Mercurial > repos > matthias > stacks2_cstacks

annotate stacks_cstacks.xml @ 3:61afc5a3cd8e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c42d129928cfd153ba7a922368c8e76e79b242b2
author matthias
date Fri, 04 Jan 2019 03:31:18 -0500
parents d31714d7f03e
children 924e7889aa05
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1 <tool id="stacks2_cstacks" name="Stacks2: cstacks" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@">
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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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12 &&
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14 ## for each input collection
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15 ## - create links all tsv files that are not catalog
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16 ## (ustacks produces ony tags, alleles, snps, ie eventually
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17 ## present catalogs are ignored)
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18 ## link name is element_identifier(.tsv)
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19 ## - create -s sample1prefix -s sample2prefix ..
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21 #set $samples = ""
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22 #for $input_file in $input_cat
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23 #set $filename = str($input_file.element_identifier)
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24 #if not filename.endswith('.tsv')
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25 #set $filename = $filename + ".tsv"
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26 #end if
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27 #if not re.search('catalog\.[a-z]+(\.tsv)?$', $filename)
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28 ln -s '${input_file}' 'stacks_inputs/$filename' &&
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30 #if $filename.endswith('.tags.tsv')
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31 #set samples += " -s 'stacks_inputs/" + $filename[:-9] + "'"
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32 #end if
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33 #end if
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34 #end for
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36 cstacks
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38 -p \${GALAXY_SLOTS:-1}
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40 #if $popmap
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41 -P stacks_inputs
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42 -M '$popmap'
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43 #else
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44 $samples
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45 -o stacks_outputs
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46 #end if
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47
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48 -n $n
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49 ## -c not implemented in Galaxy (appending can be done in Galaxy)
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51 @GAP_OPTIONS@
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52
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53 ## Advanced Options
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54 #if $k_len:
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55 --k_len $k_len
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56 #end if
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57 $report_mmatches
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58 @TEE_APPEND_LOG@
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59 @CAT_LOG_TO_STDERR@
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61 #if $popmap
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62 ## When using a popmap, cstacks writes to the input dir
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63 && mv stacks_inputs/catalog.*.tsv stacks_outputs/
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64 #end if
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66 ]]></command>
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68 <inputs>
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69 <expand macro="input_cat_macro"/>
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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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73 <param argument="-n" type="integer" value="1" label="Number of mismatches allowed between sample loci when building the catalog" help="(default 1; suggested: set to ustacks -M)"/>
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75 <expand macro="gap_options"/>
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76 <param argument="--k_len" type="integer" min="5" max="31" value="" optional="true" label="k-mer size for matching between between catalog loci" help="default: automatic"/>
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77 <param argument="--report_mmatches" type="boolean" checked="false" truevalue="--report_mmatches" falsevalue="" label="report query loci that match more than one catalog locus" />
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78 <expand macro="in_log"/>
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79 </inputs>
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81 <outputs>
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82 <expand macro="out_log"/>
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83 <expand macro="cstacks_outputs_macro"/>
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84 </outputs>
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86 <tests>
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87 <!-- TODO add test w popmap -->
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88 <!-- test w default options -->
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89 <test>
3
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90 <param name="input_cat">
0
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91 <collection type="list">
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92 <element name="PopA_01.alleles.tsv" ftype="tabular" value="ustacks/PopA_01.alleles.tsv" />
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93 <element name="PopA_01.snps.tsv" ftype="tabular" value="ustacks/PopA_01.snps.tsv" />
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94 <element name="PopA_01.tags.tsv" ftype="tabular" value="ustacks/PopA_01.tags.tsv" />
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95 <element name="PopA_02.alleles.tsv" ftype="tabular" value="ustacks/PopA_02.alleles.tsv" />
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96 <element name="PopA_02.snps.tsv" ftype="tabular" value="ustacks/PopA_02.snps.tsv" />
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97 <element name="PopA_02.tags.tsv" ftype="tabular" value="ustacks/PopA_02.tags.tsv" />
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98 </collection>
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99 </param>
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100 <param name="add_log" value="yes" />
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101 <output name="output_log"><assert_contents><has_text text="done." /></assert_contents></output>
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102 <output_collection name="catalog" type="list">
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103 <element name="catalog.alleles" file="cstacks/catalog.alleles.tsv" ftype="tabular" lines_diff="2"/>
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104 <element name="catalog.snps" file="cstacks/catalog.snps.tsv" ftype="tabular" lines_diff="2" />
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105 <element name="catalog.tags" file="cstacks/catalog.tags.tsv" ftype="tabular" lines_diff="2" />
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106 </output_collection>
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107 </test>
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108 <!-- test w non default options (wo gapped, because tested already in ustacks) -->
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109 <test>
3
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110 <param name="input_cat">
0
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111 <collection type="list">
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112 <element name="PopA_01.alleles.tsv" ftype="tabular" value="ustacks/PopA_01.alleles.tsv" />
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113 <element name="PopA_01.snps.tsv" ftype="tabular" value="ustacks/PopA_01.snps.tsv" />
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114 <element name="PopA_01.tags.tsv" ftype="tabular" value="ustacks/PopA_01.tags.tsv" />
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115 <element name="PopA_02.alleles.tsv" ftype="tabular" value="ustacks/PopA_02.alleles.tsv" />
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116 <element name="PopA_02.snps.tsv" ftype="tabular" value="ustacks/PopA_02.snps.tsv" />
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117 <element name="PopA_02.tags.tsv" ftype="tabular" value="ustacks/PopA_02.tags.tsv" />
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118 </collection>
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119 </param>
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120 <param name="n" value="2"/>
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121 <param name="k_len" value="23"/>
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122 <param name="report_mmatches" value="--report_mmatches" />
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123 <assert_command>
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124 <has_text text="--k_len 23" />
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125 <has_text text="-n 2" />
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126 <has_text text="--report_mmatches" />
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127 </assert_command>
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128 <param name="add_log" value="yes" />
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129 <output name="output_log"><assert_contents><has_text text="done." /></assert_contents></output>
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130 <output_collection name="catalog" type="list">
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131 <element name="catalog.alleles" file="cstacks/catalog.alleles.tsv" ftype="tabular" lines_diff="2"/>
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132 <element name="catalog.snps" file="cstacks/catalog.snps.tsv" ftype="tabular" lines_diff="2" />
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133 <element name="catalog.tags" file="cstacks/catalog.tags.tsv" ftype="tabular" lines_diff="2" />
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134 </output_collection>
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135 </test>
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136 </tests>
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137 <help>
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138 <![CDATA[
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139 .. class:: infomark
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140
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141 **What it does**
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142
3
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143 A catalog can be built from any set of samples processed by ustacks. 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.
0
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144
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145 --------
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146
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147 **Input files**
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148
3
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149 Output from denovo_map, refmap, or ustacks
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150
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151 **Output files**
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152
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153 - XXX.tags.tsv file:
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154
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155 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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156
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157 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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158
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159
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160 - XXX.snps.tsv file:
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161
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162 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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163
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164 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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165
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166
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167 - XXX.alleles.tsv file:
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168
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169 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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170
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171 @STACKS_INFOS@
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172 ]]>
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173 </help>
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174 <expand macro="citation" />
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175 </tool>