Mercurial > repos > greg > gene_family_aligner

comparison gene_family_aligner.xml @ 9:43341e97bb08 draft

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Uploaded
author greg
date Mon, 10 Apr 2017 12:47:18 -0400
parents 9e68bebb3d7c
children 5ad5d4204edf
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8:9e68bebb3d7c 9:43341e97bb08
6 <expand macro="requirements_gene_family_aligner" /> 6 <expand macro="requirements_gene_family_aligner" />
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <command> 8 <command>
9 <![CDATA[ 9 <![CDATA[
10 #set input_format = $input_format_cond.input_format 10 #set input_format = $input_format_cond.input_format
11 #set scaffold = $input_format_cond.scaffold
12 #set alignment_method_cond = $input_format_cond.alignment_method_cond 11 #set alignment_method_cond = $input_format_cond.alignment_method_cond
13 #set alignment_method = $alignment_method_cond.alignment_method 12 #set alignment_method = $alignment_method_cond.alignment_method
14 13
15 python $__tool_directory__/gene_family_aligner.py 14 python $__tool_directory__/gene_family_aligner.py
16 --scaffold '$scaffold.fields.path'
17 --method $input_format_cond.method
18 --alignment_method $alignment_method 15 --alignment_method $alignment_method
19 #if str($alignment_method) == 'pasta': 16 #if str($alignment_method) == 'pasta':
20 --pasta_script_path '$__tool_directory__/run_pasta.py' 17 --pasta_script_path '$__tool_directory__/run_pasta.py'
21 --pasta_iter_limit $alignment_method_cond.pasta_iter_limit 18 --pasta_iter_limit $alignment_method_cond.pasta_iter_limit
22 #end if 19 #end if
69 <option value="ptortho">Gene family clusters</option> 66 <option value="ptortho">Gene family clusters</option>
70 <option value="ptorthocs">Gene family clusters with corresponding coding sequences</option> 67 <option value="ptorthocs">Gene family clusters with corresponding coding sequences</option>
71 </param> 68 </param>
72 <when value="ptortho"> 69 <when value="ptortho">
73 <param name="input_ptortho" format="ptortho" type="data" label="Gene family clusters" /> 70 <param name="input_ptortho" format="ptortho" type="data" label="Gene family clusters" />
74 <expand macro="param_scaffold" />
75 <expand macro="param_method" />
76 <expand macro="cond_alignment_method" /> 71 <expand macro="cond_alignment_method" />
77 </when> 72 </when>
78 <when value="ptorthocs"> 73 <when value="ptorthocs">
79 <param name="input_ptorthocs" format="ptorthocs" type="data" label="Gene family clusters with corresponding coding sequences" /> 74 <param name="input_ptorthocs" format="ptorthocs" type="data" label="Gene family clusters with corresponding coding sequences" />
80 <expand macro="param_scaffold" />
81 <expand macro="param_method" />
82 <expand macro="cond_alignment_method" /> 75 <expand macro="cond_alignment_method" />
83 <expand macro="param_codon_alignments" /> 76 <expand macro="param_codon_alignments" />
84 </when> 77 </when>
85 </conditional> 78 </conditional>
86 <conditional name="options_type_cond"> 79 <conditional name="options_type_cond">
121 - **Gene family clusters** - sequences classified into gene family clusters. 114 - **Gene family clusters** - sequences classified into gene family clusters.
122 - **Gene family clusters with corresponding coding sequences** - sequences classified into gene family clusters including corresponding coding sequences. 115 - **Gene family clusters with corresponding coding sequences** - sequences classified into gene family clusters including corresponding coding sequences.
123 116
124 - **Construct orthogroup multiple codon alignments** - construct orthogroup multiple codon alignments. 117 - **Construct orthogroup multiple codon alignments** - construct orthogroup multiple codon alignments.
125 118
126 * **Gene family scaffold** - one of the PlantTribes gene family scaffolds [2-4] installed into Galaxy by the PlantTribes Scaffold Data Manager tool.
127 * **Protein clustering method** - gene family scaffold protein clustering method as described in the AssemblyPostProcessor tool.
128
129 * **Select method for multiple sequence alignments** 119 * **Select method for multiple sequence alignments**
130 120
131 - **MAFFT algorithm** - mafft algorithm. 121 - **MAFFT algorithm** - mafft algorithm.
132 - **Pasta algorithm** - pasta algorithm. 122 - **Pasta algorithm** - pasta algorithm.
133 123