annotate stacks_procrad.xml @ 11:be78e39d56b3 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 5f2ec13ecca435abaac2b99ba21f1d6497ec7139"
author iuc
date Tue, 22 Mar 2022 23:20:30 +0000
parents 57910d476be9
children eded025438db
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1 <tool id="stacks_procrad" name="Stacks: process radtags" version="@WRAPPER_VERSION@.0">
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2 <description>the Stacks demultiplexing script</description>
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3 <expand macro="bio_tools"/>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <expand macro="stdio"/>
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9 <command><![CDATA[
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11 #if $input_type.options_type_selector == "single"
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13 #if $input_type.input_single.is_of_type('fastqsanger')
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14 #set $ext = ".fq"
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15 #set inputype = "fastq"
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16 #else
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17 #set $ext = ".fq.gz"
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18 #set inputype = "gzfastq"
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19 #end if
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21 ln -s '$input_type.input_single' R1$ext &&
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22 #else
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24 #if $input_type.inputs_paired1.is_of_type('fastqsanger')
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25 #set $ext = ".fq"
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26 #set inputype = "fastq"
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27 #else
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28 #set $ext = ".fq.gz"
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29 #set inputype = "gzfastq"
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30 #end if
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32 ln -s '$input_type.inputs_paired1' R1$ext &&
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33 ln -s '$input_type.inputs_paired2' R2$ext &&
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34 #end if
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35
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36 mkdir stacks_outputs
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37
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38 &&
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39
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40 process_radtags
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41
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42 #if $input_type.options_type_selector == "single"
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43 -f R1$ext
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44 #else
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45 -1 R1$ext
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46 -2 R2$ext
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47 #end if
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48
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49 -i $inputype
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50 -b '$barcode'
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51
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52 $input_type.barcode_encoding
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53
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54 #if str( $options_enzyme.options_enzyme_selector ) == "1"
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55 -e $options_enzyme.enzyme
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56 #else
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57 --renz_1 $options_enzyme.enzyme --renz_2 $options_enzyme.enzyme2
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58 #end if
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59
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60 #if str( $outype ) != "auto"
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61 -y $outype
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62 #end if
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63
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64 $capture
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65
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66 $options_advanced.retain_header
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67
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68 #if str($options_advanced.truncate)
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69 -t $options_advanced.truncate
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70 #end if
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71
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72 -w $options_advanced.sliding
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74 $options_advanced.remove
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75
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76 $options_advanced.discard
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77 -s $options_advanced.score
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78
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79 $options_advanced.rescue
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80
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81 -o stacks_outputs
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82 ]]></command>
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83
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84 <inputs>
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85 <conditional name="input_type">
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86 <param name="options_type_selector" type="select" label="Single-end or paired-end reads files">
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87 <option value="single" selected="True">Single-end files</option>
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88 <option value="paired">Paired-end files</option>
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89 </param>
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90 <when value="single">
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91 <param name="input_single" argument="-f" format="fastqsanger,fastqsanger.gz" type="data" label="singles-end reads infile(s)" help="input files" />
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92
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93 <param name="barcode_encoding" type="select" label="Barcode location">
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94 <expand macro="barcode_encoding_single" />
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95 </param>
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96 </when>
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97 <when value="paired">
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98 <param name="inputs_paired1" argument="-1" format="fastqsanger,fastqsanger.gz" type="data" label="paired-end reads infile(s) 1" help="Files must have this syntax : name_R1_001.fastq" />
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99 <param name="inputs_paired2" argument="-2" format="fastqsanger,fastqsanger.gz" type="data" label="paired-end reads infile(s) 2" help="Files must have this syntax : name_R2_001.fastq" />
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100
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101 <param name="barcode_encoding" type="select" label="Barcode location">
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102 <expand macro="barcode_encoding_pair" />
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103 </param>
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104 </when>
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105 </conditional>
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106
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107 <param name="barcode" argument="-b" type="data" format="tabular,txt" label="Barcode file" help="Barcode file" />
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108
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109 <conditional name="options_enzyme">
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110 <param name="options_enzyme_selector" type="select" label="Number of enzymes">
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111 <option value="1">One</option>
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112 <option value="2">Two</option>
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113 </param>
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114 <when value="1">
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115 <param name="enzyme" type="select" label="Enzyme" argument="-e" help="provide the restriction enzyme used" >
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116 <expand macro="enzymes"/>
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117 </param>
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118 </when>
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119 <when value="2">
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120 <param name="enzyme" type="select" label="Enzyme" argument="--renz_1" help="provide the restriction enzyme used" >
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121 <expand macro="enzymes"/>
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122 </param>
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123 <param name="enzyme2" type="select" label="Second enzyme" argument="--renz_2" help="provide the second restriction enzyme used" >
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124 <expand macro="enzymes"/>
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125 </param>
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126 </when>
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127 </conditional>
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128
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129 <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file" />
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130
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131 <section name="options_advanced" title="advanced options" expanded="False">
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132 <param name="sliding" type="float" value="0.15" argument="-w" label="Set the size of the sliding window as a fraction of the read length, between 0 and 1 (default 0.15)" />
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133 <param name="remove" type="boolean" checked="false" truevalue="-c" falsevalue="" argument="-c" label="Clean data, remove any read with an uncalled base" />
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134 <param name="discard" type="boolean" checked="false" truevalue="-q" falsevalue="" argument="-q" label="Discard reads with low quality scores"/>
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135 <param name="score" type="integer" value="10" argument="-s" label="Set the score limit. If the average score within the sliding window drops below this value, the read is discarded (default 10)" />
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136 <param name="rescue" type="boolean" checked="false" truevalue="-r" falsevalue="" argument="-r" label="Rescue barcodes and RAD-Tags?"/>
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137 <param name="truncate" type="integer" value="" optional="True" argument="-t" label="Truncate final read length to this value" />
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138 <param name="retain_header" type="boolean" checked="false" truevalue="--retain_header" falsevalue="" argument="--retain_header" label="Retain unmodified FASTQ headers in the output" />
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139 </section>
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140
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141 <param name="outype" argument="-y" type="select" label="Output format" >
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142 <option value="auto" selected="True">Same as input</option>
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143 <option value="fastq">fastq</option>
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144 <option value="fasta">fasta</option>
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145 <option value="gzfastq">gzipped fastq</option>
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146 </param>
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147 </inputs>
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148
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149 <outputs>
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150 <data format="txt" name="output_log" label="results.log with ${tool.name} on ${on_string}: demultiplexed and cleaned reads" from_work_dir="stacks_outputs/process_radtags.log" />
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151
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152 <collection name="demultiplexed" type="list" label="Demultiplexed reads from ${on_string}">
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153 <discover_datasets pattern="(?P&lt;name&gt;.+(\.[12])?)\.fq$" ext="fastqsanger" directory="stacks_outputs" />
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154 <discover_datasets pattern="(?P&lt;name&gt;.+(\.[12])?)\.fq.gz$" ext="fastqsanger.gz" directory="stacks_outputs" />
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155 <discover_datasets pattern="(?P&lt;name&gt;.+(\.[12])?)\.fa$" ext="fasta" directory="stacks_outputs" />
0
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156 </collection>
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157 <collection name="remaining" type="list" label="Remaining orphan reads from ${on_string}">
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158 <filter>input_type['options_type_selector'] == "paired"</filter>
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159 <discover_datasets pattern="(?P&lt;name&gt;.+\.rem(\.[12])?)\.fq$" ext="fastqsanger" directory="stacks_outputs" />
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160 <discover_datasets pattern="(?P&lt;name&gt;.+\.rem(\.[12])?)\.fq.gz$" ext="fastqsanger.gz" directory="stacks_outputs" />
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161 <discover_datasets pattern="(?P&lt;name&gt;.+\.rem(\.[12])?)\.fa$" ext="fasta" directory="stacks_outputs" />
0
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162 </collection>
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163 <collection name="discarded" type="list" label="${tool.name}: discarded reads from ${on_string}">
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164 <filter>capture is True</filter>
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165 <discover_datasets pattern="(?P&lt;name&gt;.+)\.fq\.discards$" ext="fastqsanger" directory="stacks_outputs" />
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166 <discover_datasets pattern="(?P&lt;name&gt;.+)\.fq\.gz.discards$" ext="fastqsanger" directory="stacks_outputs" /> <!-- discards are never gzipped -->
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167 <discover_datasets pattern="(?P&lt;name&gt;.+)\.fa\.discards$" ext="fasta" directory="stacks_outputs" />
0
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168 </collection>
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169 </outputs>
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170
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171 <tests>
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172 <test>
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173 <param name="options_type_selector" value="single"/>
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174 <param name="input_single" ftype="fastqsanger" value="procrad/R1.fq"/>
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175 <param name="barcode" value="procrad/barcodes"/>
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176 <param name="options_enzyme_selector" value="1"/>
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177 <param name="enzyme" value="ecoRI"/>
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178 <param name="discard" value="true"/>
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179 <param name="capture" value="true"/>
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180 <output name="output_log" file="procrad/process_radtags.out" compare="sim_size"/>
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181 <output_collection name="demultiplexed">
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182 <element name="PopA_01" compare="sim_size" file="demultiplexed/PopA_01.1.fq"/>
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183 </output_collection>
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184 <output_collection name="discarded">
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185 <element name="R1">
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186 <assert_contents>
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187 <has_text text="lane1_fakedata0_11" />
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188 </assert_contents>
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189 </element>
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190 </output_collection>
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191 </test>
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192 <test>
8
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193 <param name="options_type_selector" value="single"/>
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194 <param name="input_single" ftype="fastqsanger" value="procrad/R1.fq"/>
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195 <param name="barcode" value="procrad/barcodes"/>
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196 <param name="options_enzyme_selector" value="1"/>
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197 <param name="enzyme" value="ecoRI"/>
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198 <param name="discard" value="true"/>
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199 <param name="capture" value="true"/>
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200 <param name="outype" value="gzfastq"/>
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201 <output name="output_log" file="procrad/process_radtags.out" compare="sim_size"/>
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202 <output_collection name="demultiplexed">
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203 <element name="PopA_01" ftype="fastqsanger.gz" md5="c7250f50138cbca747b85223aaae9565"/>
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204 </output_collection>
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205 <output_collection name="discarded">
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206 <element name="R1" ftype="fastqsanger" md5="786b30d864332a2d56d9179f0a53add4"/>
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207 </output_collection>
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208 </test>
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209 <test>
0
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210 <param name="options_type_selector" value="paired"/>
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211 <param name="inputs_paired1" ftype="fastqsanger" value="procrad/R1.fq"/>
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212 <param name="inputs_paired2" ftype="fastqsanger" value="procrad/R2.fq"/>
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213 <param name="barcode" value="procrad/barcodes"/>
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214 <param name="options_enzyme_selector" value="1"/>
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215 <param name="enzyme" value="ecoRI"/>
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216 <param name="discard" value="true"/>
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217 <param name="capture" value="true"/>
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218 <output name="output_log" file="procrad/process_radtags.out" compare="sim_size"/>
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219 <output_collection name="demultiplexed">
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220 <element name="PopA_01.1" compare="sim_size" file="demultiplexed/PopA_01.1.fq"/>
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221 </output_collection>
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222 <output_collection name="remaining">
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223 <element name="PopA_01.rem.1" compare="sim_size" file="demultiplexed/PopA_01.rem.1.fq"/>
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224 </output_collection>
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225 <output_collection name="discarded">
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226 <element name="R1">
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227 <assert_contents>
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228 <has_text text="lane1_fakedata0_11" />
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229 </assert_contents>
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230 </element>
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231 </output_collection>
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232 </test>
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233 <test>
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234 <param name="options_type_selector" value="paired"/>
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235 <param name="inputs_paired1" ftype="fastqsanger" value="procrad/R1.fq"/>
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236 <param name="inputs_paired2" ftype="fastqsanger" value="procrad/R2.fq"/>
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237 <param name="barcode" value="procrad/barcodes"/>
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238 <param name="options_enzyme_selector" value="1"/>
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239 <param name="enzyme" value="ecoRI"/>
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240 <param name="discard" value="true"/>
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241 <param name="capture" value="true"/>
6
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242 <param name="retain_header" value="true"/>
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243 <output name="output_log" file="procrad/process_radtags.out" compare="sim_size"/>
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244 <output_collection name="demultiplexed">
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245 <element name="PopA_01.1" compare="sim_size" file="demultiplexed/PopA_01.1.fq.header"/>
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246 </output_collection>
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247 <output_collection name="remaining">
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248 <element name="PopA_01.rem.1" compare="sim_size" file="demultiplexed/PopA_01.rem.1.fq"/>
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249 </output_collection>
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250 <output_collection name="discarded">
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251 <element name="R1">
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252 <assert_contents>
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253 <has_text text="lane1_fakedata0_11" />
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254 </assert_contents>
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255 </element>
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256 </output_collection>
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257 </test>
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258 <test>
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259 <param name="options_type_selector" value="paired"/>
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260 <param name="inputs_paired1" ftype="fastqsanger" value="procrad/R1.fq"/>
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261 <param name="inputs_paired2" ftype="fastqsanger" value="procrad/R2.fq"/>
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262 <param name="barcode" value="procrad/barcodes"/>
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263 <param name="options_enzyme_selector" value="1"/>
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264 <param name="enzyme" value="ecoRI"/>
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265 <param name="discard" value="true"/>
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266 <param name="capture" value="true"/>
0
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267 <param name="outype" value="fasta"/>
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268 <output name="output_log" file="procrad/process_radtags.out" compare="sim_size"/>
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269 <output_collection name="demultiplexed">
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270 <element name="PopA_01.1" compare="sim_size" file="demultiplexed/PopA_01.1.fa"/>
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271 </output_collection>
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272 <output_collection name="remaining">
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273 <element name="PopA_01.rem.1" compare="sim_size" file="demultiplexed/PopA_01.rem.1.fa"/>
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274 </output_collection>
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275 <output_collection name="discarded">
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276 <element name="R1">
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277 <assert_contents>
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278 <has_text text="lane1_fakedata0_11" />
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279 </assert_contents>
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280 </element>
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281 </output_collection>
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282 </test>
8
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283 <test>
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284 <param name="options_type_selector" value="single"/>
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285 <param name="input_single" ftype="fastqsanger" value="procrad/R1.fq.gzip"/>
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286 <param name="barcode" value="procrad/barcodes"/>
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287 <param name="options_enzyme_selector" value="1"/>
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288 <param name="enzyme" value="ecoRI"/>
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289 <param name="discard" value="true"/>
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290 <param name="capture" value="true"/>
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291 <output name="output_log" file="procrad/process_radtags.out" compare="sim_size"/>
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292 <output_collection name="demultiplexed">
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293 <element name="PopA_01" compare="sim_size" file="demultiplexed/PopA_01.1.fq"/>
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294 </output_collection>
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295 <output_collection name="discarded">
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296 <element name="R1">
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297 <assert_contents>
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298 <has_text text="lane1_fakedata0_11" />
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299 </assert_contents>
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300 </element>
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301 </output_collection>
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302 </test>
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303 <test>
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304 <param name="options_type_selector" value="single"/>
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305 <param name="input_single" ftype="fastqsanger.gz" value="procrad/R1.fq.gzip"/>
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306 <param name="barcode" value="procrad/barcodes"/>
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307 <param name="options_enzyme_selector" value="1"/>
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308 <param name="enzyme" value="ecoRI"/>
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309 <param name="discard" value="true"/>
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310 <param name="capture" value="true"/>
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311 <param name="outype" value="gzfastq"/>
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312 <output name="output_log" file="procrad/process_radtags.out" compare="sim_size"/>
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313 <output_collection name="demultiplexed">
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314 <element name="PopA_01" compare="sim_size" file="demultiplexed/PopA_01.1.fq.gzip"/>
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315 </output_collection>
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316 <output_collection name="discarded">
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317 <element name="R1" ftype="fastqsanger" md5="786b30d864332a2d56d9179f0a53add4"/>
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318 </output_collection>
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319 </test>
0
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320 </tests>
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321
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322
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323
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324 <help>
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325 <![CDATA[
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326 .. class:: infomark
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327
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328 **What it does**
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329
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330 This program examines raw reads from an Illumina sequencing run and first, checks that the barcode and the RAD cutsite are intact, and demultiplexes the data. If there are errors in the barcode or the RAD site within a certain allowance process_radtags can correct them. Second, it slides a window down the length of the read and checks the average quality score within the window. If the score drops below 90% probability of being correct (a raw phred score of 10), the read is discarded. This allows for some seqeuncing errors while elimating reads where the sequence is degrading as it is being sequenced. By default the sliding window is 15% of the length of the read, but can be specified on the command line (the threshold and window size can be adjusted).
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331
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332 The process_radtags program can:
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333
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334 - handle data that is barcoded, either inline or using an index, or unbarcoded.
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335 - use combinatorial barcodes.
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336 - check and correct for a restriction enzyme cutsite for single or double-digested data.
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337 - filter adapter sequence while allowing for sequencing error in the adapter pattern.
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338 - process individual files or whole directories of files.
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339 - directly read gzipped data
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340 - filter reads based on Illumina's Chastity filter
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341
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342 **Help**
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343
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344 Input files:
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345
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346 - FASTQ
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347
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348 - Barcode File Format
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349
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350 The barcode file is a very simple format:
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351
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352 ======= ===========
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353 Barcode Sample name
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354 ======= ===========
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355 ATGGGG PopA_01
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356 GGGTAA PopA_02
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357 AGGAAA PopA_03
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358 TTTAAG PopA_04
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359 GGTGTG PopA_05
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360 TGATGT PopA_06
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361 ======= ===========
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362
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363 Combinatorial barcodes are specified, one per column, separated by a tab:
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364
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365 ======== ======== ===========
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366 Barcode1 Barcode2 Sample name
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367 ======== ======== ===========
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368 CGATA ACGTA PopA_01
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369 CGGCG CGTA PopA_02
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370 GAAGC CGTA PopA_03
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371 GAGAT CGTA PopA_04
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372 CGATA AGCA PopA_05
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373 CGGCG AGCA PopA_06
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374 ======== ======== ===========
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375
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376 @STACKS_INFOS@
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377 ]]>
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378 </help>
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379 <expand macro="citation" />
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380 </tool>