Mercurial > repos > greg > gene_family_aligner

comparison gene_family_aligner.xml @ 57:9c9c2ea494ba draft

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author greg
date Mon, 09 Oct 2017 08:56:27 -0400
parents f782812220e1
children c2b9081064f0
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56:f782812220e1 57:9c9c2ea494ba
47 #end if 47 #end if
48 #end if 48 #end if
49 #end if 49 #end if
50 ]]></command> 50 ]]></command>
51 <inputs> 51 <inputs>
52 <param name="input" format="fasta" type="data_collection" collection_type="list" label="Proteins orthogroup fasta files" /> 52 <param name="input" format="fasta" type="data_collection" collection_type="list" label="Integrated orthogroup fasta files" />
53 <conditional name="alignment_method_cond"> 53 <conditional name="alignment_method_cond">
54 <param name="alignment_method" type="select" force_select="true" label="Multiple sequence alignment method"> 54 <param name="alignment_method" type="select" force_select="true" label="Multiple sequence alignment method">
55 <option value="mafft" selected="true">MAFFT</option> 55 <option value="mafft" selected="true">MAFFT</option>
56 <option value="pasta">PASTA</option> 56 <option value="pasta">PASTA</option>
57 </param> 57 </param>
90 <when value="yes"> 90 <when value="yes">
91 <param name="remove_sequences_with_gaps_of" type="float" optional="true" min="0" max="1" label="Coverage score" /> 91 <param name="remove_sequences_with_gaps_of" type="float" optional="true" min="0" max="1" label="Coverage score" />
92 <param name="iterative_realignment" type="integer" optional="true" min="0" label="Realignment iteration limit" /> 92 <param name="iterative_realignment" type="integer" optional="true" min="0" label="Realignment iteration limit" />
93 </when> 93 </when>
94 </conditional> 94 </conditional>
95 <param name="output_pristine_alignments" type="select" display="radio" label="Output non-filtered, non-trimmed alignemnts?" help="In addition to trimmed/filtered alignments"> 95 <param name="output_pristine_alignments" type="select" display="radio" label="Output primary and intermediate alignemnts?" help="In addition to trimmed/filtered alignments">
96 <option value="no" selected="true">No</option> 96 <option value="no" selected="true">No</option>
97 <option value="yes">Yes</option> 97 <option value="yes">Yes</option>
98 </param> 98 </param>
99 </when> 99 </when>
100 </conditional> 100 </conditional>
144 144
145 ----- 145 -----
146 146
147 **Required options** 147 **Required options**
148 148
149 * **Classified orthogroup fasta files** - orthogroup fasta files produced by the GeneFamilyClassifier tool selected from your history. Depending on how the GeneFamilyClassifier tool was executed, these could either be proteins or proteins and their corresponding coding sequences. 149 * **Integrated orthogroup fasta files** - orthogroup fasta files produced by the GeneFamilyIntegrator tool selected from your history. Depending on how the GeneFamilyClassifier tool was executed, these could either be proteins or proteins and their corresponding coding sequences.
150 150
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. 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.
152 152
153 - **PASTA iteration limit** - number of PASTA iterations. By default, PASTA performs 3 iterations. 153 - **PASTA iteration limit** - number of PASTA iterations. By default, PASTA performs 3 iterations.
154 154
166 166
167 - **Coverage score** - minimum fraction of sites without gaps for a sequence in a multiple sequence alignment. The score is restricted to the range 0.0 - 1.0. Zero value has no effect. 167 - **Coverage score** - minimum fraction of sites without gaps for a sequence in a multiple sequence alignment. The score is restricted to the range 0.0 - 1.0. Zero value has no effect.
168 168
169 - **Realignment iteration limit** - number of iterations to perform trimming, removal of sequences, and realignment of orthogroup sequences. Zero value has no effect. 169 - **Realignment iteration limit** - number of iterations to perform trimming, removal of sequences, and realignment of orthogroup sequences. Zero value has no effect.
170 170
171 * **Output additional dataset collection of files** - selecting 'Yes' will produce an additional output dataset collection whose elements are copies of the directories of files (these elements can be viewed with visualization tools). 171 * **Output primary and intermediate alignments** - selecting 'Yes' will produce a dataset collection of primary and intermediate alignments, the elements of which can be viewed with viaula tools, in addition to the final trimmed and/or filtered alignments dataset collection.
172 172
173 .. _trimAl: http://trimal.cgenomics.org 173 .. _trimAl: http://trimal.cgenomics.org
174 174
175 </help> 175 </help>
176 <citations> 176 <citations>