Mercurial > repos > iuc > stacks_sstacks

annotate stacks_sstacks.xml @ 3:344cfdb7dd48 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
author iuc
date Sat, 25 Jun 2016 17:28:25 -0400
parents 17469af4e858
children 679f97ac0dd5
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1 <tool id="stacks_sstacks" name="Stacks: sstacks" version="@WRAPPER_VERSION@.1">
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2 <description>match stacks to a catalog</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 $catalog = ""
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16 #for $input_file in $input_cat:
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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 = $filename + ".tsv"
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20 #end if
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21 #if re.search('catalog\.[a-z]+(\.tsv)?$', $filename):
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22 ln -s "${input_file}" "stacks_inputs/$filename" &&
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24 #if $filename.endswith('.tags.tsv'):
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25 #set catalog += " -c \"stacks_inputs/"+$filename[:-17] + "\""
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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 #set $samples = ""
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31 #for $input_file in $input_tags:
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32 #set $filename = str($input_file.element_identifier)
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33 #if not filename.endswith('.tsv'):
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34 #set $filename = $filename + ".tsv"
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35 #end if
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36 #if not re.search('catalog\.[a-z]+(\.tsv)?$', $filename):
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37 ln -s "${input_file}" "stacks_inputs/$filename" &&
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39 #if $filename.endswith('.tags.tsv'):
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40 #set samples += " -s \"stacks_inputs/"+$filename[:-9] + "\""
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41 #end if
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42 #end if
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43 #end for
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45 sstacks
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47 -p \${GALAXY_SLOTS:-1}
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49 $catalog
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51 $samples
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53 ## Batch description
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54 -b 1
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56 $g
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57
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58 $check_haplo
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60 $gapped
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62 -o stacks_outputs
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64 > sstacks.log 2>&1
0
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65 ]]></command>
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67 <inputs>
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68 <param name="input_cat" format="tabular,txt" type="data_collection" collection_type="list" label="Catalog files" help="output from a previous Stacks pipeline steps e.g. denovo_map, refmap or cstacks" />
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69 <param name="input_tags" format="tabular,txt" type="data_collection" collection_type="list" label="Samples stacks" help="output from previous Stacks pipeline steps e.g. denovo_map, refmap or ustacks/pstacks" />
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71 <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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73 <param name="check_haplo" argument="-x" type="boolean" checked="false" truevalue="-x" falsevalue="" label="Don't verify haplotype of matching locus" />
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75 <param name="gapped" argument="--gapped" type="boolean" checked="false" truevalue="--gapped" falsevalue="" label="Perform gapped alignments between stacks" />
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76 </inputs>
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78 <outputs>
3
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79 <data format="txt" name="output_log" label="sstacks.log with ${tool.name} on ${on_string}" from_work_dir="sstacks.log" />
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80
0
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81 <collection name="matches" type="list" label="Matches to the catalog on ${on_string}">
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82 <discover_datasets pattern="(?P&lt;name&gt;.+\.matches)\.tsv$" ext="tabular" directory="stacks_outputs" />
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83 </collection>
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84 </outputs>
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85
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86 <tests>
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87 <test>
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88 <param name="input_cat">
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89 <collection type="list">
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90 <element name="batch_1.catalog.alleles.tsv" ftype="tabular" value="genotypes/batch_1.catalog.alleles.tsv" />
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91 <element name="batch_1.catalog.snps.tsv" ftype="tabular" value="genotypes/batch_1.catalog.snps.tsv" />
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92 <element name="batch_1.catalog.tags.tsv" ftype="tabular" value="genotypes/batch_1.catalog.tags.tsv" />
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93 </collection>
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94 </param>
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95 <param name="input_tags">
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96 <collection type="list">
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97 <element name="PopA_01.alleles.tsv" ftype="tabular" value="genotypes/PopA_01.alleles.tsv" />
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98 <element name="PopA_01.matches.tsv" ftype="tabular" value="genotypes/PopA_01.matches.tsv" />
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99 <element name="PopA_01.snps.tsv" ftype="tabular" value="genotypes/PopA_01.snps.tsv" />
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100 <element name="PopA_01.tags.tsv" ftype="tabular" value="genotypes/PopA_01.tags.tsv" />
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101 <element name="PopA_02.alleles.tsv" ftype="tabular" value="genotypes/PopA_02.alleles.tsv" />
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102 <element name="PopA_02.matches.tsv" ftype="tabular" value="genotypes/PopA_02.matches.tsv" />
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103 <element name="PopA_02.snps.tsv" ftype="tabular" value="genotypes/PopA_02.snps.tsv" />
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104 <element name="PopA_02.tags.tsv" ftype="tabular" value="genotypes/PopA_02.tags.tsv" />
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105 </collection>
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106 </param>
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107
3
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108 <output name="output_log">
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109 <assert_contents>
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110 <has_text text="Outputing to file" />
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111 </assert_contents>
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112 </output>
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113
0
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114 <output_collection name="matches">
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115 <element name="PopA_01.matches">
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116 <assert_contents>
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117 <has_text text="generated on " />
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118 </assert_contents>
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119 </element>
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120 </output_collection>
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121 </test>
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122
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123 <test>
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124 <param name="input_cat">
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125 <collection type="list">
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126 <element name="batch_1.catalog.alleles.tsv" ftype="tabular" value="genotypes/batch_1.catalog.alleles.tsv" />
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127 <element name="batch_1.catalog.snps.tsv" ftype="tabular" value="genotypes/batch_1.catalog.snps.tsv" />
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128 <element name="batch_1.catalog.tags.tsv" ftype="tabular" value="genotypes/batch_1.catalog.tags.tsv" />
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129 </collection>
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130 </param>
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131 <param name="input_tags">
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132 <collection type="list">
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133 <element name="PopA_01.alleles.tsv" ftype="tabular" value="genotypes/PopA_01.alleles.tsv" />
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134 <element name="PopA_01.matches.tsv" ftype="tabular" value="genotypes/PopA_01.matches.tsv" />
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135 <element name="PopA_01.snps.tsv" ftype="tabular" value="genotypes/PopA_01.snps.tsv" />
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136 <element name="PopA_01.tags.tsv" ftype="tabular" value="genotypes/PopA_01.tags.tsv" />
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137 <element name="PopA_02.alleles.tsv" ftype="tabular" value="genotypes/PopA_02.alleles.tsv" />
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138 <element name="PopA_02.matches.tsv" ftype="tabular" value="genotypes/PopA_02.matches.tsv" />
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139 <element name="PopA_02.snps.tsv" ftype="tabular" value="genotypes/PopA_02.snps.tsv" />
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140 <element name="PopA_02.tags.tsv" ftype="tabular" value="genotypes/PopA_02.tags.tsv" />
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141 </collection>
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142 </param>
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143 <param name="gapped" value="true" />
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144 <param name="check_haplo" value="true" />
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145
3
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146 <output name="output_log">
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147 <assert_contents>
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148 <has_text text="Outputing to file" />
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149 </assert_contents>
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150 </output>
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151
0
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152 <output_collection name="matches">
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153 <element name="PopA_01.matches">
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154 <assert_contents>
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155 <has_text text="generated on " />
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156 </assert_contents>
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157 </element>
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158 </output_collection>
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159 </test>
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160 </tests>
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161
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162 <help>
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163 <![CDATA[
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164 .. class:: infomark
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165
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166 **What it does**
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167
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168 Sets of stacks constructed by the ustacks or pstacks programs can be searched against a catalog produced by cstacks. In the case of a genetic map, stacks from the progeny would be matched against the catalog to determine which progeny contain which parental alleles.
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169
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170 --------
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171
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172 **Input files**
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173
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174 Output from denovo_map, refmap or cstacks/ustacks/pstacks
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175
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176 **Output files**
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177
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178 - XXX.tags.tsv file:
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179
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180 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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182 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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183
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184
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185 - XXX.snps.tsv file:
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187 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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189 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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190
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192 - XXX.alleles.tsv file:
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194 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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195
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196 - XXX.matches.tsv file:
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197
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198 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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200 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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201
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202 @STACKS_INFOS@
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203 ]]>
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204 </help>
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205 <expand macro="citation" />
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206 </tool>
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207