Mercurial > repos > iuc > stacks_cstacks

annotate stacks_cstacks.xml @ 8:759ba5c7faca draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
author iuc
date Thu, 27 Apr 2017 04:18:23 -0400
parents a62f7e799494
children be3df81c0353
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1 <tool id="stacks_cstacks" name="Stacks: cstacks" version="@WRAPPER_VERSION@.0">
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2 <description>build a catalogue of loci</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 #import re
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11 mkdir stacks_inputs stacks_outputs
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13 &&
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15 #set $samples = ""
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16 #for $input_file in $input_col
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17 #set $filename = str($input_file.element_identifier)
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18 #if not filename.endswith('.tsv')
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19 #set $filename = $filename + ".tsv"
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20 #end if
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21 #if not re.search('catalog\.[a-z]+(\.tsv)?$', $filename)
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22 ln -s '${input_file}' 'stacks_inputs/$filename' &&
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24 #if $filename.endswith('.tags.tsv')
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25 #set samples += " -s 'stacks_inputs/" + $filename[:-9] + "'"
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26 #end if
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27 #end if
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28 #end for
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30 cstacks
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31
8
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32 ## Batch description
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33 -b 1
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34
0
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35 -p \${GALAXY_SLOTS:-1}
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36
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37 #if $popmap
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38 -P stacks_inputs -M '$popmap'
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39 #else
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40 $samples
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41 -o stacks_outputs
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42 #end if
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43
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44 $g
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46 -n $n
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48 $include_multiple
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49
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50 #if $gapped.use_gapped == "yes"
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51 --gapped
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52 --max_gaps $gapped.max_gaps
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53 --min_aln_len $gapped.min_aln_len
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54 #end if
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55
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56 2>&1 | tee cstacks.log
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58 #if $popmap
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59 ## When using a popmap, stacks write to the input dir
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60 && mv stacks_inputs/batch_1.catalog.*.tsv stacks_outputs/
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61 #end if
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63 &&
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64
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65 stacks_summary.py --stacks-prog cstacks --res-dir stacks_outputs --logfile cstacks.log --summary stacks_outputs/summary.html
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66 ]]></command>
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67
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68 <inputs>
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69 <param name="input_col" format="tabular,txt" type="data_collection" collection_type="list" label="Output from previous Stacks pipeline steps (e.g. denovo_map, refmap, ustacks or pstacks)" />
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70
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71 <param name="popmap" type="data" format="tabular,txt" label="Population map" help="If set, the catalog will be built from samples listed in this file" optional="true" argument="-M" />
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72
0
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73 <param name="g" argument="-g" type="boolean" checked="false" truevalue="-g" falsevalue="" label="Base catalog matching on genomic location, not sequence identity" />
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74
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75 <param name="n" argument="-n" type="integer" value="1" label="Number of mismatches allowed between sample tags when building the catalog"/>
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77 <param name="include_multiple" argument="-m" type="boolean" checked="false" truevalue="-m" falsevalue="" label="Include tags in the catalog that match to more than one entry" />
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78
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79 <conditional name="gapped">
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80 <param name="use_gapped" argument="--gapped" type="select" label="Perform gapped alignments between stacks">
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81 <option value="no" selected="true">No</option>
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82 <option value="yes">Yes</option>
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83 </param>
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84 <when value="no"/>
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85 <when value="yes">
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86 <param name="max_gaps" argument="--max_gaps" type="integer" value="2" label="Number of gaps allowed between stacks before merging"/>
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87 <param name="min_aln_len" argument="--min_aln_len" type="float" value="0.8" min="0.0" max="1.0" label="Minimum length of aligned sequence in a gapped alignment"/>
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88 </when>
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89 </conditional>
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90 </inputs>
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91
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92 <outputs>
3
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93 <data format="txt" name="output_log" label="cstacks.log with ${tool.name} on ${on_string}" from_work_dir="cstacks.log" />
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94
8
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95 <data format="html" name="output_summary" label="Summary from ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/summary.html" />
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96
0
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97 <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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98 <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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99 <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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100 </outputs>
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101
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102 <tests>
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103 <test>
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104 <param name="input_col">
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105 <collection type="list">
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106 <element name="batch_1.catalog.alleles.tsv" ftype="tabular" value="genotypes/batch_1.catalog.alleles.tsv" />
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107 <element name="batch_1.catalog.snps.tsv" ftype="tabular" value="genotypes/batch_1.catalog.snps.tsv" />
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108 <element name="batch_1.catalog.tags.tsv" ftype="tabular" value="genotypes/batch_1.catalog.tags.tsv" />
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109 <element name="PopA_01.alleles.tsv" ftype="tabular" value="genotypes/PopA_01.alleles.tsv" />
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110 <element name="PopA_01.matches.tsv" ftype="tabular" value="genotypes/PopA_01.matches.tsv" />
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111 <element name="PopA_01.snps.tsv" ftype="tabular" value="genotypes/PopA_01.snps.tsv" />
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112 <element name="PopA_01.tags.tsv" ftype="tabular" value="genotypes/PopA_01.tags.tsv" />
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113 <element name="PopA_02.alleles.tsv" ftype="tabular" value="genotypes/PopA_02.alleles.tsv" />
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114 <element name="PopA_02.matches.tsv" ftype="tabular" value="genotypes/PopA_02.matches.tsv" />
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115 <element name="PopA_02.snps.tsv" ftype="tabular" value="genotypes/PopA_02.snps.tsv" />
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116 <element name="PopA_02.tags.tsv" ftype="tabular" value="genotypes/PopA_02.tags.tsv" />
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117 </collection>
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118 </param>
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119
3
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120 <output name="output_log">
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121 <assert_contents>
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122 <has_text text="done." />
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123 </assert_contents>
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124 </output>
8
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125 <output name="output_summary">
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126 <assert_contents>
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127 <has_text text="Stacks Statistics" />
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128 </assert_contents>
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129 </output>
3
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130
0
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131 <!-- catalog -->
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132 <output name="catalogtags">
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133 <assert_contents>
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134 <has_text text="catalog generated on" />
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135 </assert_contents>
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136 </output>
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137 <output name="catalogsnps">
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138 <assert_contents>
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139 <has_text text="catalog generated on" />
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140 </assert_contents>
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141 </output>
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142 <output name="catalogalleles">
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143 <assert_contents>
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144 <has_text text="catalog generated on" />
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145 </assert_contents>
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146 </output>
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147 </test>
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148
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149 <test>
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150 <param name="input_col">
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151 <collection type="list">
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152 <element name="batch_1.catalog.alleles.tsv" ftype="tabular" value="genotypes/batch_1.catalog.alleles.tsv" />
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153 <element name="batch_1.catalog.snps.tsv" ftype="tabular" value="genotypes/batch_1.catalog.snps.tsv" />
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154 <element name="batch_1.catalog.tags.tsv" ftype="tabular" value="genotypes/batch_1.catalog.tags.tsv" />
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155 <element name="PopA_01.alleles.tsv" ftype="tabular" value="genotypes/PopA_01.alleles.tsv" />
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156 <element name="PopA_01.matches.tsv" ftype="tabular" value="genotypes/PopA_01.matches.tsv" />
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157 <element name="PopA_01.snps.tsv" ftype="tabular" value="genotypes/PopA_01.snps.tsv" />
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158 <element name="PopA_01.tags.tsv" ftype="tabular" value="genotypes/PopA_01.tags.tsv" />
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159 <element name="PopA_02.alleles.tsv" ftype="tabular" value="genotypes/PopA_02.alleles.tsv" />
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160 <element name="PopA_02.matches.tsv" ftype="tabular" value="genotypes/PopA_02.matches.tsv" />
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161 <element name="PopA_02.snps.tsv" ftype="tabular" value="genotypes/PopA_02.snps.tsv" />
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162 <element name="PopA_02.tags.tsv" ftype="tabular" value="genotypes/PopA_02.tags.tsv" />
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163 </collection>
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164 </param>
8
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165 <param name="gapped|use_gapped" value="yes" />
0
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166
3
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167 <output name="output_log">
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168 <assert_contents>
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169 <has_text text="done." />
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170 </assert_contents>
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171 </output>
8
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172 <output name="output_summary">
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173 <assert_contents>
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174 <has_text text="Stacks Statistics" />
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175 </assert_contents>
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176 </output>
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177
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178 <!-- catalog -->
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179 <output name="catalogtags">
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180 <assert_contents>
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181 <has_text text="catalog generated on" />
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182 </assert_contents>
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183 </output>
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184 <output name="catalogsnps">
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185 <assert_contents>
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186 <has_text text="catalog generated on" />
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187 </assert_contents>
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188 </output>
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189 <output name="catalogalleles">
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190 <assert_contents>
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191 <has_text text="catalog generated on" />
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192 </assert_contents>
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193 </output>
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194 </test>
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195
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196 <test>
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197 <param name="input_col">
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198 <collection type="list">
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199 <element name="batch_1.catalog.alleles.tsv" ftype="tabular" value="genotypes/batch_1.catalog.alleles.tsv" />
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200 <element name="batch_1.catalog.snps.tsv" ftype="tabular" value="genotypes/batch_1.catalog.snps.tsv" />
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201 <element name="batch_1.catalog.tags.tsv" ftype="tabular" value="genotypes/batch_1.catalog.tags.tsv" />
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202 <element name="PopA_01.alleles.tsv" ftype="tabular" value="genotypes/PopA_01.alleles.tsv" />
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203 <element name="PopA_01.matches.tsv" ftype="tabular" value="genotypes/PopA_01.matches.tsv" />
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204 <element name="PopA_01.snps.tsv" ftype="tabular" value="genotypes/PopA_01.snps.tsv" />
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205 <element name="PopA_01.tags.tsv" ftype="tabular" value="genotypes/PopA_01.tags.tsv" />
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206 <element name="PopA_02.alleles.tsv" ftype="tabular" value="genotypes/PopA_02.alleles.tsv" />
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207 <element name="PopA_02.matches.tsv" ftype="tabular" value="genotypes/PopA_02.matches.tsv" />
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208 <element name="PopA_02.snps.tsv" ftype="tabular" value="genotypes/PopA_02.snps.tsv" />
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209 <element name="PopA_02.tags.tsv" ftype="tabular" value="genotypes/PopA_02.tags.tsv" />
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210 </collection>
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211 </param>
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212
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213 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
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214
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215 <output name="output_log">
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216 <assert_contents>
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217 <has_text text="done." />
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218 </assert_contents>
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219 </output>
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220 <output name="output_summary">
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221 <assert_contents>
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222 <has_text text="Stacks Statistics" />
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223 </assert_contents>
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224 </output>
3
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225
0
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226 <!-- catalog -->
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227 <output name="catalogtags">
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228 <assert_contents>
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229 <has_text text="catalog generated on" />
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230 </assert_contents>
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231 </output>
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232 <output name="catalogsnps">
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233 <assert_contents>
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234 <has_text text="catalog generated on" />
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235 </assert_contents>
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236 </output>
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237 <output name="catalogalleles">
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238 <assert_contents>
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239 <has_text text="catalog generated on" />
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240 </assert_contents>
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241 </output>
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242 </test>
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243 </tests>
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244
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245 <help>
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246 <![CDATA[
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247 .. class:: infomark
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248
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249 **What it does**
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250
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251 A catalog can be built from any set of samples processed by the ustacks or pstacks programs. It will create a set of consensus loci, merging alleles together. In the case of a genetic cross, a catalog would be constructed from the parents of the cross to create a set of all possible alleles expected in the progeny of the cross.
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252
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253 --------
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254
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255 **Input files**
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256
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257 Output from denovo_map, refmap, ustacks or pstacks
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258
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259 **Output files**
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260
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261 - XXX.tags.tsv file:
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262
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263 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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264
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265 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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266
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267
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268 - XXX.snps.tsv file:
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270 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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272 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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273
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275 - XXX.alleles.tsv file:
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277 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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278
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279 @STACKS_INFOS@
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280 ]]>
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281 </help>
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282 <expand macro="citation" />
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283 </tool>