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comparison t_coffee.xml @ 9:e3507be607eb draft default tip

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/t_coffee commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty
author earlhaminst
date Mon, 24 Feb 2025 11:00:35 +0000
parents ae69d14b6fbf
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8:ae69d14b6fbf 9:e3507be607eb
85 <option value="probcons_msa">probcons_msa</option> 85 <option value="probcons_msa">probcons_msa</option>
86 <option value="muscle_msa">muscle_msa</option> 86 <option value="muscle_msa">muscle_msa</option>
87 <option value="t_coffee_msa">t_coffee_msa</option> 87 <option value="t_coffee_msa">t_coffee_msa</option>
88 <option value="kalign_msa">kalign_msa</option> 88 <option value="kalign_msa">kalign_msa</option>
89 </param> 89 </param>
90 <param name="outputs" type="select" multiple="true" optional="false" display="checkboxes" label="Output formats"> 90 <param name="outputs" type="select" multiple="true" optional="false" label="Output formats">
91 <option value="clustalw_aln">clustalw_aln</option> 91 <option value="clustalw_aln">clustalw_aln</option>
92 <option value="dnd" selected="true">dnd</option> 92 <option value="dnd" selected="true">dnd</option>
93 <option value="fasta_aln">fasta_aln</option> 93 <option value="fasta_aln">fasta_aln</option>
94 <option value="fasta_seq">fasta_seq</option> 94 <option value="fasta_seq">fasta_seq</option>
95 <option value="msf_aln">msf_aln</option> 95 <option value="msf_aln">msf_aln</option>
154 <param name="input" value="input.fasta" ftype="fasta" /> 154 <param name="input" value="input.fasta" ftype="fasta" />
155 <param name="method03" value="clustalw_pair,t_coffee_pair" /> 155 <param name="method03" value="clustalw_pair,t_coffee_pair" />
156 <param name="method01" value="sap_pair,mustang_pair,TMalign_pair" /> 156 <param name="method01" value="sap_pair,mustang_pair,TMalign_pair" />
157 <param name="method02" value="mafft_msa,clustalw_msa,dialigntx_msa,poa_msa,probcons_msa,muscle_msa,t_coffee_msa,kalign_msa" /> 157 <param name="method02" value="mafft_msa,clustalw_msa,dialigntx_msa,poa_msa,probcons_msa,muscle_msa,t_coffee_msa,kalign_msa" />
158 <param name="outputs" value="clustalw_aln,dnd,fasta_aln,fasta_seq,msf_aln,phylip,pir_aln,pir_seq,score_ascii,score_html" /> 158 <param name="outputs" value="clustalw_aln,dnd,fasta_aln,fasta_seq,msf_aln,phylip,pir_aln,pir_seq,score_ascii,score_html" />
159 <output name="clustalw_aln" file="output3.clustal" /> 159 <output name="clustalw_aln">
160 <assert_contents>
161 <has_size size="44953" delta="1000" />
162 </assert_contents>
163 </output>
160 <output name="dnd" file="output3.nhx" /> 164 <output name="dnd" file="output3.nhx" />
161 <output name="fasta_aln" file="output3.fasta_aln" /> 165 <output name="fasta_aln">
166 <assert_contents>
167 <has_size size="21797" delta="500" />
168 </assert_contents>
169 </output>
162 <output name="fasta_seq" file="output3.fasta_seq" /> 170 <output name="fasta_seq" file="output3.fasta_seq" />
163 <output name="msf_aln" file="output3.msf" /> 171 <output name="msf_aln">
164 <output name="phylip" file="output3.phylip" /> 172 <assert_contents>
165 <output name="pir_aln" file="output3.pir_aln" /> 173 <has_size size="41823" delta="1000" />
174 </assert_contents>
175 </output>
176 <output name="phylip">
177 <assert_contents>
178 <has_size size="27310" delta="600" />
179 </assert_contents>
180 </output>
181 <output name="pir_aln">
182 <assert_contents>
183 <has_size size="21827" delta="500" />
184 </assert_contents>
185 </output>
166 <output name="pir_seq" file="output3.pir_seq" /> 186 <output name="pir_seq" file="output3.pir_seq" />
167 <output name="score_ascii" file="output3.txt" /> 187 <output name="score_ascii">
188 <assert_contents>
189 <has_size size="42613" delta="1000" />
190 </assert_contents>
191 </output>
168 <output name="score_html"> 192 <output name="score_html">
169 <assert_contents> 193 <assert_contents>
170 <has_text text="ENSMUST00000091" /> 194 <has_text text="ENSMUST00000091" />
171 <has_text text="ENSCAFT00000026" /> 195 <has_text text="ENSCAFT00000026" />
172 <has_text text="ENSMUST00000005" /> 196 <has_text text="ENSMUST00000005" />
181 205
182 This tool is a wrapper for the T-Coffee multiple sequence alignment suite. The input is a set of sequences in FASTA format. Apart from running on the complete FASTA input, it can also run on a subset of sequences by providing a list of the FASTA IDs. 206 This tool is a wrapper for the T-Coffee multiple sequence alignment suite. The input is a set of sequences in FASTA format. Apart from running on the complete FASTA input, it can also run on a subset of sequences by providing a list of the FASTA IDs.
183 207
184 This wrapper offers selected advanced T-Coffee options like the selection of the alignment methods to use: ''Pairwise Structual Method'', ''Multiple Sequence Alignment Methods'' or ''Pairwise Sequence Alignment Methods''. 208 This wrapper offers selected advanced T-Coffee options like the selection of the alignment methods to use: ''Pairwise Structual Method'', ''Multiple Sequence Alignment Methods'' or ''Pairwise Sequence Alignment Methods''.
185 209
186 The T-Coffee documentation can be found at http://www.tcoffee.org/Projects/tcoffee/ . 210 The T-Coffee documentation can be found at https://tcoffee.org/Projects/tcoffee/index.html .
187 211
188 **Example** 212 **Example**
189 213
190 Suppose you have 5 sequences in FASTA format:: 214 Suppose you have 5 sequences in FASTA format::
191 215