Mercurial > repos > iuc > stacks_refmap

annotate stacks_refmap.xml @ 5:12aa3ad29980 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 9401451df4a985ef5686864eaadafa077ffc0877
author iuc
date Mon, 27 Feb 2017 05:44:36 -0500
parents 827c8c6ec4c1
children c209e3f3359b
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827c8c6ec4c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
iuc
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1 <tool id="stacks_refmap" name="Stacks: reference map" version="@WRAPPER_VERSION@.0">
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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12aa3ad29980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 9401451df4a985ef5686864eaadafa077ffc0877
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14 #if $input_parent.is_of_type('sam'):
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15 #set $data_path = splitext($input_parent.element_identifier)[0]
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.element_identifier)[0]
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20 #set $data_path = re.sub(r'\.1$', '', $data_path)
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21 #set $data_path = $data_path + ".bam"
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22 #end if
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24 ln -s "${input_parent}" "${data_path}" &&
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25 #end for
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27 #for $input_progeny in $options_usage.progeny_alignments:
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28
3
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29 #if $input_progeny:
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30 #if $input_progeny.is_of_type('sam'):
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31 #set $data_path = splitext($input_progeny.element_identifier)[0]
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32 #set $data_path = re.sub(r'\.1$', '', $data_path)
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33 #set $data_path = $data_path + ".sam"
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34 #else:
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35 #set $data_path = splitext($input_progeny.element_identifier)[0]
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36 #set $data_path = re.sub(r'\.1$', '', $data_path)
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37 #set $data_path = $data_path + ".bam"
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38 #end if
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39
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40 ln -s "${input_progeny}" "${data_path}" &&
0
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41 #end if
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42 #end for
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43 #else:
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44 #for $input_indiv in $options_usage.individual_sample:
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45
5
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46 #if $input_indiv.is_of_type('sam'):
3
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47 #set $data_path = splitext($input_indiv.element_identifier)[0]
0
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48 #set $data_path = re.sub(r'\.1$', '', $data_path)
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49 #set $data_path = $data_path + ".sam"
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50 #else:
3
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51 #set $data_path = splitext($input_indiv.element_identifier)[0]
0
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52 #set $data_path = re.sub(r'\.1$', '', $data_path)
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53 #set $data_path = $data_path + ".bam"
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54 #end if
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56 ln -s "${input_indiv}" "${data_path}" &&
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57 #end for
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58 #end if
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60 mkdir stacks_outputs
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62 &&
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64 ref_map.pl
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65
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66 -T \${GALAXY_SLOTS:-1}
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67
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68 #if str( $options_usage.rad_analysis_type ) == "genetic":
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69 #for $input_parent in $options_usage.parent_alignments:
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70 #if $input_parent.is_of_type('sam'):
3
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71 #set $data_path = splitext($input_parent.element_identifier)[0]
0
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72 #set $data_path = re.sub(r'\.1$', '', $data_path)
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73 #set $data_path = $data_path + ".sam"
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74 #else:
3
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75 #set $data_path = splitext($input_parent.element_identifier)[0]
0
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76 #set $data_path = re.sub(r'\.1$', '', $data_path)
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77 #set $data_path = $data_path + ".bam"
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78 #end if
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80 -p "${data_path}"
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81 #end for
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83 -A $options_usage.cross_type
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84
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85 #for $input_progeny in $options_usage.progeny_alignments:
3
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86 #if $input_progeny:
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87 #if $input_progeny.is_of_type('sam'):
3
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88 #set $data_path = splitext($input_progeny.element_identifier)[0]
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89 #set $data_path = re.sub(r'\.1$', '', $data_path)
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90 #set $data_path = $data_path + ".sam"
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91 #else:
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92 #set $data_path = splitext($input_progeny.element_identifier)[0]
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93 #set $data_path = re.sub(r'\.1$', '', $data_path)
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94 #set $data_path = $data_path + ".bam"
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95 #end if
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96
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97 -r "${data_path}"
0
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98 #end if
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99 #end for
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100 #else:
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101 #for $input_indiv in $options_usage.individual_sample:
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102
5
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103 #if $input_indiv.is_of_type('sam'):
3
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104 #set $data_path = splitext($input_indiv.element_identifier)[0]
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 + ".sam"
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107 #else:
3
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108 #set $data_path = splitext($input_indiv.element_identifier)[0]
0
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109 #set $data_path = re.sub(r'\.1$', '', $data_path)
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110 #set $data_path = $data_path + ".bam"
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111 #end if
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112
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113 -s "${data_path}"
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114 #end for
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115 -O "$options_usage.popmap"
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116 #end if
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117
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118 #if str($m):
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119 -m $m
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120 #end if
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121 #if str($P):
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122 -P $P
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123 #end if
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124
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125 ## Batch description
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126 -b 1
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127
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128 ## No SQL recording
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129 -S
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130
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131 ## snp_model
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132 #if str( $snp_options.select_model.model_type) == "bounded":
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133 --bound_low $snp_options.select_model.bound_low
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134 --bound_high $snp_options.select_model.bound_high
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135 --alpha $snp_options.select_model.alpha
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136 #else if str( $snp_options.select_model.model_type) == "snp":
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137 --alpha $snp_options.select_model.alpha
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138 #end if
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139
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140 -o stacks_outputs
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141
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142 #if str( $options_usage.rad_analysis_type ) == "genetic":
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143 @NORM_GENOTYPES_OUTPUT_LIGHT@
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144 #end if
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145
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146 ## If input is in bam format, stacks will output gzipped files (no option to control this)
3
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147 && if ls stacks_outputs/*.gz > /dev/null 2>&1; then gunzip stacks_outputs/*.gz; fi
0
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148 ]]></command>
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149
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150 <inputs>
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151 <conditional name="options_usage">
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152 <param name="rad_analysis_type" type="select" label="Select your usage">
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153 <option value="genetic" selected="true">Genetic map</option>
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154 <option value="population">Population</option>
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155 </param>
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156 <when value="genetic">
3
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157 <param name="parent_alignments" format="sam,bam" type="data" multiple="true" label="Files containing parent alignments" argument="-p" help="Dataset names will be used as sample name (no space allowed)." />
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158 <param name="progeny_alignments" format="sam,bam" type="data" multiple="true" optional="true" label="Files containing progeny alignments" argument="-r" help="Dataset names will be used as sample name (no space allowed)." />
0
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159
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160 <param name="cross_type" argument="-A" type="select" label="Cross type">
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161 <expand macro="cross_types"/>
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162 </param>
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163 </when>
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164 <when value="population">
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165 <param name="individual_sample" format="sam,bam" type="data" multiple="true" label="Files containing an individual sample from a population" argument="-s" help="Dataset names will be used as sample name (no space allowed)." />
0
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166 <param name="popmap" type="data" format="tabular,txt" label="Specify a population map" argument="-O" />
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167 </when>
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168 </conditional>
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169
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170 <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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171 <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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172
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173 <!-- SNP Model options -->
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174 <section name="snp_options" title="SNP_Model_Options" expanded="False">
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175 <expand macro="snp_options"/>
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176 </section>
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177 </inputs>
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178 <outputs>
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179 <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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180
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181 <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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182 <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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183 <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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184
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185 <expand macro="genotypes_output_light"/>
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186 <expand macro="populations_output_light"/>
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187
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188 <collection name="tags" type="list" label="Assembled loci (tags) from ${on_string}">
3
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189 <discover_datasets pattern="(?P&lt;name&gt;.+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs" />
0
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190 </collection>
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191
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192 <collection name="snps" type="list" label="Model calls (snps) from each locus on ${on_string}">
3
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193 <discover_datasets pattern="(?P&lt;name&gt;.+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs" />
0
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194 </collection>
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195
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196 <collection name="alleles" type="list" label="Haplotypes (alleles) recorded from each locus on ${on_string}">
3
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197 <discover_datasets pattern="(?P&lt;name&gt;.+\.alleles)\.tsv$" ext="tabular" directory="stacks_outputs" />
0
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198 </collection>
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199
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200 <collection name="matches" type="list" label="Matches to the catalog on ${on_string}">
3
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201 <discover_datasets pattern="(?P&lt;name&gt;.+\.matches)\.tsv$" ext="tabular" directory="stacks_outputs" />
0
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202 </collection>
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203
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204 <collection name="all_output" type="list" label="Full output from ref_map on ${on_string}">
3
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205 <discover_datasets pattern="(?P&lt;name&gt;.+\.(tags|snps|alleles|matches))\.tsv$" ext="tabular" directory="stacks_outputs" />
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206 <discover_datasets pattern="(?P&lt;name&gt;.+\.(haplotypes|genotypes|markers|hapstats|sumstats|sumstats_summary))\.tsv$" ext="tabular" directory="stacks_outputs" />
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207 <discover_datasets pattern="(?P&lt;name&gt;.+\.(genotypes))\.(loc|txt)$" ext="txt" directory="stacks_outputs" />
0
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208 </collection>
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209 </outputs>
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210
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211 <tests>
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212 <test>
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213 <param name="options_usage|rad_analysis_type" value="genetic"/>
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214 <param name="options_usage|parent_alignments" value="refmap/PopA_01.bam" />
3
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215 <output name="output_log">
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216 <assert_contents>
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217 <has_text text="ref_map.pl completed" />
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218 </assert_contents>
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219 </output>
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220
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221 <!-- catalog -->
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222 <output name="catalogsnps">
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223 <assert_contents>
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224 <has_text text="catalog generated" />
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225 </assert_contents>
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226 </output>
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227 <output name="catalogalleles">
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228 <assert_contents>
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229 <has_text text="catalog generated" />
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230 </assert_contents>
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231 </output>
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232 <output name="catalogtags">
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233 <assert_contents>
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234 <has_text text="catalog generated" />
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235 </assert_contents>
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236 </output>
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237
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238 <!-- genotypes -->
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239 <output name="out_generic_haplo">
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240 <assert_contents>
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241 <has_text text="Catalog ID" />
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242 </assert_contents>
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243 </output>
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244 <output name="out_sql_markers">
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245 <assert_contents>
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246 <has_text text="Total Genotypes" />
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247 </assert_contents>
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248 </output>
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249 <output name="out_joinmap">
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250 <assert_contents>
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251 <has_text text="batch_1.genotypes_" />
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252 </assert_contents>
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253 </output>
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254 <output name="out_sql_genotypes">
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255 <assert_contents>
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256 <has_text text="SQL ID" />
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257 </assert_contents>
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258 </output>
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259 <output name="out_generic_haplo">
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260 <assert_contents>
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261 <has_text text="Seg Dist" />
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parents: 0
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262 </assert_contents>
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
263 </output>
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
264 <output name="out_sql_markers">
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
265 <assert_contents>
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
266 <has_text text="Total Genotypes" />
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
267 </assert_contents>
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
268 </output>
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
269
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
270 <!-- samples -->
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
271 <output_collection name="tags">
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
272 <element name="PopA_01.tags">
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
273 <assert_contents>
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
274 <has_text text="generated on " />
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
275 </assert_contents>
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
276 </element>
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
277 </output_collection>
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
278 <output_collection name="snps">
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
279 <element name="PopA_01.snps">
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
280 <assert_contents>
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
281 <has_text text="generated on " />
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
282 </assert_contents>
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
283 </element>
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
284 </output_collection>
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
285 <output_collection name="alleles">
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
286 <element name="PopA_01.alleles">
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
287 <assert_contents>
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
288 <has_text text="generated on " />
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
289 </assert_contents>
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
290 </element>
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
291 </output_collection>
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
292 <output_collection name="matches">
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
293 <element name="PopA_01.matches">
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
294 <assert_contents>
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
295 <has_text text="generated on " />
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
296 </assert_contents>
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
297 </element>
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
298 </output_collection>
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
299 </test>
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
300 <test>
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
301 <param name="options_usage|rad_analysis_type" value="genetic"/>
26ad8a52d9fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 0
diff changeset
302 <param name="options_usage|parent_alignments" value="refmap/PopA_01.bam" />
0
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
303 <param name="options_usage|progeny_alignments" value="refmap/PopA_02.bam" />
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
304 <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
305 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
306 <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
parents:
diff changeset
307 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
308 </output>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
309
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
310 <!-- catalog -->
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
311 <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
312 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
313 <has_text text="catalog generated" />
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 </output>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
316 <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
317 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
318 <has_text text="catalog generated" />
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 </output>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
321 <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
322 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
323 <has_text text="catalog generated" />
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
324 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
325 </output>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
326
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
327 <!-- genotypes -->
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
328 <output name="out_generic_haplo">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
329 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
330 <has_text text="Catalog ID" />
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 </output>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
333 <output name="out_sql_markers">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
334 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
335 <has_text text="Total Genotypes" />
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
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 </output>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
338 <output name="out_joinmap">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
339 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
340 <has_text text="batch_1.genotypes_" />
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 </output>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
343 <output name="out_sql_genotypes">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
344 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
345 <has_text text="SQL ID" />
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 </output>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
348 <output name="out_generic_haplo">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
349 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
350 <has_text text="Seg Dist" />
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
351 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
352 </output>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
353 <output name="out_sql_markers">
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="Total Genotypes" />
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 </output>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
358
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
359 <!-- samples -->
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
360 <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
361 <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
362 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
363 <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
364 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
365 </element>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
366 </output_collection>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
367 <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
368 <element name="PopA_01.snps">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
369 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
370 <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
371 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
372 </element>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
373 </output_collection>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
374 <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
375 <element name="PopA_01.alleles">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
376 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
377 <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
378 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
379 </element>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
380 </output_collection>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
381 <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
382 <element name="PopA_01.matches">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
383 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
384 <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
385 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
386 </element>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
387 </output_collection>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
388 </test>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
389 <test>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
390 <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
parents:
diff changeset
391 <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
392 <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
393 <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
394 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
395 <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
parents:
diff changeset
396 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
397 </output>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
398
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
399 <!-- catalog -->
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
400 <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
401 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
402 <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
403 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
404 </output>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
405 <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
406 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
407 <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
408 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
409 </output>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
410 <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
411 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
412 <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
413 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
414 </output>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
415
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
416 <!-- populations -->
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
417 <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
418 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
419 <has_text text="PopA_01" />
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
420 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
421 </output>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
422 <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
423 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
424 <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
parents:
diff changeset
425 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
426 </output>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
427 <output name="out_populations_log">
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
428 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
429 <has_text text="populations version" />
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
430 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
431 </output>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
432 <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
433 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
434 <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
435 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
436 </output>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
437 <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
438 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
439 <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
440 </assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
441 </output>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
442
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
443 <!-- samples -->
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
444 <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
445 <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
446 <assert_contents>
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
447 <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
448 </assert_contents>
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449 </element>
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450 </output_collection>
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451 <output_collection name="snps">
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452 <element name="PopA_01.snps">
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453 <assert_contents>
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454 <has_text text="generated on " />
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455 </assert_contents>
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456 </element>
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457 </output_collection>
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458 <output_collection name="alleles">
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459 <element name="PopA_01.alleles">
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460 <assert_contents>
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461 <has_text text="generated on " />
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462 </assert_contents>
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463 </element>
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464 </output_collection>
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465 <output_collection name="matches">
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466 <element name="PopA_01.matches">
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467 <assert_contents>
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468 <has_text text="generated on " />
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469 </assert_contents>
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470 </element>
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471 </output_collection>
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472 </test>
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473 </tests>
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474
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475 <help>
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476 <![CDATA[
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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477 .. class:: infomark
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478
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479 **What it does**
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480
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481 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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482
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483 --------
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484
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485 **Input files**
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486
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487 - SAM, BAM
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488
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489 - Population map::
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490
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491 indv_01 1
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492 indv_02 1
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493 indv_03 1
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494 indv_04 2
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495 indv_05 2
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496 indv_06 2
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497
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498 **Output files**
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499
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500 - XXX.tags.tsv file:
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501
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502 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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503
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504 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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505
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506
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507 - XXX.snps.tsv file:
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508
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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509 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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510
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511 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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512
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513
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514 - XXX.alleles.tsv file:
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515
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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diff changeset
516 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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diff changeset
517
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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diff changeset
518
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519 - XXX.matches.tsv file:
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diff changeset
520
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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521 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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522
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523 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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524
66d3c1ae3937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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525
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526 - other files:
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527
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528 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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529
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530 @STACKS_INFOS@
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531 ]]>
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532 </help>
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533 <expand macro="citation" />
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534 </tool>