annotate stacks_refmap.xml @ 1:eea53e013f9e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 64069b03d33644632275cb79a017f5425323c75e
author iuc
date Wed, 15 Jun 2016 05:40:54 -0400
parents 66d3c1ae3937
children 26ad8a52d9fd
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1 <tool id="stacks_refmap" name="Stacks: reference map" version="@WRAPPER_VERSION@.0">
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2 <description>the Stacks pipeline with a reference genome (ref_map.pl)</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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9 #from os.path import splitext
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10 #import re
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11
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12 #if str( $options_usage.rad_analysis_type ) == "genetic":
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13 #for $input_parent in $options_usage.parent_alignments:
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14 #if $input_parent.ext == "sam":
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15 #set $data_path = splitext($input_parent.name)[0]
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16 #set $data_path = re.sub(r'\.1$', '', $data_path)
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17 #set $data_path = $data_path + ".sam"
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18 #else:
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19 #set $data_path = splitext($input_parent.name)[0]
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20 #set $data_path = re.sub(r'\.1$', '', $data_path)
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21 #set $data_path = $data_path + ".bam"
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22 #end if
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23
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24 ln -s "${input_parent}" "${data_path}" &&
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25 #end for
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26
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27 #for $input_progeny in $options_usage.progeny_alignments:
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28
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29 #if $input_progeny.ext == "sam":
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30 #set $data_path = splitext($input_progeny.name)[0]
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31 #set $data_path = re.sub(r'\.1$', '', $data_path)
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32 #set $data_path = $data_path + ".sam"
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33 #else:
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34 #set $data_path = splitext($input_progeny.name)[0]
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35 #set $data_path = re.sub(r'\.1$', '', $data_path)
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36 #set $data_path = $data_path + ".bam"
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37 #end if
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38
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39 ln -s "${input_progeny}" "${data_path}" &&
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40 #end for
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41 #else:
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42 #for $input_indiv in $options_usage.individual_sample:
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43
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44 #if $input_indiv.ext == "sam":
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45 #set $data_path = splitext($input_indiv.name)[0]
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46 #set $data_path = re.sub(r'\.1$', '', $data_path)
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47 #set $data_path = $data_path + ".sam"
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48 #else:
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49 #set $data_path = splitext($input_indiv.name)[0]
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50 #set $data_path = re.sub(r'\.1$', '', $data_path)
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51 #set $data_path = $data_path + ".bam"
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52 #end if
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53
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54 ln -s "${input_indiv}" "${data_path}" &&
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55 #end for
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56 #end if
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57
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58 mkdir stacks_outputs
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59
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60 &&
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61
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62 ref_map.pl
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63
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64 -T \${GALAXY_SLOTS:-1}
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65
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66 #if str( $options_usage.rad_analysis_type ) == "genetic":
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67 #for $input_parent in $options_usage.parent_alignments:
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68 #if $input_parent.ext == "sam":
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69 #set $data_path = splitext($input_parent.name)[0]
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70 #set $data_path = re.sub(r'\.1$', '', $data_path)
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71 #set $data_path = $data_path + ".sam"
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72 #else:
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73 #set $data_path = splitext($input_parent.name)[0]
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74 #set $data_path = re.sub(r'\.1$', '', $data_path)
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75 #set $data_path = $data_path + ".bam"
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76 #end if
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77
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78 -p "${data_path}"
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79 #end for
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80
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81 -A $options_usage.cross_type
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82
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83 #for $input_progeny in $options_usage.progeny_alignments:
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84 #if $input_progeny.ext == "sam":
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85 #set $data_path = splitext($input_progeny.name)[0]
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86 #set $data_path = re.sub(r'\.1$', '', $data_path)
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87 #set $data_path = $data_path + ".sam"
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88 #else:
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89 #set $data_path = splitext($input_progeny.name)[0]
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90 #set $data_path = re.sub(r'\.1$', '', $data_path)
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91 #set $data_path = $data_path + ".bam"
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92 #end if
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93
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94 -r "${data_path}"
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95 #end for
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96 #else:
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97 #for $input_indiv in $options_usage.individual_sample:
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98
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99 #if $input_indiv.ext == "sam":
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100 #set $data_path = splitext($input_indiv.name)[0]
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101 #set $data_path = re.sub(r'\.1$', '', $data_path)
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102 #set $data_path = $data_path + ".sam"
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103 #else:
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104 #set $data_path = splitext($input_indiv.name)[0]
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105 #set $data_path = re.sub(r'\.1$', '', $data_path)
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106 #set $data_path = $data_path + ".bam"
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107 #end if
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108
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109 -s "${data_path}"
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110 #end for
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111 -O "$options_usage.popmap"
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112 #end if
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113
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114 #if str($m):
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115 -m $m
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116 #end if
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117 #if str($P):
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118 -P $P
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119 #end if
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120
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121 ## Batch description
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122 -b 1
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123
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124 ## No SQL recording
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125 -S
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126
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127 ## snp_model
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128 #if str( $snp_options.select_model.model_type) == "bounded":
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129 --bound_low $snp_options.select_model.bound_low
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130 --bound_high $snp_options.select_model.bound_high
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131 --alpha $snp_options.select_model.alpha
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132 #else if str( $snp_options.select_model.model_type) == "snp":
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133 --alpha $snp_options.select_model.alpha
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134 #end if
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135
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136 -o stacks_outputs
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137
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138 #if str( $options_usage.rad_analysis_type ) == "genetic":
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139 @NORM_GENOTYPES_OUTPUT_LIGHT@
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140 #end if
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141
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142 ## If input is in bam format, stacks will output gzipped files (no option to control this)
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143 && gunzip stacks_outputs/*.gz
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144 ]]></command>
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145
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146 <inputs>
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147 <conditional name="options_usage">
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148 <param name="rad_analysis_type" type="select" label="Select your usage">
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149 <option value="genetic" selected="true">Genetic map</option>
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150 <option value="population">Population</option>
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151 </param>
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152 <when value="genetic">
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153 <param name="parent_alignments" format="sam,bam" type="data" multiple="true" label="Files containing parent alignments" argument="-p" />
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154 <param name="progeny_alignments" format="sam,bam" type="data" multiple="true" optional="true" label="Files containing progeny alignments" argument="-r" />
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155
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156 <param name="cross_type" argument="-A" type="select" label="Cross type">
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157 <expand macro="cross_types"/>
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158 </param>
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159 </when>
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160 <when value="population">
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161 <param name="individual_sample" format="sam,bam" type="data" multiple="true" label="Files containing an individual sample from a population" argument="-s" />
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162 <param name="popmap" type="data" format="tabular,txt" label="Specify a population map" argument="-O" />
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163 </when>
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164 </conditional>
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165
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166 <param name="m" type="integer" value="3" label="Minimum depth of coverage" help="specify the minimum depth of coverage to report a stack in pstacks" argument="-m" />
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167 <param name="P" type="integer" value="" optional="true" label="Minimum depth of coverage in 'progeny' individuals" help="specify the minimum depth of coverage to report a stack in pstacks for 'progeny' individuals" argument="-P" />
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168
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169 <!-- SNP Model options -->
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170 <section name="snp_options" title="SNP_Model_Options" expanded="False">
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171 <expand macro="snp_options"/>
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172 </section>
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173 </inputs>
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174 <outputs>
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175 <data format="txt" name="output_log" label="ref_map.log with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/ref_map.log" />
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176
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177 <data format="tabular" name="catalogtags" label="Catalog assembled loci (tags) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.tags.tsv" />
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178 <data format="tabular" name="catalogsnps" label="Catalog model calls (snps) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.snps.tsv" />
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179 <data format="tabular" name="catalogalleles" label="Catalog haplotypes (alleles) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.alleles.tsv" />
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180
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181 <expand macro="genotypes_output_light"/>
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182 <expand macro="populations_output_light"/>
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183
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184 <collection name="tags" type="list" label="Assembled loci (tags) from ${on_string}">
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185 <discover_datasets pattern="(?P&lt;name&gt;.+\.tags)\.tsv" ext="tabular" directory="stacks_outputs" />
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186 </collection>
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187
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188 <collection name="snps" type="list" label="Model calls (snps) from each locus on ${on_string}">
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189 <discover_datasets pattern="(?P&lt;name&gt;.+\.snps)\.tsv" ext="tabular" directory="stacks_outputs" />
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190 </collection>
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191
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192 <collection name="alleles" type="list" label="Haplotypes (alleles) recorded from each locus on ${on_string}">
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193 <discover_datasets pattern="(?P&lt;name&gt;.+\.alleles)\.tsv" ext="tabular" directory="stacks_outputs" />
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194 </collection>
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195
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196 <collection name="matches" type="list" label="Matches to the catalog on ${on_string}">
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197 <discover_datasets pattern="(?P&lt;name&gt;.+\.matches)\.tsv" ext="tabular" directory="stacks_outputs" />
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198 </collection>
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199
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200 <collection name="all_output" type="list" label="Full output from ref_map on ${on_string}">
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201 <discover_datasets pattern="(?P&lt;name&gt;.+\.(tags|snps|alleles|matches))\.tsv" ext="tabular" directory="stacks_outputs" />
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202 <discover_datasets pattern="(?P&lt;name&gt;.+\.(haplotypes|genotypes|markers|hapstats|sumstats|sumstats_summary))\.tsv" ext="tabular" directory="stacks_outputs" />
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203 <discover_datasets pattern="(?P&lt;name&gt;.+\.(genotypes))\.(loc|txt)" ext="txt" directory="stacks_outputs" />
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204 </collection>
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205 </outputs>
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206
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207 <tests>
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208 <test>
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209 <param name="options_usage|rad_analysis_type" value="genetic"/>
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210 <param name="options_usage|parent_alignments" value="refmap/PopA_01.bam" />
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211 <param name="options_usage|progeny_alignments" value="refmap/PopA_02.bam" />
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212 <output name="output_log">
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213 <assert_contents>
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214 <has_text text="ref_map.pl completed" />
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215 </assert_contents>
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216 </output>
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217
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218 <!-- catalog -->
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219 <output name="catalogsnps">
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220 <assert_contents>
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221 <has_text text="catalog generated" />
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222 </assert_contents>
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223 </output>
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224 <output name="catalogalleles">
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225 <assert_contents>
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226 <has_text text="catalog generated" />
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227 </assert_contents>
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228 </output>
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229 <output name="catalogtags">
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230 <assert_contents>
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231 <has_text text="catalog generated" />
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232 </assert_contents>
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233 </output>
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234
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235 <!-- genotypes -->
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236 <output name="out_generic_haplo">
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237 <assert_contents>
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238 <has_text text="Catalog ID" />
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239 </assert_contents>
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240 </output>
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241 <output name="out_sql_markers">
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242 <assert_contents>
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243 <has_text text="Total Genotypes" />
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244 </assert_contents>
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245 </output>
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246 <output name="out_joinmap">
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247 <assert_contents>
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248 <has_text text="batch_1.genotypes_" />
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249 </assert_contents>
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250 </output>
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251 <output name="out_sql_genotypes">
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252 <assert_contents>
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253 <has_text text="SQL ID" />
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254 </assert_contents>
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255 </output>
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256 <output name="out_generic_haplo">
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257 <assert_contents>
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258 <has_text text="Seg Dist" />
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259 </assert_contents>
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260 </output>
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261 <output name="out_sql_markers">
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262 <assert_contents>
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263 <has_text text="Total Genotypes" />
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264 </assert_contents>
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265 </output>
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iuc
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diff changeset
266
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
267 <!-- samples -->
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
268 <output_collection name="tags">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
269 <element name="PopA_01.tags">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
270 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
271 <has_text text="generated on " />
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
272 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
273 </element>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
274 </output_collection>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
275 <output_collection name="snps">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
276 <element name="PopA_01.snps">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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diff changeset
277 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
278 <has_text text="generated on " />
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
279 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
280 </element>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
281 </output_collection>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
282 <output_collection name="alleles">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
283 <element name="PopA_01.alleles">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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diff changeset
284 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
285 <has_text text="generated on " />
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
286 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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diff changeset
287 </element>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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288 </output_collection>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
289 <output_collection name="matches">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
290 <element name="PopA_01.matches">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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diff changeset
291 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
292 <has_text text="generated on " />
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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293 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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diff changeset
294 </element>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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295 </output_collection>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
296 </test>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
297 <test>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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diff changeset
298 <param name="options_usage|rad_analysis_type" value="population"/>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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299 <param name="options_usage|individual_sample" value="refmap/PopA_01.bam,refmap/PopA_02.bam,refmap/PopA_03.bam,refmap/PopA_04.bam,refmap/PopB_01.bam,refmap/PopB_02.bam,refmap/PopB_03.bam,refmap/PopB_04.bam" />
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
300 <param name="options_usage|popmap" value="denovo_map/popmap.tsv" />
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
301 <output name="output_log">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
302 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
303 <has_text text="ref_map.pl completed" />
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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diff changeset
304 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
305 </output>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
306
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
307 <!-- catalog -->
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
308 <output name="catalogtags">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
309 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
310 <has_text text="catalog generated on" />
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
311 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
312 </output>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
313 <output name="catalogsnps">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
314 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
315 <has_text text="catalog generated on" />
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
316 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
317 </output>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
318 <output name="catalogalleles">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
319 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
320 <has_text text="catalog generated on" />
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
321 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
322 </output>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
323
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
324 <!-- populations -->
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
325 <output name="out_haplotypes">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
326 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
327 <has_text text="PopA_01" />
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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diff changeset
328 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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diff changeset
329 </output>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
330 <output name="out_hapstats">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
331 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
332 <has_text text="Smoothed Gene Diversity" />
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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diff changeset
333 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
334 </output>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
335 <output name="out_populations_log">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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336 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
337 <has_text text="populations version" />
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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338 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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diff changeset
339 </output>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
340 <output name="out_sumstats_sum">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
341 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
342 <has_text text="Polymorphic Sites" />
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
343 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
344 </output>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
345 <output name="out_sumstats">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
346 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
347 <has_text text="Smoothed Pi" />
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
348 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
349 </output>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
350
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
351 <!-- samples -->
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
352 <output_collection name="tags">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
353 <element name="PopA_01.tags">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
354 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
355 <has_text text="generated on " />
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
356 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
357 </element>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
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358 </output_collection>
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359 <output_collection name="snps">
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360 <element name="PopA_01.snps">
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361 <assert_contents>
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362 <has_text text="generated on " />
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363 </assert_contents>
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364 </element>
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365 </output_collection>
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366 <output_collection name="alleles">
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367 <element name="PopA_01.alleles">
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368 <assert_contents>
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369 <has_text text="generated on " />
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370 </assert_contents>
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371 </element>
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372 </output_collection>
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373 <output_collection name="matches">
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374 <element name="PopA_01.matches">
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375 <assert_contents>
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376 <has_text text="generated on " />
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377 </assert_contents>
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378 </element>
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379 </output_collection>
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380 </test>
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381 </tests>
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382
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383 <help>
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384 <![CDATA[
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385 .. class:: infomark
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386
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387 **What it does**
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388
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389 This program expects data that have been aligned to a reference genome, and can accept data directly from Bowtie, or from any aligner that can produce SAM format. To avoid datasets names problems, we recommand the use of the *Map with BWA for STACKS tool*. This program will execute each of the Stacks components: first, running pstacks on each of the samples specified, building loci (based on the reference alignment) and calling SNPs in each. Second, cstacks will be run to create a catalog of all loci specified as 'parents' or 'samples' on the command line, again using alignment to match loci in the catalog. Finally, sstacks will be executed to match each sample against the catalog. The ref_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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390
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391 --------
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392
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393 **Input files**
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394
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395 - SAM, BAM
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396
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397 - Population map::
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398
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399 indv_01 1
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400 indv_02 1
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401 indv_03 1
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402 indv_04 2
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403 indv_05 2
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404 indv_06 2
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405
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406 **Output files**
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407
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408 - XXX.tags.tsv file:
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409
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410 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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411
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412 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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413
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414
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415 - XXX.snps.tsv file:
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416
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417 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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418
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419 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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420
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421
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422 - XXX.alleles.tsv file:
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423
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424 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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425
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426
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427 - XXX.matches.tsv file:
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428
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429 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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430
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431 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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432
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433
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434 - other files:
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435
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436 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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437
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438 @STACKS_INFOS@
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439 ]]>
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440 </help>
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441 <expand macro="citation" />
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442 </tool>