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 |
|---|---|
| date | Thu, 27 Apr 2017 04:19:10 -0400 |
| parents | 969a09779e3c |
| children | 00f4a4e553ae |
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| 7:639f2db87df0 | 8:8dc6a3afbe83 |
|---|---|
| 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> |