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annotate sickle.xml @ 0:a5f56370e870 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1
author iuc
date Thu, 12 Nov 2015 07:05:48 -0500
parents
children 43e081d32f90
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0
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1
iuc
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1 <tool id="sickle" name="Sickle" version="1.33">
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1
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2 <description>windowed adaptive trimming of FASTQ data</description>
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1
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3 <requirements>
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iuc
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4 <requirement type="package" version="1.33">sickle</requirement>
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5 </requirements>
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6 <version_command>sickle --version | head -n 1</version_command>
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7 <command>
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8 sickle
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9
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10 #if str($readtype.single_or_paired) == "se":
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11 se -f "${readtype.input_single}" -o "$output_single"
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1
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12
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13 #if $readtype.input_single.ext in ("fastq", "fastqsanger"):
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1
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14 -t sanger
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1
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15 #else if $readtype.input_single.ext == "fastqillumina":
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1
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16 -t illumina
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17 #else if $readtype.input_single.ext == "fastqsolexa":
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1
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18 -t solexa
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19 #end if
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20 #end if
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21
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22 #if str($readtype.single_or_paired) == "pe_combo":
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23 #if $readtype.output_n:
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24 pe -c "${readtype.input_combo}" -M "$output_combo"
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25 #else
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26 pe -c "${readtype.input_combo}" -m "$output_combo" -s "$output_combo_single"
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1
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27 #end if
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28
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29 #if $readtype.input_combo.ext in ("fastq", "fastqsanger"):
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1
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30 -t sanger
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31 #else if $readtype.input_combo.ext == "fastqillumina":
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1
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32 -t illumina
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33 #else if $readtype.input_combo.ext == "fastqsolexa":
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1
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34 -t solexa
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35 #end if
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36 #end if
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37
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38 #if str($readtype.single_or_paired) == "pe_sep":
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1
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39 pe -f "${readtype.input_paired1}" -r "${readtype.input_paired2}" -o "$output_paired1" -p "$output_paired2" -s "$output_paired_single"
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1
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40
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41 #if $readtype.input_paired1.ext in ("fastq", "fastqsanger"):
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42 -t sanger
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43 #else if $readtype.input_paired1.ext == "fastqillumina":
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1
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44 -t illumina
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45 #else if $readtype.input_paired1.ext == "fastqsolexa":
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46 -t solexa
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47 #end if
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48 #end if
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49
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50 #if str($qual_threshold) != "":
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51 -q $qual_threshold
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52 #end if
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53
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54 #if str($length_threshold) != "":
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55 -l $length_threshold
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56 #end if
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57
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58 #if $no_five_prime:
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59 -x
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60 #end if
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61
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62 #if $trunc_n:
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63 -n
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64 #end if
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65 </command>
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66
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67 <inputs>
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68 <conditional name="readtype">
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69 <param name="single_or_paired" type="select" label="Single-end or paired-end reads?" help="Note: Sickle will infer the quality type of the file from its datatype. I.e., if the datatype is fastqsanger, then the quality type is sanger. The default is fastqsanger.">
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70 <option value="se" selected="true">Single-end</option>
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71 <option value="pe_combo">Paired-end (one interleaved input file)</option>
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72 <option value="pe_sep">Paired-end (two separate input files)</option>
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73 </param>
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74
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75 <when value="se">
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76 <param format="fastq" name="input_single" type="data" label="Single-end FASTQ reads" help="(-f)" />
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77 </when>
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78
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79 <when value="pe_combo">
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80 <param format="fastq" name="input_combo" type="data" label="Paired-end interleaved FASTQ reads" help="(-c)" />
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81 <param name="output_n" type="boolean" label="Output only one file with all reads" help="This will output only one file with all the reads, where the reads that did not pass filter will be replaced with a single 'N', rather than discarded."/>
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82 </when>
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83
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84 <when value="pe_sep">
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85 <param format="fastq" name="input_paired1" type="data" label="Paired-end forward strand FASTQ reads" help="(-f)" />
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86 <param format="fastq" name="input_paired2" type="data" label="Paired-end reverse strand FASTQ reads" help="(-r)" />
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87 </when>
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88 </conditional>
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89
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90 <param name="qual_threshold" value="20" min="0" type="integer" optional="true" label="Quality threshold" help="Threshold for trimming based on average quality in a window (-q)" />
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91
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92 <param name="length_threshold" value="20" min="0" type="integer" optional="true" label="Length threshold" help="Threshold to keep a read based on length after trimming (-l)" />
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93
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94 <param name="no_five_prime" type="boolean" label="Don't do 5' trimming" help="(-x)" />
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95 <param name="trunc_n" type="boolean" label="Truncate sequences with Ns at first N position" help="(-n)" />
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96 </inputs>
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97
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98 <outputs>
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99 <data name="output_single" format_source="input_single" label="Single-end output of ${tool.name} on ${on_string}">
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100 <filter>readtype['single_or_paired'] == 'se'</filter>
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101 </data>
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102
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103 <data name="output_combo" format_source="input_combo" label="Paired-end interleaved output of ${tool.name} on ${on_string}">
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104 <filter>readtype['single_or_paired'] == 'pe_combo'</filter>
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105 </data>
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106
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107 <data name="output_combo_single" format_source="input_combo" label="Singletons from paired-end interleaved output of ${tool.name} on ${on_string}">
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108 <filter>readtype['single_or_paired'] == 'pe_combo' and not readtype['output_n']</filter>
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109 </data>
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110
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111 <data name="output_paired1" format_source="input_paired1" label="Paired-end forward strand output of ${tool.name} on ${on_string}">
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112 <filter>readtype['single_or_paired'] == 'pe_sep'</filter>
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113 </data>
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114
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115 <data name="output_paired2" format_source="input_paired2" label="Paired-end reverse strand output of ${tool.name} on ${on_string}">
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116 <filter>readtype['single_or_paired'] == 'pe_sep'</filter>
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117 </data>
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118
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119 <data name="output_paired_single" format_source="input_paired1" label="Singletons from paired-end output of ${tool.name} on ${on_string}">
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120 <filter>readtype['single_or_paired'] == 'pe_sep'</filter>
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121 </data>
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122 </outputs>
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123 <tests>
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124 <test>
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125 <param name="single_or_paired" value="pe_combo" />
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126 <param name="input_combo" value="test.fastq" />
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127 <param name="qual_threshold" value="34" />
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128 <output name="output_combo" file="output.c1.fastq" />
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129 <output name="output_combo_single" file="output.s.fastq" />
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130 </test>
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131 <test>
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132 <param name="single_or_paired" value="pe_combo" />
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133 <param name="input_combo" value="test.fastq" />
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134 <param name="qual_threshold" value="34" />
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135 <param name="output_n" value="true" />
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136 <output name="output_combo" file="output.c2.fastq" />
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137 </test>
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138 <test>
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139 <param name="single_or_paired" value="pe_sep" />
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140 <param name="input_paired1" value="test.f.fastq" />
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141 <param name="input_paired2" value="test.r.fastq" />
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142 <param name="qual_threshold" value="34" />
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143 <output name="output_paired1" file="output.f.fastq" />
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144 <output name="output_paired2" file="output.r.fastq" />
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145 <output name="output_paired_single" file="output.s.fastq" />
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146 </test>
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147 </tests>
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148 <help>
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149 **What it does**
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150
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151 Most modern sequencing technologies produce reads that have
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152 deteriorating quality towards the 3'-end and some towards the 5'-end
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153 as well. Incorrectly called bases in both regions negatively impact
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154 assembles, mapping, and downstream bioinformatics analyses.
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155
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156 Sickle is a tool that uses sliding windows along with quality and
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157 length thresholds to determine when quality is sufficiently low to
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158 trim the 3'-end of reads and also determines when the quality is
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159 sufficiently high enough to trim the 5'-end of reads. It will also
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160 discard reads based upon the length threshold. It takes the quality
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161 values and slides a window across them whose length is 0.1 times the
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162 length of the read. If this length is less than 1, then the window is
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163 set to be equal to the length of the read. Otherwise, the window
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164 slides along the quality values until the average quality in the
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165 window rises above the threshold, at which point the algorithm
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166 determines where within the window the rise occurs and cuts the read
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167 and quality there for the 5'-end cut. Then when the average quality
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168 in the window drops below the threshold, the algorithm determines
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169 where in the window the drop occurs and cuts both the read and quality
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170 strings there for the 3'-end cut. However, if the length of the
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171 remaining sequence is less than the minimum length threshold, then the
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172 read is discarded entirely (or replaced with an "N" record). 5'-end
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173 trimming can be disabled. Sickle also has an option to truncate reads
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174 with Ns at the first N position.
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175
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176 Sickle supports three types of quality values: Illumina, Solexa, and
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177 Sanger. Note that the Solexa quality setting is an approximation (the
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178 actual conversion is a non-linear transformation). The end
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179 approximation is close. Illumina quality refers to qualities encoded
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180 with the CASAVA pipeline between versions 1.3 and 1.7. Illumina
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181 quality using CASAVA >= 1.8 is Sanger encoded. The quality value will
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182 be determined from the datatype of the data, i.e. a fastqsanger datatype
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183 is assumed to be Sanger encoded.
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184
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185 Note that Sickle will remove the 2nd FASTQ record header (on the "+"
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186 line) and replace it with simply a "+". This is the default format for
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187 CASAVA >= 1.8.
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188
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189 -----
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190
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191 **Options**
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192
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193 **Single-end**
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194
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195 This option takes one single-end input file and outputs one single-end
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196 output file of reads that passed the filters.
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197
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198 **Paired-End (one interleaved input file)**
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199
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200 This option takes as input one interleaved paired-end file. If you then
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201 check the "Output only one file with all reads" checkbox, it will output
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202 one interleaved file where any read that did not pass filter will be replaced
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203 with a FASTQ record where the sequence is a single "N" and the quality is the
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204 lowest quality possible for that quality type. This will preserve the paired
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205 nature of the data. If you leave the checkbox unchecked, it will output two files,
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206 one interleaved file with all the passed pairs and one singletons file where only
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207 one of the pair passed filter.
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208
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209 **Paired-End (two separate input files)**
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210
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211 This option takes two separate (forward and reverse) paired-end files as input.
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212 The output is three files: Two paired-end files with pairs that passed filter and
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213 a singletons file where only one of the pair passed filter.
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214
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215 **Quality threshold**
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216
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217 Input your desired quality threshold. This threshold is phred-scaled, which is typically
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218 values between 0-41 for FASTQ data.
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219
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220 **Length threshold**
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221
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222 Input your desired length threshold. This is the threshold to determine if a read is kept
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223 after all the trimming steps are done.
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224
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225 **Disable 5-prime trimming**
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226
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227 An option to disable trimming the read on the 5-prime end. This trimming trims the read
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228 if the average quality values dip below the quality threshold at the 5-prime end.
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229
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230 **Truncate sequences with Ns**
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231
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232 This option will trim a read at the first "N" base in the read after doing quality trimming.
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233 It is then still subject to the length threshold.
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234
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235 -----
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236
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237 Copyright: Nikhil Joshi
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238
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239 http://bioinformatics.ucdavis.edu
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240
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241 http://github.com/najoshi/sickle
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242 </help>
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243 <citations>
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244 <citation type="bibtex">
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245 @unpublished{sickle_link,
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246 author = {Joshi, Nikhil A. and Fass, Joseph N.},
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247 title = {Sickle: A windowed adaptive trimming tool for FASTQ files using quality},
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248 year = 2011,
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249 url = { https://github.com/najoshi/sickle }
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250 }
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251 </citation>
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252 </citations>
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253 </tool>