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annotate quality.xml @ 6:9fb9fed71486 draft

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planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
author nml
date Fri, 12 Oct 2018 09:16:03 -0400
parents b69e898b8109
children dcd43b402eb3
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1 <tool id="quality" name="Quality control" version="0.4.2">
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2 <description>Performs quality control on FASTQ reads.</description>
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3 <requirements>
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4 <requirement type="package" version="0.4.2">quasitools</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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8 quasitools quality
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10 ## Preparing file input.
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11 #if $data_type.type == "paired":
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13 '$data_type.fastq_input1'
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14 '$data_type.fastq_input2'
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16 #elif $data_type.type == "collection":
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18 '$data_type.fastq_input1.forward'
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19 '$data_type.fastq_input1.reverse'
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21 #elif $data_type.type == "single":
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23 '$data_type.fastq_input1'
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25 #end if
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27 #if $length_cutoff:
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28 -lc '$length_cutoff'
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29 #end if
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31 #if $score_cutoff:
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32 -sc '$score_cutoff'
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33 #end if
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35 #if $min_read_qual:
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36 -rq '$min_read_qual'
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37 #end if
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39 #if $low_quality.qual_selector == "filter_ns":
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40 --ns
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41 #elif $low_quality.qual_selector == "mask_reads":
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42 --mask_reads
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43 #end if
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45 #if $score_type.score_selector == "median":
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46 --median
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47 #elif $score_type.score_selector == "mean":
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48 --mean
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49 #end if
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51 $trim_reads
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53 -o output
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55 ]]></command>
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56 <inputs>
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57 <conditional name="data_type">
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58 <param name="type" type="select" label="Specify the read type.">
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59 <option value="single">Single-end Data</option>
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60 <option value="paired">Paired-end Data</option>
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61 <option value="collection">Collection Paired-end Data</option>
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62 </param>
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63 <when value="single">
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64 <param name="fastq_input1" type="data" format="fastq" label="Single end read file(s)"/>
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65 </when>
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66 <when value="paired">
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67 <param name="fastq_input1" type="data" format="fastq" label="Forward paired-end read file"/>
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68 <param name="fastq_input2" type="data" format="fastq" label="Reverse paired-end read file"/>
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69 </when>
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70 <when value="collection">
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71 <param name="fastq_input1" type="data_collection" label="Paired-end reads collection" optional="false" format="fastq" collection_type="paired" />
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72 </when>
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73 </conditional>
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74 <param name="length_cutoff" type="integer" optional="true" min="1" max="1000" label="Length cutoff" value="100" help="Reads which fall short of the specified length will be filtered out. Defaults to 100." />
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75 <param name="score_cutoff" type="integer" optional="true" min="0" max="40" label="Score cutoff" value="30" help="Reads whose median or mean quality score (depending on the score type specified) is less than the specified score cutoff value will be filtered out. Defaults to 30." />
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76 <param name="min_read_qual" type="integer" optional="true" min="1" max="100" label="Minimum quality" value="30" help="Minimum required quality for a position in a read not to be masked, is masking is enabled. Defaults to 30." />
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77 <param name="trim_reads" type="boolean" optional="true" checked="false" truevalue="-tr" falsevalue="" label="Trim reads" help="Iteratively trim reads based on filter values if enabled." />
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78 <conditional name="low_quality">
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79 <param name="qual_selector" type="select" label="Filter out regions masked, or mask low coverage regions with n's." multiple="false" display="radio">
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80 <option value="filter_ns">Filter out regions with n's</option>
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81 <option value="mask_reads">Mask low coverage regions with n's</option>
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82 <option value="neither" selected="true">Do not filter or mask low coverage regions.</option>
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83 </param>
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84 <when value="filter_ns">
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85 </when>
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86 <when value="mask_reads">
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87 </when>
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88 <when value="neither">
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89 </when>
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90 </conditional>
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91 <conditional name="score_type">
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92 <param name="score_selector" type="select" label="Use either median score (default) or mean score for the score cutoff value." multiple="false" display="radio">
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93 <option value="median" selected="true">Use median score</option>
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94 <option value="mean">Use mean score</option>
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95 </param>
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96 <when value="median">
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97 </when>
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98 <when value="mean">
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99 </when>
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100 </conditional>
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101 </inputs>
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102 <outputs>
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103 <data format="fastq" label="Quality control output" name="output_filtered" from_work_dir="output/filtered.fastq" />
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104 </outputs>
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105 <tests>
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106 <test>
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107 <param name="type" value="single"/>
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108 <param name="fastq_input1" value="forward.fastq" />
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109 <param name="score_selector" value="median" />
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110 <output name="output_filtered">
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111 <assert_contents>
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112 <has_text text="@M01647:10:000000000-ACPHB:1:1101:18589:1580 1:N:0:86" />
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113 <has_text text="CCCCCGG@FFGGGGGGGGGGGGCGGGGGGGGDGFFFGGGGGDEGCFGCFFFGGGGGGGGGGGGGGGGFGGGGGGGGGGFCFCGGGGCGFGGGGFGEGGGGGGGGGGGGGGGGGGGGGFEFGGGGGGF" />
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114 </assert_contents>
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115 </output>
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116 </test>
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117 <test>
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118 <param name="type" value="single"/>
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119 <param name="fastq_input1" value="forward.fastq" />
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120 <param name="score_selector" value="median" />
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121 <param name="qual_selector" value="filter_ns" />
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122 <output name="output_filtered">
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123 <assert_contents>
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124 <has_text text="@M01647:10:000000000-ACPHB:1:1101:18589:1580 1:N:0:86" />
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125 <has_text text="CCCCCGG@FFGGGGGGGGGGGGCGGGGGGGGDGFFFGGGGGDEGCFGCFFFGGGGGGGGGGGGGGGGFGGGGGGGGGGFCFCGGGGCGFGGGGFGEGGGGGGGGGGGGGGGGGGGGGFEFGGGGGGF" />
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126 </assert_contents>
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127 </output>
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128 </test>
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129 <test>
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130 <param name="type" value="single"/>
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131 <param name="fastq_input1" value="forward.fastq" />
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132 <param name="score_selector" value="median" />
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133 <param name="trim_reads" value="-tr" />
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134 <output name="output_filtered">
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135 <assert_contents>
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136 <has_text text="@M01647:10:000000000-ACPHB:1:1101:18589:1580 1:N:0:86" />
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137 <has_text text="CCCCCGG@FFGGGGGGGGGGGGCGGGGGGGGDGFFFGGGGGDEGCFGCFFFGGGGGGGGGGGGGGGGFGGGGGGGGGGFCFCGGGGCGFGGGGFGEGGGGGGGGGGGGGGGGGGGGGFEFGGGGGGF" />
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138 </assert_contents>
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139 </output>
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140 </test>
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141 <test>
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142 <param name="type" value="single"/>
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143 <param name="fastq_input1" value="forward.fastq" />
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144 <param name="score_selector" value="median" />
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145 <param name="qual_selector" value="mask_reads" />
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146 <output name="output_filtered">
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147 <assert_contents>
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148 <has_text text="@M01647:10:000000000-ACPHB:1:1101:18589:1580 1:N:0:86" />
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149 <has_text text="NNNNNNTACCACATCCCNCNNNNTTNNNNNNNNNNANNTCNNTNNCNNTNCTNNNTNTNNNTGNTGCNTNTTTTTCAGTTCCCTTNGNTGNNGNCTTCAGNNNNTATACTGCATTTACCNTNCNT" />
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150 </assert_contents>
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151 </output>
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152 </test>
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153 <test>
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154 <param name="type" value="single"/>
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155 <param name="fastq_input1" value="forward.fastq" />
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156 <param name="score_selector" value="mean" />
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157 <output name="output_filtered">
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158 <assert_contents>
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159 <has_text text="@M01647:10:000000000-ACPHB:1:1101:10485:1674 1:N:0:86" />
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160 <has_text text="CCCCCGG@FFGGGGGGGGGGGGCGGGGGGGGDGFFFGGGGGDEGCFGCFFFGGGGGGGGGGGGGGGGFGGGGGGGGGGFCFCGGGGCGFGGGGFGEGGGGGGGGGGGGGGGGGGGGGFEFGGGGGGF" />
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161 </assert_contents>
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162 </output>
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163 </test>
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164 </tests>
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165 <help><![CDATA[
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166 Quality Control
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167 ===============
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168
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169 Perform quality control on FASTQ reads.]]></help>
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170 <citations>
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171 </citations>
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172 </tool>