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1 <tool id="STACKSassembleperead" name="STACKS : assemble read pairs by locus" version="1.1.1">
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2 <description>Run the STACKS sort_read_pairs.pl and exec_velvet.pl wrappers</description>
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3
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4 <requirements>
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5 <requirement type="package" version="1.18">stacks</requirement>
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6 <requirement type="package" version="1.2.10">velvet</requirement>
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7 </requirements>
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8 <command interpreter="python">
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9
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10 STACKS_sort_read_pairs.py
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11 -a $STACKS_archive
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12 -e $samples_archive
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13 #if str( $options_whitelist.whitelist_selector) == "yes"
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14 -b $whitelist
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15 #end if
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16 #if str( $options_filter.reads_selector) == "yes"
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17 -c $options_filter.threshold
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18 #end if
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19 #if str( $options_filter2.length_selector) == "yes"
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20 -d $options_filter2.threshold2
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21 #end if
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22 -o $output
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23
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24
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25 </command>
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26
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27 <inputs>
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28 <param name="STACKS_archive" format="zip,tar.gz" type="data" label="Archive from STACKS pipeline regrouping all outputs" />
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29
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30 <param name="samples_archive" format="zip,fastq.gz,tar.gz,tar.bz2" type="data" label="Archive with raw reads used to execute previous STACKS pipeline" />
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31
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32 <conditional name="options_whitelist">
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33 <param name="whitelist_selector" type="select" label="Have you got a whitelist?" >
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34 <option value="no" selected="true">No</option>
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35 <option value="yes">Yes</option>
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36 </param>
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37 <when value="no"></when>
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38 <when value="yes">
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39 <param name="whitelist" format="txt, tabular" type="data" label="Whitelist file containing loci that we want to assemble: those that have SNPs" />
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40 </when>
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41 </conditional>
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42
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43
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44 <conditional name="options_filter">
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45 <param name="reads_selector" type="select" label="Specify a treshold for the minimum number of reads by locus?" >
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46 <option value="no" selected="true">No</option>
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47 <option value="yes">Yes</option>
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48 </param>
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49 <when value="no"></when>
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50 <when value="yes">
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51 <param name="threshold" type="integer" value="10" label="Minimum number of reads by locus"/>
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52 </when>
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53 </conditional>
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54 <conditional name="options_filter2">
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55 <param name="length_selector" type="select" label="Specify a minimum length for asssembled contigs?" >
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56 <option value="no" selected="true">No</option>
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57 <option value="yes">Yes</option>
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58 </param>
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59 <when value="no"></when>
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60 <when value="yes">
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61 <param name="threshold2" type="integer" value="200" label="Minimum length for asssembled contigs"/>
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62 </when>
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63 </conditional>
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64
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65 </inputs>
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66 <outputs>
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67 <data format="fasta" name="output" label="collated.fa : ${tool.name} on ${on_string}" />
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68 </outputs>
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69 <stdio>
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70 <exit_code range="1" level="fatal" description="Error" />
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71 </stdio>
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72 <help>
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73
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74 .. class:: infomark
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75
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76 **What it does**
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77
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78 This program will run each of the Stacks sort_read_pairs.pl and exec_velvet.pl utilities to assemble pair-end reads from STACKS pipeline results
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79
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80 --------
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81
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82 **Created by:**
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83
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84 Stacks was developed by Julian Catchen with contributions from Angel Amores, Paul Hohenlohe, and Bill Cresko
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85
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86 --------
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87
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88 **Example:**
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89
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90 Input file:
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91
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92 Output archives of STACKS : Reference map or STACKS : De novo map, in zip or tar.gz format
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93
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94
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95 Output file:
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96
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97 A collated.fa file containing assembled contigs for each locus
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98
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99
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100 Instructions to add the functionality of archives management in Galaxy on the `eBiogenouest HUB wiki <https://www.e-biogenouest.org/wiki/ManArchiveGalaxy>`_ .
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101
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102 --------
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103
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104
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105 **Project links:**
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106
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107 `STACKS website <http://creskolab.uoregon.edu/stacks/>`_ .
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108
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109 `STACKS manual <http://creskolab.uoregon.edu/stacks/stacks_manual.pdf>`_ .
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110
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111 `STACKS google group <https://groups.google.com/forum/#!forum/stacks-users>`_ .
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112
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113 --------
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114
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115 **References:**
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116
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117 -J. Catchen, P. Hohenlohe, S. Bassham, A. Amores, and W. Cresko. Stacks: an analysis tool set for population genomics. Molecular Ecology. 2013.
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118
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119 -J. Catchen, S. Bassham, T. Wilson, M. Currey, C. O'Brien, Q. Yeates, and W. Cresko. The population structure and recent colonization history of Oregon threespine stickleback determined using restriction-site associated DNA-sequencing. Molecular Ecology. 2013.
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120
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121 -J. Catchen, A. Amores, P. Hohenlohe, W. Cresko, and J. Postlethwait. Stacks: building and genotyping loci de novo from short-read sequences. G3: Genes, Genomes, Genetics, 1:171-182, 2011.
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122
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123 -A. Amores, J. Catchen, A. Ferrara, Q. Fontenot and J. Postlethwait. Genome evolution and meiotic maps by massively parallel DNA sequencing: Spotted gar, an outgroup for the teleost genome duplication. Genetics, 188:799'808, 2011.
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124
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125 -P. Hohenlohe, S. Amish, J. Catchen, F. Allendorf, G. Luikart. RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow trout and westslope cutthroat trout. Molecular Ecology Resources, 11(s1):117-122, 2011.
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126
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127 -K. Emerson, C. Merz, J. Catchen, P. Hohenlohe, W. Cresko, W. Bradshaw, C. Holzapfel. Resolving postglacial phylogeography using high-throughput sequencing. Proceedings of the National Academy of Science, 107(37):16196-200, 2010.
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128
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129 --------
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130
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131 **Integrated by:**
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132
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133 Yvan Le Bras and Cyril Monjeaud
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134
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135 GenOuest Bio-informatics Core Facility
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136
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137 UMR 6074 IRISA INRIA-CNRS-UR1 Rennes (France)
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138
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139 support@genouest.org
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140
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141 If you use this tool in Galaxy, please cite :
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142
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143 `Y. Le Bras, A. Roult, C. Monjeaud, M. Bahin, O. Quenez, C. Heriveau, A. Bretaudeau, O. Sallou, O. Collin, Towards a Life Sciences Virtual Research Environment : an e-Science initiative in Western France. JOBIM 2013. <https://www.e-biogenouest.org/resources/128>`_
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144
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145
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146 </help>
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147 <citations>
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148 <citation type="doi">10.1111/mec.12354</citation>
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149 <citation type="doi">10.1111/mec.12330</citation>
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150 <citation type="doi">10.1534/g3.111.000240</citation>
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151 <citation type="doi">10.1534/genetics.111.127324</citation>
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152 <citation type="doi">10.1111/j.1755-0998.2010.02967.x</citation>
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153 <citation type="doi">10.1073/pnas.1006538107</citation>
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154
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155 <citation type="bibtex">@INPROCEEDINGS{JOBIM2013,
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156 author = {Le Bras, Y. and ROULT, A. and Monjeaud, C. and Bahin, M. and Quenez, O. and Heriveau, C. and Bretaudeau, A. and Sallou, O. and Collin, O.},
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157 title = {Towards a Life Sciences Virtual Research Environment: An e-Science initiative in Western France},
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158 booktitle = {JOBIM 2013 Proceedings},
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159 year = {2013},
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160 url = {https://www.e-biogenouest.org/resources/128},
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161 pages = {97-106}
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162 }</citation>
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163 </citations>
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164 </tool>
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