTEIN"/>
175 <section name="multiple_alignments">
176 <param name="MATRIX" value="BLOSUM"/>
177 <param name="GAPOPEN" value="3"/>
178 <param name="GAPEXT" value="1"/>
179 <param name="ENDGAPS" value="true"/>
180 <param name="GAPDIST" value="2"/>
181 <param name="NOPGAP" value="true"/>
182 <param name="NOHGAP" value="true"/>
183 <param name="MAXDIV" value="1"/>
184 <param name="NEGATIVE" value="true"/>
185 <param name="TRANSWEIGHT" value="1"/>
186 </section>
187 <conditional name="algorithm_conditional">
188 <param name="selector" value="-QUICKTREE"/>
189 <section name="fast_pairwise_alignments">
190 <param name="KTUPLE" value="1"/>
191 <param name="TOPDIAGS" value="1"/>
192 <param name="WINDOW" value="2"/>
193 <param name="PAIRGAP" value="2"/>
194 <param name="SCORE" value="PERCENT"/>
195 </section>
196 </conditional>
197 </conditional>
198 <output name="output" file="rgClustal_testout03.aln" ftype="clustal"/>
199 <output name="dnd" file="rgClustal_testout03.dnd" ftype="nhx"/>
200 </test>
78 </tests> 201 </tests>
79 <help><![CDATA[ 202 <help><![CDATA[
203 .. class:: infomark
204
80 **Note** 205 **Note**
81 206
82 This tool allows you to run a multiple sequence alignment with ClustalW_ using the default options. 207 This tool allows you to run a multiple sequence alignment with ClustalW_.
83
84 You can align DNA or protein sequences in the input file which should be multiple sequences to be aligned in a FASTA file. 208 You can align DNA or protein sequences in the input file which should be multiple sequences to be aligned in a FASTA file.
85 209
86 The alignments will appear as a clustal format file or optionally, as PHYLIP or FASTA format files in your history. If you choose FASTA as 210 The alignments will appear as a clustal format file or optionally, as PHYLIP or FASTA format files in your history. If you choose FASTA as
87 the output format, you can create a 'Logo' image using the Sequence Logo tool. 211 the output format, you can create a 'Logo' image using the Sequence Logo tool.
88 212
90 214
91 A subsequence of the alignment can be output by setting the Output complete parameter to "Partial" and defining the offset and end of the subsequence to be output. 215 A subsequence of the alignment can be output by setting the Output complete parameter to "Partial" and defining the offset and end of the subsequence to be output.
92 216
93 ---- 217 ----
94 218
219 .. class:: infomark
220
95 **Attribution** 221 **Attribution**
96 222
97 The first iteration of this Galaxy wrapper was written by Hans-Rudolf Hotz. 223 The first iteration of this Galaxy wrapper was written by Hans-Rudolf Hotz.
98 224
99 It was modified by Ross Lazarus for the rgenetics project - tests and some additional parameters were added. 225 It was modified by Ross Lazarus for the rgenetics project - tests and some additional parameters were added. Cristóbal Gallardo included the remaining parameters.
100 226
101 This wrapper is released licensed under the LGPL_. 227 This wrapper is released licensed under the LGPL_.
102 228
103 .. _ClustalW: http://www.clustal.org/clustal2/ 229 .. _ClustalW: http://www.clustal.org/clustal2/
104 230