Mercurial > repos > iuc > stacks_assembleperead

annotate stacks_assembleperead.xml @ 4:ae705d244e28 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
author iuc
date Mon, 26 Sep 2016 11:43:58 -0400
parents ee52d9cfaffc
children e6919d8ae34d
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1 <tool id="stacks_assembleperead" name="Stacks: assemble read pairs by locus" version="@WRAPPER_VERSION@.0">
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2 <description>run the STACKS sort_read_pairs.pl and exec_velvet.pl wrappers</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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10 mkdir stacks_inputs reads stacks_outputs
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12 &&
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14 #for $input_file in $stacks_col:
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15 #set $ext = ""
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16 #if not str($input_file.element_identifier).endswith('.tsv'):
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17 #set $ext = ".tsv"
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18 #end if
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19 ln -s "${input_file}" "stacks_inputs/${input_file.element_identifier}${ext}" &&
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20 #end for
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22 #for $input_file in $reads:
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23 #set $name = str($input_file.element_identifier)
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24 ## sort_read_pairs is expecting strange fastq names: <sample_name>.fq_2
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25 #if $name.endswith('.1.fq'):
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26 ## handle a common case
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27 #set $name = $name[:-5]+".fq_1"
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28 #else if $name.endswith('.2.fq'):
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29 ## handle a common case
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30 #set $name = $name[:-5]+".fq_2"
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31 #else if not $name.endswith('.fq') and not $name.endswith('.fq_2'):
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32 ## no extension, consider it's a fq_2 file
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33 #set $name = $name + ".fq_2"
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34 #end if
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35 ln -s "${input_file}" "reads/${name}" &&
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36 #end for
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38 sort_read_pairs.pl
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39 -p stacks_inputs
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40 -s 'reads'
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42 #if $whitelist:
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43 -w '$whitelist'
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44 #end if
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46 #if $threshold:
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47 -r $threshold
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48 #end if
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49
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50 -o stacks_outputs
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51
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52 #if $velvet.use_velvet:
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53 ## remove possible empty files
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54 && find stacks_outputs -type f -size 0 -delete
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55
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56 &&
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57 mkdir assembled
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58 &&
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59 velvet_path=`which velveth` && velvet_path=`dirname "\$velvet_path"`
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60 &&
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61 exec_velvet.pl -s stacks_outputs -o assembled -c -M ${velvet.contig_length} -e "\$velvet_path"
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62 #end if
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63
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64 ]]></command>
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65 <inputs>
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66 <param name="stacks_col" argument="-p" format="tabular,txt" type="data_collection" collection_type="list" label="Output from previous Stacks pipeline steps (e.g. denovo_map or refmap)" />
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67 <param name="reads" argument="-s" format="fastqsanger" type="data" multiple="true" label="Files containing reads to assemble" help="only R2 reads" />
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68
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69 <param name="whitelist" argument="-w" format="txt,tabular" type="data" optional="true" label="White list of catalog IDs to include" />
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70 <param name="threshold" argument="-r" type="integer" value="" optional="true" label="Minimum number of reads by locus"/>
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71
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72 <conditional name="velvet">
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73 <param name="use_velvet" type="boolean" checked="false" label="Perform assembly with Velvet" help="If not selected, the tool will only produce of collection of fasta files (one per locus) containing reads ready to assemble." />
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74 <when value="false"></when>
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75 <when value="true">
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76 <param name="contig_length" type="integer" value="200" label="Minimum length for asssembled contigs"/>
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77 </when>
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78 </conditional>
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79 </inputs>
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80 <outputs>
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81 <collection name="collated" type="list" label="Collated FASTA files per locus on ${on_string}">
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82 <filter>not velvet['use_velvet']</filter>
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83 <discover_datasets pattern="(?P&lt;name&gt;.+)\.fa(sta)?$" ext="fasta" directory="stacks_outputs" />
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84 </collection>
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85
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86 <data format="fasta" name="contigs" label="Assembled contigs on ${on_string}" from_work_dir="assembled/collated.fa">
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87 <filter>velvet['use_velvet']</filter>
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88 </data>
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89 </outputs>
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90
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91 <tests>
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92 <test>
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93 <param name="stacks_col">
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94 <collection type="list">
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95 <element name="batch_1.catalog.alleles.tsv" ftype="tabular" value="genotypes/batch_1.catalog.alleles.tsv" />
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96 <element name="batch_1.catalog.snps.tsv" ftype="tabular" value="genotypes/batch_1.catalog.snps.tsv" />
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97 <element name="batch_1.catalog.tags.tsv" ftype="tabular" value="genotypes/batch_1.catalog.tags.tsv" />
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98 <element name="PopA_01.alleles.tsv" ftype="tabular" value="genotypes/PopA_01.alleles.tsv" />
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99 <element name="PopA_01.matches.tsv" ftype="tabular" value="genotypes/PopA_01.matches.tsv" />
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100 <element name="PopA_01.snps.tsv" ftype="tabular" value="genotypes/PopA_01.snps.tsv" />
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101 <element name="PopA_01.tags.tsv" ftype="tabular" value="genotypes/PopA_01.tags.tsv" />
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102 <element name="PopA_02.alleles.tsv" ftype="tabular" value="genotypes/PopA_02.alleles.tsv" />
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103 <element name="PopA_02.matches.tsv" ftype="tabular" value="genotypes/PopA_02.matches.tsv" />
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104 <element name="PopA_02.snps.tsv" ftype="tabular" value="genotypes/PopA_02.snps.tsv" />
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105 <element name="PopA_02.tags.tsv" ftype="tabular" value="genotypes/PopA_02.tags.tsv" />
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106 </collection>
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107 </param>
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108 <param name="reads" value="demultiplexed/PopA_01.2.fq,demultiplexed/PopA_02.2.fq" ftype="fastqsanger" />
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109
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110 <output_collection name="collated">
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111 <element name="1">
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112 <assert_contents>
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113 <has_text text="CCGATCAGCATCAGTAGTTTTCAACGAGCTGGCCCAATGGTGTATAACTATGTGGTAGAGAGAAACTGCTGCTATCACTCACGATATAAGCCCTCTGACG" />
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114 </assert_contents>
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115 </element>
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116 </output_collection>
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117 </test>
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118 <test>
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119 <param name="stacks_col">
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120 <collection type="list">
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121 <element name="batch_1.catalog.alleles.tsv" ftype="tabular" value="genotypes/batch_1.catalog.alleles.tsv" />
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122 <element name="batch_1.catalog.snps.tsv" ftype="tabular" value="genotypes/batch_1.catalog.snps.tsv" />
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123 <element name="batch_1.catalog.tags.tsv" ftype="tabular" value="genotypes/batch_1.catalog.tags.tsv" />
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124 <element name="PopA_01.alleles.tsv" ftype="tabular" value="genotypes/PopA_01.alleles.tsv" />
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125 <element name="PopA_01.matches.tsv" ftype="tabular" value="genotypes/PopA_01.matches.tsv" />
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126 <element name="PopA_01.snps.tsv" ftype="tabular" value="genotypes/PopA_01.snps.tsv" />
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127 <element name="PopA_01.tags.tsv" ftype="tabular" value="genotypes/PopA_01.tags.tsv" />
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128 <element name="PopA_02.alleles.tsv" ftype="tabular" value="genotypes/PopA_02.alleles.tsv" />
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129 <element name="PopA_02.matches.tsv" ftype="tabular" value="genotypes/PopA_02.matches.tsv" />
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130 <element name="PopA_02.snps.tsv" ftype="tabular" value="genotypes/PopA_02.snps.tsv" />
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131 <element name="PopA_02.tags.tsv" ftype="tabular" value="genotypes/PopA_02.tags.tsv" />
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132 </collection>
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133 </param>
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134 <param name="reads" value="demultiplexed/PopA_01.2.fq,demultiplexed/PopA_02.2.fq" ftype="fastqsanger" />
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135 <param name="velvet|use_velvet" value="true" />
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136 <param name="velvet|contig_length" value="20" />
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137
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138 <output name="contigs">
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139 <assert_contents>
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140 <has_text text="TGTATTCTCCCATGCGACAGCAGGACATCCCATCCCCCTCTGATGTTATCAATCATAAGA" />
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141 </assert_contents>
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142 </output>
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143 </test>
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144 </tests>
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145
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146 <help>
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147 <![CDATA[
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148 .. class:: infomark
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149
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150 **What it does**
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151
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152 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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153
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154 --------
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155
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156 **Input file**
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157
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158 Output from denovo_map or ref_map
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159
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160
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161 **Output file**
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162
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163 A collated.fa file containing assembled contigs for each locus
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164
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165 @STACKS_INFOS@
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166 ]]>
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167 </help>
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168 <expand macro="citation" />
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169 </tool>