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comparison kaks_analysis.xml @ 20:887a918134da draft

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author greg
date Fri, 03 Mar 2017 14:16:09 -0500
parents e188f52adf1d
children eca17c50d2e0
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19:e188f52adf1d 20:887a918134da
33 #set fit_components = 'no' 33 #set fit_components = 'no'
34 #set set_lower_ks_limit = 'no' 34 #set set_lower_ks_limit = 'no'
35 #set set_upper_ks_limit = 'no' 35 #set set_upper_ks_limit = 'no'
36 #end if 36 #end if
37 KaKsAnalysis 37 KaKsAnalysis
38 --config_dir '$scaffold.fields.path'
39 --num_threads \${GALAXY_SLOTS:-4} 38 --num_threads \${GALAXY_SLOTS:-4}
40 --coding_sequences_species_1 '$coding_sequences_species_1' 39 --coding_sequences_species_1 '$coding_sequences_species_1'
41 --proteins_species_1 '$proteins_species_1' 40 --proteins_species_1 '$proteins_species_1'
42 --comparison $comparison 41 --comparison $comparison
43 #if str($comparison) == 'orthologs': 42 #if str($comparison) == 'orthologs':
97 <when value="orthologs"> 96 <when value="orthologs">
98 <param name="coding_sequences_species_2" format="fasta" type="data" label="Coding sequences (CDS) fasta file for species2" /> 97 <param name="coding_sequences_species_2" format="fasta" type="data" label="Coding sequences (CDS) fasta file for species2" />
99 <param name="proteins_species_2" format="fasta" type="data" label="Aamino acids (proteins) sequences fasta file for species2" /> 98 <param name="proteins_species_2" format="fasta" type="data" label="Aamino acids (proteins) sequences fasta file for species2" />
100 </when> 99 </when>
101 </conditional> 100 </conditional>
102 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold" help="Selection specifies default configuration files">
103 <options from_data_table="plant_tribes_scaffolds" />
104 <validator type="no_options" message="No PlantTribes scaffolds are available. Use the PlantTribes Scaffolds Download Data Manager tool in Galaxy to install and populate the PlantTribes scaffolds data table."/>
105 </param>
106 <conditional name="options_type"> 101 <conditional name="options_type">
107 <param name="options_type_selector" type="select" label="Options Configuration"> 102 <param name="options_type_selector" type="select" label="Options Configuration">
108 <option value="basic" selected="true">Basic</option> 103 <option value="basic" selected="true">Basic</option>
109 <option value="advanced">Advanced</option> 104 <option value="advanced">Advanced</option>
110 </param> 105 </param>
145 <option value="no" selected="true">No</option> 140 <option value="no" selected="true">No</option>
146 <option value="yes">Yes</option> 141 <option value="yes">Yes</option>
147 </param> 142 </param>
148 <when value="no" /> 143 <when value="no" />
149 <when value="yes"> 144 <when value="yes">
150 <param name="num_of_components" type="integer" value="0" min="0" label="Number components to fit to synonymous subsitutions (ks) distribution" /> 145 <param name="num_of_components" type="integer" value="0" min="0" label="Number of components to fit to synonymous subsitutions (ks) distribution" />
151 </when> 146 </when>
152 </conditional> 147 </conditional>
153 <conditional name="set_lower_ks_limit_cond"> 148 <conditional name="set_lower_ks_limit_cond">
154 <param name="set_lower_ks_limit" type="select" label="Set lower limit of synonymous subsitutions (ks)?" help="Reduces background noise from young paralogous pairs due to normal gene births and deaths in a genome"> 149 <param name="set_lower_ks_limit" type="select" label="Set lower limit of synonymous subsitutions (ks)?" help="Reduces background noise from young paralogous pairs due to normal gene births and deaths in a genome">
155 <option value="no" selected="true">No</option> 150 <option value="no" selected="true">No</option>
217 * **Required** 212 * **Required**
218 213
219 - **Coding sequences (CDS) fasta file for species1** - Coding sequences (CDS) fasta file for species1. 214 - **Coding sequences (CDS) fasta file for species1** - Coding sequences (CDS) fasta file for species1.
220 - **Aamino acids (proteins) sequences fasta file for species1** - Aamino acids (proteins) sequences fasta file for species1 215 - **Aamino acids (proteins) sequences fasta file for species1** - Aamino acids (proteins) sequences fasta file for species1
221 - **Select method for pairwise sequence comparison to determine homolgous pairs** - Pairwise sequence comparison to determine homolgous pairs (cross species comparison requires selection of inputs for species2). 216 - **Select method for pairwise sequence comparison to determine homolgous pairs** - Pairwise sequence comparison to determine homolgous pairs (cross species comparison requires selection of inputs for species2).
222 - **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data installed into Galaxy by the PlantTribes Scaffolds Download Data Manager tool.
223 217
224 * **Optional** 218 * **Optional**
225 219
226 - **Minimum sequence pairwise coverage length between homologous pairs** - Minimum sequence pairwise coverage length between homologous pairs (e.g., 0.5 results in 50% coverage. Legal values lie between 0.3 and 1.0. 220 - **Minimum sequence pairwise coverage length between homologous pairs** - Minimum sequence pairwise coverage length between homologous pairs (e.g., 0.5 results in 50% coverage. Legal values lie between 0.3 and 1.0.
227 - **Evolutionary rate for recalibrating synonymous subsitutions (ks) of species** - (applies to paralogous ks analysis) Recalibrate synonymous subsitutions (ks) of species using a predetermined evoutionary rate that can be determined from a species tree inferred from a collection single copy genes from taxa of interest (Cui et al., 2006). 221 - **Evolutionary rate for recalibrating synonymous subsitutions (ks) of species** - (applies to paralogous ks analysis) Recalibrate synonymous subsitutions (ks) of species using a predetermined evoutionary rate that can be determined from a species tree inferred from a collection single copy genes from taxa of interest (Cui et al., 2006).