Mercurial > repos > greg > kaks_analysis

comparison kaks_analysis.xml @ 5:a0c58fecc07b draft

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author greg
date Wed, 01 Mar 2017 13:40:40 -0500
parents 7fc692c81c02
children ed921c8159bf
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4:7fc692c81c02 5:a0c58fecc07b
11 <regex match="Error:" /> 11 <regex match="Error:" />
12 <regex match="Exception:" /> 12 <regex match="Exception:" />
13 </stdio> 13 </stdio>
14 <command> 14 <command>
15 <![CDATA[ 15 <![CDATA[
16 #set output_dir = 'kaksAnalysis_dir'
16 #set comparison = $comparison_cond.comparison 17 #set comparison = $comparison_cond.comparison
17 #if str($options_type.options_type_selector) == 'advanced': 18 #if str($options_type.options_type_selector) == 'advanced':
18 #set codeml_ctl_file_cond = $options_type.codeml_ctl_file_cond 19 #set codeml_ctl_file_cond = $options_type.codeml_ctl_file_cond
19 #set codeml_ctl_file_select = $codeml_ctl_file_cond.codeml_ctl_file_select 20 #set codeml_ctl_file_select = $codeml_ctl_file_cond.codeml_ctl_file_select
20 #set fit_components_cond = $options_type.fit_components_cond 21 #set fit_components_cond = $options_type.fit_components_cond
42 --num_of_components $fit_components_cond.num_of_components 43 --num_of_components $fit_components_cond.num_of_components
43 --min_ks $fit_components_cond.min_ks 44 --min_ks $fit_components_cond.min_ks
44 --max_ks $fit_components_cond.max_ks 45 --max_ks $fit_components_cond.max_ks
45 #end if 46 #end if
46 #end if 47 #end if
48 && mv $output_dir/species1.fna '$output_species1_fna'
49 && mv $output_dir/species1.faa '$output_species1_faa'
50 #if str($comparison) == 'orthologs':
51 && mv $output_dir/species1.fna.blastn.paralogs '$output_species1_paralog'
52 #end if
53 #if str($comparison) == 'orthologs':
54 && mv $output_dir/species2.faa '$output_species2_faa'
55 && mv $output_dir/species2.fna '$output_species2_fna'
56 && mv $output_dir/species1.fna.blastn.orthologs '$output_species1_ortholog'
57 && mv $output_dir/species2.fna.blastn.orthologs '$output_species2_ortholog'
58 #end if
59 && mv $output_dir/*.rbhb '$output_rbhb'
60 && mv $output_dir/*.kaks '$output_kaks'
61 #if str($fit_components) == 'yes':
62 && mv $output_dir/*.components '$output_components'
63 #end if
47 ]]> 64 ]]>
48 </command> 65 </command>
49 <inputs> 66 <inputs>
50 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold">
51 <options from_data_table="plant_tribes_scaffolds" />
52 <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."/>
53 </param>
54 <param name="coding_sequences_species_1" format="fasta" type="data" label="Coding sequences (CDS) fasta file for the species" /> 67 <param name="coding_sequences_species_1" format="fasta" type="data" label="Coding sequences (CDS) fasta file for the species" />
55 <param name="proteins_species_1" format="fasta" type="data" label="Aamino acids (proteins) sequences fasta file for the species" /> 68 <param name="proteins_species_1" format="fasta" type="data" label="Aamino acids (proteins) sequences fasta file for the species" />
56 <conditional name="comparison_cond"> 69 <conditional name="comparison_cond">
57 <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"> 70 <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">
58 <option value="paralogs" selected="true">Self species comparison</option> 71 <option value="paralogs" selected="true">Self species comparison</option>
62 <when value="orthologs"> 75 <when value="orthologs">
63 <param name="coding_sequences_species_2" format="fasta" type="data" label="Coding sequences (CDS) fasta file for the second species" /> 76 <param name="coding_sequences_species_2" format="fasta" type="data" label="Coding sequences (CDS) fasta file for the second species" />
64 <param name="proteins_species_2" format="fasta" type="data" label="Aamino acids (proteins) sequences fasta file for the second species" /> 77 <param name="proteins_species_2" format="fasta" type="data" label="Aamino acids (proteins) sequences fasta file for the second species" />
65 </when> 78 </when>
66 </conditional> 79 </conditional>
80 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold" help="Selection specifies default configuration files">
81 <options from_data_table="plant_tribes_scaffolds" />
82 <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."/>
83 </param>
67 <conditional name="options_type"> 84 <conditional name="options_type">
68 <param name="options_type_selector" type="select" label="Options Configuration"> 85 <param name="options_type_selector" type="select" label="Options Configuration">
69 <option value="basic" selected="true">Basic</option> 86 <option value="basic" selected="true">Basic</option>
70 <option value="advanced">Advanced</option> 87 <option value="advanced">Advanced</option>
71 </param> 88 </param>
97 </conditional> 114 </conditional>
98 </when> 115 </when>
99 </conditional> 116 </conditional>
100 </inputs> 117 </inputs>
101 <outputs> 118 <outputs>
102 <collection name="ks_files" type="list"> 119 <data name="output_species1_fna" format="fasta" label="KaKs analysis (coding sequences) on ${on_string}" />
103 <discover_datasets pattern="__name__" directory="kaksAnalysis_dir" visible="false" ext="fasta" /> 120 <data name="output_species1_faa" format="fasta" label="KaKs analysis (amino acids) on ${on_string}" />
104 </collection> 121 <data name="output_species2_fna" format="fasta" label="KaKs analysis (coding sequences) on ${on_string}">
122 <filter>comparison_cond['comparison'] == 'orthologs'</filter>
123 </data>
124 <data name="output_species2_faa" format="fasta" label="KaKs analysis (amino acids) on ${on_string}">
125 <filter>comparison_cond['comparison'] == 'orthologs'</filter>
126 </data>
127 <data name="output_species1_paralog" format="tabular" label="KaKs analysis (blastn results) on ${on_string}">
128 <filter>comparison_cond['comparison'] == 'paralogs'</filter>
129 </data>
130 <data name="output_species1_ortholog" format="tabular" label="KaKs analysis (blastn results) on ${on_string}">
131 <filter>comparison_cond['comparison'] == 'orthologs'</filter>
132 </data>
133 <data name="output_species2_ortholog" format="tabular" label="KaKs analysis (blastn results) on ${on_string}">
134 <filter>comparison_cond['comparison'] == 'orthologs'</filter>
135 </data>
136 <data name="output_rbhb" format="tabular" label="KaKs analysis (paralogous pairs) on ${on_string}" />
137 <data name="output_kaks" format="tabular" label="KaKs analysis on ${on_string}" />
138 <data name="output_components" format="tabular" label="KaKs analysis (significant components in the ks distribution) on ${on_string}">
139 <filter>options_type[options_type_selector'] == 'advanced' and options_type['fit_components_cond']['fit_components'] == 'yes</filter>
140 </data>
105 </outputs> 141 </outputs>
106 <tests> 142 <tests>
107 <test> 143 <test>
108 </test> 144 </test>
109 </tests> 145 </tests>