Mercurial > repos > iuc > stacks_genotypes
comparison stacks_genotypes.xml @ 8:8dc6a3afbe83 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
author | iuc |
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date | Thu, 27 Apr 2017 04:19:10 -0400 |
parents | 969a09779e3c |
children | 00f4a4e553ae |
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7:639f2db87df0 | 8:8dc6a3afbe83 |
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10 | 10 |
11 mkdir stacks_outputs | 11 mkdir stacks_outputs |
12 | 12 |
13 && | 13 && |
14 | 14 |
15 #for $input_file in $input_col: | 15 #for $input_file in $input_col |
16 #set $filename = str($input_file.element_identifier) | 16 #set $filename = str($input_file.element_identifier) |
17 #if not $filename.endswith('.tsv'): | 17 #if not $filename.endswith('.tsv') |
18 #set $filename = $filename + ".tsv" | 18 #set $filename = $filename + ".tsv" |
19 #end if | 19 #end if |
20 #if re.search('\.(tags|snps|alleles|matches)(\.tsv)?$', $filename): | 20 #if re.search('\.(tags|snps|alleles|matches)(\.tsv)?$', $filename) |
21 ln -s "${input_file}" "stacks_outputs/${filename}" && | 21 ln -s '${input_file}' 'stacks_outputs/${filename}' && |
22 #end if | 22 #end if |
23 #end for | 23 #end for |
24 | 24 |
25 genotypes | 25 genotypes |
26 | 26 |
28 -b $advanced_options.batchid | 28 -b $advanced_options.batchid |
29 | 29 |
30 -t $options_usage.cross_type | 30 -t $options_usage.cross_type |
31 -o $options_usage.map_out.map_out_type | 31 -o $options_usage.map_out.map_out_type |
32 | 32 |
33 #if str( $options_usage.map_out.map_out_type ) == "genomic": | 33 #if str( $options_usage.map_out.map_out_type ) == "genomic" |
34 -e ${options_usage.map_out.enzyme} | 34 -e ${options_usage.map_out.enzyme} |
35 #end if | 35 #end if |
36 | 36 |
37 #if str($advanced_options.minprogeny): | 37 #if str($advanced_options.minprogeny) |
38 -r $advanced_options.minprogeny | 38 -r $advanced_options.minprogeny |
39 #end if | 39 #end if |
40 | 40 |
41 #if str($advanced_options.mindepth): | 41 #if str($advanced_options.mindepth) |
42 -m $advanced_options.mindepth | 42 -m $advanced_options.mindepth |
43 #end if | 43 #end if |
44 | 44 |
45 #if str($advanced_options.lnl): | 45 #if str($advanced_options.lnl) |
46 --lnl_lim $advanced_options.lnl | 46 --lnl_lim $advanced_options.lnl |
47 #end if | 47 #end if |
48 | 48 |
49 #if $advanced_options.blacklist: | 49 #if $advanced_options.blacklist |
50 -B "$advanced_options.blacklist" | 50 -B '$advanced_options.blacklist' |
51 #end if | 51 #end if |
52 #if $advanced_options.whitelist: | 52 #if $advanced_options.whitelist |
53 -W "$advanced_options.whitelist" | 53 -W '$advanced_options.whitelist' |
54 #end if | 54 #end if |
55 | 55 |
56 #if $advanced_options.manual_cor: | 56 #if $advanced_options.manual_cor |
57 --corr_path "$advanced_options.manual_cor" | 57 --corr_path '$advanced_options.manual_cor' |
58 #end if | 58 #end if |
59 | 59 |
60 #if $options_autocorr.corrections: | 60 #if $options_autocorr.corrections |
61 -c | 61 -c |
62 --min_hom_seqs $options_autocorr.hom | 62 --min_hom_seqs $options_autocorr.hom |
63 --min_het_seqs $options_autocorr.het | 63 --min_het_seqs $options_autocorr.het |
64 --max_het_seqs $options_autocorr.hetmax | 64 --max_het_seqs $options_autocorr.hetmax |
65 #end if | 65 #end if |
66 | 66 |
67 ## output SQL file (as denovo/refmap) | 67 ## output SQL file (as denovo/refmap) |
68 -s | 68 -s |
69 | 69 |
70 @NORM_GENOTYPES_OUTPUT_FULL@ | 70 @NORM_GENOTYPES_OUTPUT_FULL@ |
71 | |
72 && | |
73 | |
74 stacks_summary.py --stacks-prog genotypes --res-dir stacks_outputs --summary stacks_outputs/summary.html | |
71 ]]></command> | 75 ]]></command> |
72 <inputs> | 76 <inputs> |
73 <param name="input_col" format="tabular,txt" type="data_collection" collection_type="list" label="Output from previous Stacks pipeline steps (e.g. denovo_map or refmap)" /> | 77 <param name="input_col" format="tabular,txt" type="data_collection" collection_type="list" label="Output from previous Stacks pipeline steps (e.g. denovo_map or refmap)" /> |
74 | 78 |
75 <section name="options_usage" title="Genotyping options"> | 79 <section name="options_usage" title="Genotyping options"> |
83 <option value="joinmap">JoinMap</option> | 87 <option value="joinmap">JoinMap</option> |
84 <option value="onemap">OneMap</option> | 88 <option value="onemap">OneMap</option> |
85 <option value="rqtl">R/QTL</option> | 89 <option value="rqtl">R/QTL</option> |
86 <option value="genomic">Genomic</option> | 90 <option value="genomic">Genomic</option> |
87 </param> | 91 </param> |
92 <when value="joinmap"/> | |
93 <when value="onemap"/> | |
94 <when value="rqtl"/> | |
88 <when value="genomic"> | 95 <when value="genomic"> |
89 <param name="enzyme" argument="-e" type="select" label="Restriction enzyme used" help="Only needed for Genomic output format"> | 96 <param name="enzyme" argument="-e" type="select" label="Restriction enzyme used" help="Only needed for Genomic output format"> |
90 <expand macro="enzymes"/> | 97 <expand macro="enzymes"/> |
91 </param> | 98 </param> |
92 </when> | 99 </when> |
118 <param name="batchid" type="integer" value="1" label="Batch ID to examine when exporting from the catalog" help="Only useful if you analyse data that was processed outside galaxy" /> | 125 <param name="batchid" type="integer" value="1" label="Batch ID to examine when exporting from the catalog" help="Only useful if you analyse data that was processed outside galaxy" /> |
119 </section> | 126 </section> |
120 </inputs> | 127 </inputs> |
121 <outputs> | 128 <outputs> |
122 <expand macro="genotypes_output_full"/> | 129 <expand macro="genotypes_output_full"/> |
130 | |
131 <data format="html" name="output_summary" label="Summary from ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/summary.html" /> | |
123 </outputs> | 132 </outputs> |
124 | 133 |
125 <tests> | 134 <tests> |
126 <test> | 135 <test> |
127 <param name="input_col"> | 136 <param name="input_col"> |
141 </param> | 150 </param> |
142 <param name="map_out_type" value="joinmap" /> | 151 <param name="map_out_type" value="joinmap" /> |
143 <param name="cross_type" value="CP" /> | 152 <param name="cross_type" value="CP" /> |
144 <param name="advanced_options|minprogeny" value="1" /> | 153 <param name="advanced_options|minprogeny" value="1" /> |
145 | 154 |
155 <output name="output_summary"> | |
156 <assert_contents> | |
157 <has_text text="Stacks Statistics" /> | |
158 </assert_contents> | |
159 </output> | |
160 | |
146 <!-- genotypes --> | 161 <!-- genotypes --> |
147 <output name="out_generic_haplo"> | 162 <output name="out_generic_haplo"> |
148 <assert_contents> | 163 <assert_contents> |
149 <has_text text="Catalog ID" /> | 164 <has_text text="Catalog ID" /> |
150 </assert_contents> | 165 </assert_contents> |