Mercurial > repos > greg > kaks_analysis

comparison kaks_analysis.xml @ 3:bbc153dbaee7 draft

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author greg
date Wed, 01 Mar 2017 11:13:06 -0500
parents db3e35944c09
children 7fc692c81c02
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2:db3e35944c09 3:bbc153dbaee7
23 --config_dir '$scaffold.fields.path' 23 --config_dir '$scaffold.fields.path'
24 --num_threads \${GALAXY_SLOTS:-4} 24 --num_threads \${GALAXY_SLOTS:-4}
25 --coding_sequences_species_1 '$coding_sequences_species_1' 25 --coding_sequences_species_1 '$coding_sequences_species_1'
26 --proteins_species_1 '$proteins_species_1' 26 --proteins_species_1 '$proteins_species_1'
27 --comparison $comparison 27 --comparison $comparison
28 #if str($comparison) == 'orthologs': 28 #if str($comparison_cond.comparison) == 'orthologs':
29 --coding_sequences_species_2 '$comparison_cond.coding_sequences_species_2' 29 --coding_sequences_species_2 '$comparison_cond.coding_sequences_species_2'
30 --proteins_species_2 '$comparison_cond.proteins_species_2' 30 --proteins_species_2 '$comparison_cond.proteins_species_2'
31 #end if 31 #end if
32 #if str($options_type.options_type_selector) == 'advanced': 32 #if str($options_type.options_type_selector) == 'advanced':
33 --min_coverage $min_coverage 33 --min_coverage $min_coverage
49 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold"> 49 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold">
50 <options from_data_table="plant_tribes_scaffolds" /> 50 <options from_data_table="plant_tribes_scaffolds" />
51 <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."/> 51 <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."/>
52 </param> 52 </param>
53 <param name="coding_sequences_species_1" format="fasta" type="data" label="Coding sequences (CDS) fasta file for the species" /> 53 <param name="coding_sequences_species_1" format="fasta" type="data" label="Coding sequences (CDS) fasta file for the species" />
54 <param name="proteins_species_1" format="fasta" type="data" label="Aamino acids (FNA) sequences fasta file for the species" /> 54 <param name="proteins_species_1" format="fasta" type="data" label="Aamino acids (proteins) sequences fasta file for the species" />
55 <conditional name="comparison_cond"> 55 <conditional name="comparison_cond">
56 <param name="comparison" type="select" label="Select method for pairwise sequence comparison to determine homolgous pairs" help="Cross species comparison requires selection of inputs for second species"> 56 <param name="comparison" type="select" label="Select method for pairwise sequence comparison to determine homolgous pairs" help="Cross species comparison requires selection of inputs for second species">
57 <option value="paralogs" selected="true">Self species comparison</option> 57 <option value="paralogs" selected="true">Self species comparison</option>
58 <option value="orthologs">Cross species comparison</option> 58 <option value="orthologs">Cross species comparison</option>
59 </param> 59 </param>
60 <when value="paralogs" /> 60 <when value="paralogs" />
61 <when value="orthologs"> 61 <when value="orthologs">
62 <param name="coding_sequences_species_2" format="fasta" type="data" label="Coding sequences (CDS) fasta file for the second species" /> 62 <param name="coding_sequences_species_2" format="fasta" type="data" label="Coding sequences (CDS) fasta file for the second species" />
63 <param name="proteins_species_2" format="fasta" type="data" label="Aamino acids (FNA) sequences fasta file for the second species" /> 63 <param name="proteins_species_2" format="fasta" type="data" label="Aamino acids (proteins) sequences fasta file for the second species" />
64 </when> 64 </when>
65 </conditional> 65 </conditional>
66 <conditional name="options_type"> 66 <conditional name="options_type">
67 <param name="options_type_selector" type="select" label="Options Configuration"> 67 <param name="options_type_selector" type="select" label="Options Configuration">
68 <option value="basic" selected="true">Basic</option> 68 <option value="basic" selected="true">Basic</option>