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comparison stacks_rxstacks.xml @ 8:1919e1ecb90d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
author iuc
date Thu, 27 Apr 2017 04:19:22 -0400
parents fec69a2d92d7
children 3e43e51b3c3b
comparison
equal deleted inserted replaced
7:f4a15ab64300 8:1919e1ecb90d
9 9
10 mkdir stacks_inputs stacks_outputs 10 mkdir stacks_inputs stacks_outputs
11 11
12 && 12 &&
13 13
14 #for $input_file in $input_col: 14 #for $input_file in $input_col
15 #set $ext = "" 15 #set $ext = ""
16 #if not str($input_file.element_identifier).endswith('.tsv'): 16 #if not str($input_file.element_identifier).endswith('.tsv')
17 #set $ext = ".tsv" 17 #set $ext = ".tsv"
18 #end if 18 #end if
19 ln -s "${input_file}" "stacks_inputs/${input_file.element_identifier}${ext}" && 19 ln -s '${input_file}' 'stacks_inputs/${input_file.element_identifier}${ext}' &&
20 #end for 20 #end for
21 21
22 rxstacks 22 rxstacks
23 23
24 -t \${GALAXY_SLOTS:-1} 24 -t \${GALAXY_SLOTS:-1}
26 -P stacks_inputs 26 -P stacks_inputs
27 27
28 ## Batch description 28 ## Batch description
29 -b 1 29 -b 1
30 30
31 #if str($options_filtering.lnl): 31 #if str($options_filtering.lnl)
32 --lnl_filter 32 --lnl_filter
33 --lnl_lim $options_filtering.lnl 33 --lnl_lim $options_filtering.lnl
34 #end if 34 #end if
35 35
36 $options_filtering.lnl_dist 36 $options_filtering.lnl_dist
37 37
38 #if str($options_filtering.conf): 38 #if str($options_filtering.conf)
39 --conf_filter 39 --conf_filter
40 --conf_lim $options_filtering.conf 40 --conf_lim $options_filtering.conf
41 #end if 41 #end if
42 42
43 #if $options_filtering.prune.prune_haplo: 43 #if $options_filtering.prune.prune_haplo == "yes"
44 --prune_haplo 44 --prune_haplo
45 #if str($options_filtering.prune.max_haplo): 45 #if str($options_filtering.prune.max_haplo)
46 --max_haplo $options_filtering.prune.max_haplo 46 --max_haplo $options_filtering.prune.max_haplo
47 #end if 47 #end if
48 #end if 48 #end if
49 49
50 ## snp_model 50 ## snp_model
51 #if str( $snp_options.select_model.model_type) == "bounded": 51 #if str( $snp_options.select_model.model_type) == "bounded"
52 --model_type bounded 52 --model_type bounded
53 --bound_low $snp_options.select_model.bound_low 53 --bound_low $snp_options.select_model.bound_low
54 --bound_high $snp_options.select_model.bound_high 54 --bound_high $snp_options.select_model.bound_high
55 --alpha $snp_options.select_model.alpha 55 --alpha $snp_options.select_model.alpha
56 #else if str( $snp_options.select_model.model_type) == "snp": 56 #else if str( $snp_options.select_model.model_type) == "snp"
57 --model_type snp 57 --model_type snp
58 --alpha $snp_options.select_model.alpha 58 --alpha $snp_options.select_model.alpha
59 #else 59 #else
60 --model_type fixed 60 --model_type fixed
61 #end if 61 #end if
71 <param name="lnl_dist" argument="--lnl_dist" truevalue="--lnl_dist" falsevalue="" type="boolean" checked="false" label="Print distribution of mean log likelihoods for catalog loci." /> 71 <param name="lnl_dist" argument="--lnl_dist" truevalue="--lnl_dist" falsevalue="" type="boolean" checked="false" label="Print distribution of mean log likelihoods for catalog loci." />
72 72
73 <param name="conf" type="float" value="0.75" optional="true" argument="--conf_lim" min="0.0" max="1.0" label="Proportion of loci in population that must be confounded relative to the catalog locus (between 0.0 and 1.0)."/> 73 <param name="conf" type="float" value="0.75" optional="true" argument="--conf_lim" min="0.0" max="1.0" label="Proportion of loci in population that must be confounded relative to the catalog locus (between 0.0 and 1.0)."/>
74 74
75 <conditional name="prune"> 75 <conditional name="prune">
76 <param name="prune_haplo" argument="--prune_haplo" type="boolean" checked="false" label="Prune out non-biological haplotypes unlikely to occur in the population." /> 76 <param name="prune_haplo" argument="--prune_haplo" type="select" label="Prune out non-biological haplotypes unlikely to occur in the population.">
77 <when value="false"></when> 77 <option value="no" selected="true">No</option>
78 <when value="true"> 78 <option value="yes">Yes</option>
79 </param>
80 <when value="no"/>
81 <when value="yes">
79 <param name="max_haplo" argument="--max_haplo" type="integer" value="" optional="true" label="Only consider haplotypes for pruning if they occur in fewer than this value."/> 82 <param name="max_haplo" argument="--max_haplo" type="integer" value="" optional="true" label="Only consider haplotypes for pruning if they occur in fewer than this value."/>
80 </when> 83 </when>
81 </conditional> 84 </conditional>
82 </section> 85 </section>
83 86
128 <element name="PopA_02.tags.tsv" ftype="tabular" value="genotypes/PopA_02.tags.tsv" /> 131 <element name="PopA_02.tags.tsv" ftype="tabular" value="genotypes/PopA_02.tags.tsv" />
129 </collection> 132 </collection>
130 </param> 133 </param>
131 <param name="options_filtering|lnl" value="-10.0" /> 134 <param name="options_filtering|lnl" value="-10.0" />
132 <param name="options_filtering|lnl_dist" value="true" /> 135 <param name="options_filtering|lnl_dist" value="true" />
133 <param name="options_filtering|prune_haplo" value="true" /> 136 <param name="options_filtering|prune_haplo" value="yes" />
134 <param name="options_filtering|max_haplo" value="1" /> 137 <param name="options_filtering|max_haplo" value="1" />
135 138
136 <output name="output_log"> 139 <output name="output_log">
137 <assert_contents> 140 <assert_contents>
138 <has_text text="rxstacks executed" /> 141 <has_text text="rxstacks executed" />