Mercurial > repos > iuc > stacks_rxstacks

annotate stacks_rxstacks.xml @ 5:73dce6ae6b7f 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 04:16:18 -0400
parents 01414bf05198
children 571245acc8a4
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1 <tool id="stacks_rxstacks" name="Stacks: rxstacks" version="@WRAPPER_VERSION@.0">
0
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2 <description>make corrections to genotype and haplotype calls</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8 <command><![CDATA[
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10 mkdir stacks_inputs stacks_outputs
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12 &&
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5
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14 #for $input_file in $input_col
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15 #set $ext = ""
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16 #if not str($input_file.element_identifier).endswith('.tsv')
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17 #set $ext = ".tsv"
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18 #end if
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19 ln -s '${input_file}' 'stacks_inputs/${input_file.element_identifier}${ext}' &&
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20 #end for
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22 rxstacks
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24 -t \${GALAXY_SLOTS:-1}
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26 -P stacks_inputs
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27
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28 ## Batch description
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29 -b 1
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30
5
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31 #if str($options_filtering.lnl)
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32 --lnl_filter
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33 --lnl_lim $options_filtering.lnl
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34 #end if
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35
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36 $options_filtering.lnl_dist
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37
5
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38 #if str($options_filtering.conf)
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39 --conf_filter
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40 --conf_lim $options_filtering.conf
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41 #end if
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42
5
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43 #if $options_filtering.prune.prune_haplo == "yes"
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44 --prune_haplo
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45 #if str($options_filtering.prune.max_haplo)
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46 --max_haplo $options_filtering.prune.max_haplo
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47 #end if
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48 #end if
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49
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50 ## snp_model
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51 #if str( $snp_options.select_model.model_type) == "bounded"
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52 --model_type bounded
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53 --bound_low $snp_options.select_model.bound_low
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54 --bound_high $snp_options.select_model.bound_high
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55 --alpha $snp_options.select_model.alpha
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56 #else if str( $snp_options.select_model.model_type) == "snp"
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57 --model_type snp
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58 --alpha $snp_options.select_model.alpha
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59 #else
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60 --model_type fixed
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61 #end if
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62
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63 -o stacks_outputs
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64 ]]></command>
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65
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66 <inputs>
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67 <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)" />
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68
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69 <section name="options_filtering" title="Data filtering options" expanded="true">
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70 <param name="lnl" type="float" value="" optional="true" argument="--lnl_lim" label="Filter loci with log likelihood values below this threshold" />
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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." />
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72
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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)."/>
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74
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75 <conditional name="prune">
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76 <param name="prune_haplo" argument="--prune_haplo" type="select" label="Prune out non-biological haplotypes unlikely to occur in the population.">
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77 <option value="no" selected="true">No</option>
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78 <option value="yes">Yes</option>
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79 </param>
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80 <when value="no"/>
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81 <when value="yes">
0
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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."/>
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83 </when>
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84 </conditional>
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85 </section>
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86
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87 <!-- SNP Model options -->
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88 <section name="snp_options" title="SNP Model Options (ustacks options)" expanded="False">
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89 <expand macro="snp_options"/>
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90 </section>
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91 </inputs>
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92
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93 <outputs>
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94 <data format="txt" name="output_log" label="rxstacks.log with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.rxstacks.log" />
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95
caf3e2905cf3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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96 <data format="txt" name="output_lnl_dist" label="Distribution of mean log likelihoods with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.rxstacks_lnls.tsv">
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97 <filter>options_filtering['lnl_dist']</filter>
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98 </data>
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99
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100 <collection name="tags" type="list" label="Assembled loci filtered from ${on_string}">
caf3e2905cf3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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101 <discover_datasets pattern="(?P&lt;name&gt;.+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs" />
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102 </collection>
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103
caf3e2905cf3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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104 <collection name="snps" type="list" label="Model calls from each locus filtered from ${on_string}">
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105 <discover_datasets pattern="(?P&lt;name&gt;.+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs" />
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106 </collection>
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107
caf3e2905cf3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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108 <collection name="alleles" type="list" label="Haplotypes/alleles recorded from each locus filtered from ${on_string}">
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109 <discover_datasets pattern="(?P&lt;name&gt;.+\.alleles)\.tsv$" ext="tabular" directory="stacks_outputs" />
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110 </collection>
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111
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112 <collection name="all_output" type="list" label="Full output from rxstacks on ${on_string}">
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113 <discover_datasets pattern="(?P&lt;name&gt;.+\.(tags|snps|alleles))\.tsv$" ext="tabular" directory="stacks_outputs" />
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114 </collection>
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115 </outputs>
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116
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117 <tests>
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118 <test>
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119 <param name="input_col">
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120 <collection type="list">
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121 <element name="batch_1.catalog.alleles.tsv" ftype="tabular" value="genotypes/batch_1.catalog.alleles.tsv" />
caf3e2905cf3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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122 <element name="batch_1.catalog.snps.tsv" ftype="tabular" value="genotypes/batch_1.catalog.snps.tsv" />
caf3e2905cf3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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123 <element name="batch_1.catalog.tags.tsv" ftype="tabular" value="genotypes/batch_1.catalog.tags.tsv" />
caf3e2905cf3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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124 <element name="PopA_01.alleles.tsv" ftype="tabular" value="genotypes/PopA_01.alleles.tsv" />
caf3e2905cf3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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125 <element name="PopA_01.matches.tsv" ftype="tabular" value="genotypes/PopA_01.matches.tsv" />
caf3e2905cf3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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126 <element name="PopA_01.snps.tsv" ftype="tabular" value="genotypes/PopA_01.snps.tsv" />
caf3e2905cf3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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127 <element name="PopA_01.tags.tsv" ftype="tabular" value="genotypes/PopA_01.tags.tsv" />
caf3e2905cf3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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128 <element name="PopA_02.alleles.tsv" ftype="tabular" value="genotypes/PopA_02.alleles.tsv" />
caf3e2905cf3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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129 <element name="PopA_02.matches.tsv" ftype="tabular" value="genotypes/PopA_02.matches.tsv" />
caf3e2905cf3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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130 <element name="PopA_02.snps.tsv" ftype="tabular" value="genotypes/PopA_02.snps.tsv" />
caf3e2905cf3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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131 <element name="PopA_02.tags.tsv" ftype="tabular" value="genotypes/PopA_02.tags.tsv" />
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132 </collection>
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133 </param>
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134 <param name="options_filtering|lnl" value="-10.0" />
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135 <param name="options_filtering|lnl_dist" value="true" />
5
73dce6ae6b7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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136 <param name="options_filtering|prune_haplo" value="yes" />
0
caf3e2905cf3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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137 <param name="options_filtering|max_haplo" value="1" />
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138
caf3e2905cf3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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139 <output name="output_log">
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140 <assert_contents>
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141 <has_text text="rxstacks executed" />
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142 </assert_contents>
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143 </output>
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144
caf3e2905cf3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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145 <output name="output_lnl_dist">
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146 <assert_contents>
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147 <has_text text="Median" />
caf3e2905cf3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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148 </assert_contents>
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149 </output>
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150
caf3e2905cf3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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151 <!-- samples -->
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152 <output_collection name="tags">
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153 <element name="PopA_01.tags">
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154 <assert_contents>
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155 <has_text text="lane1_fakedata7_0" />
caf3e2905cf3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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156 </assert_contents>
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157 </element>
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158 </output_collection>
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159 <output_collection name="snps">
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160 <element name="PopA_01.snps">
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161 <assert_contents>
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162 <has_text text="24.950" />
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163 </assert_contents>
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164 </element>
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165 </output_collection>
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166 <output_collection name="alleles">
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167 <element name="PopA_01.alleles">
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168 <assert_contents>
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169 <has_text text="AC" />
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170 </assert_contents>
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171 </element>
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172 </output_collection>
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173 </test>
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174 </tests>
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175
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176 <help>
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177 <![CDATA[
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178 .. class:: infomark
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179
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180 **What it does**
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181
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182 This program will run each of the Stacks components: first, running ustacks on each of the samples specified, building loci and calling SNPs in each. Second, cstacks will be run to create a catalog of all loci that were marked as 'parents' or 'samples' on the command line, and finally, sstacks will be executed to match each sample against the catalog. A bit more detail on this process can be found in the FAQ. The denovo_map.pl program will also load the results of each stage of the analysis: individual loci, the catalog, and matches against the catalog into the database (although this can be disabled). After matching, the program will build a database index to speed up access (index_radtags.pl) and enable web-based filtering.
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183
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184 --------
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185
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186 **Input files**
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187
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188 Output from denovo_map or ref_map
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189
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190 **Output files**
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191
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192 - XXX.tags.tsv file:
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193
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194 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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195
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196 Notes: For the tags file, each stack will start in the file with a consensus sequence for the entire stack followed by the flags for that stack. Then, each individual read that was merged into that stack will follow. The next stack will start with another consensus sequence.
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197
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198
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199 - XXX.snps.tsv file:
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200
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201 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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202
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203 Notes: If a stack has two SNPs called within it, then there will be two lines in this file listing each one.
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204
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205
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206 - XXX.alleles.tsv file:
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207
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208 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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209
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210 - XXX.matches.tsv file:
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211
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212 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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213
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214 Notes: Each line in this file records a match between a catalog locus and a locus in an individual, for a particular haplotype. The Batch ID plus the Catalog ID together represent a unique locus in the entire population, while the Sample ID and the Stack ID together represent a unique locus in an individual sample.
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215
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216 @STACKS_INFOS@
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217 ]]>
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218 </help>
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219 <expand macro="citation" />
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220 </tool>