Mercurial > repos > greg > gene_family_aligner

comparison gene_family_aligner.xml @ 58:c2b9081064f0 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author greg
date Fri, 13 Oct 2017 14:24:30 -0400
parents 9c9c2ea494ba
children 0e1041ee1926
comparison
equal deleted inserted replaced
57:9c9c2ea494ba 58:c2b9081064f0
59 <when value="pasta"> 59 <when value="pasta">
60 <param name="pasta_iter_limit" type="integer" value="3" min="1" label="PASTA iteration limit" /> 60 <param name="pasta_iter_limit" type="integer" value="3" min="1" label="PASTA iteration limit" />
61 </when> 61 </when>
62 </conditional> 62 </conditional>
63 <param name="codon_alignments" type="select" label="Codon alignments"> 63 <param name="codon_alignments" type="select" label="Codon alignments">
64 <option value="yes" selected="true">Yes</option> 64 <option value="no" selected="true">No</option>
65 <option value="no">No</option> 65 <option value="yes">Yes</option>
66 </param> 66 </param>
67 <conditional name="remove_gappy_sequences_cond"> 67 <conditional name="remove_gappy_sequences_cond">
68 <param name="remove_gappy_sequences" type="select" label="Alignment post-processing configuration"> 68 <param name="remove_gappy_sequences" type="select" label="Alignment post-processing configuration">
69 <option value="no" selected="true">No</option> 69 <option value="no" selected="true">No</option>
70 <option value="yes">Yes</option> 70 <option value="yes">Yes</option>
133 <filter>codon_alignments == 'yes' and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['output_pristine_alignments'] == 'yes'</filter> 133 <filter>codon_alignments == 'yes' and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['output_pristine_alignments'] == 'yes'</filter>
134 </collection> 134 </collection>
135 </outputs> 135 </outputs>
136 <tests> 136 <tests>
137 <test> 137 <test>
138 <param name="input">
139 <collection type="list">
140 <element name="3722.faa" value="3722.faa"/>
141 <element name="3722.fna" value="3722.fna"/>
142 <element name="38889.faa" value="38889.faa"/>
143 <element name="38889.fna" value="38889.fna"/>
144 <element name="39614.faa" value="39614.faa"/>
145 <element name="39614.fna" value="39614.fna"/>
146 </collection>
147 </param>
148 <output_collection name="primary_faa" type="list">
149 <element name="3722.faa.aln" file="3722.faa.aln" ftype="fasta"/>
150 <element name="38889.faa.aln" file="38889.faa.aln" ftype="fasta"/>
151 <element name="39614.faa.aln" file="39614.faa.aln" ftype="fasta"/>
152 </output_collection>
153 <output_collection name="primary_fna" type="list">
154 <element name="3722.fna.aln" file="3722.fna.aln" ftype="fasta"/>
155 <element name="38889.fna.aln" file="38889.fna.aln" ftype="fasta"/>
156 <element name="39614.fna.aln" file="39614.fna.aln" ftype="fasta"/>
157 </output_collection>
138 </test> 158 </test>
139 </tests> 159 </tests>
140 <help> 160 <help>
141 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary 161 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary
142 analyses of genome-scale gene families and transcriptomes. This tool estimates protein and codon multiple sequence alignments 162 analyses of genome-scale gene families and transcriptomes. This tool estimates protein and codon multiple sequence alignments
150 170
151 * **Multiple sequence alignment method** - method for estimating orthogroup multiple sequence alignments. PlantTribes estimates alignments using either MAFFT's L-INS-i algorithm or the divide and conquer approach implemented in the PASTA pipeline for large alignments. 171 * **Multiple sequence alignment method** - method for estimating orthogroup multiple sequence alignments. PlantTribes estimates alignments using either MAFFT's L-INS-i algorithm or the divide and conquer approach implemented in the PASTA pipeline for large alignments.
152 172
153 - **PASTA iteration limit** - number of PASTA iterations. By default, PASTA performs 3 iterations. 173 - **PASTA iteration limit** - number of PASTA iterations. By default, PASTA performs 3 iterations.
154 174
155 * **Codon alignments** - select 'Yes' to create codon multiple sequence alignments. This option requires protein and their corresponding coding sequences to be provided as input data. 175 * **Codon alignments** - select 'Yes' to create codon multiple sequence alignments. This option requires both protein and their corresponding coding sequence orthogroup fasta files to be present in the GeneFamilyAligner input data that was produced by the GeneFamilyIntegrator.
156 176
157 **Other options** 177 **Other options**
158 178
159 * **Alignment post-processing configuration** - select 'Yes' to enable multiple sequence alignment post-processing configuration options. 179 * **Alignment post-processing configuration** - select 'Yes' to enable multiple sequence alignment post-processing configuration options.
160 180