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author nml
date Tue, 15 Dec 2015 14:19:42 -0500
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1 <?xml version="1.0"?>
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2 <tool id="spolpred" name="SpolPred" version="1.0.0">
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3 <description>with options and commands</description>
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4 <requirements>
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5 <requirement type="package" version="1.0.0">spolpred</requirement>
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6 </requirements>
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7 <command interpreter="bash">
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8
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9 #set $output=$input_file.name
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10
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11 spolpred.sh "$input_file.name" $input_file
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12
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13 -l $read_length -b $type_reads -d $more_details -s $screening_options.stop_screening
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14
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15 #if $screening_options.stop_screening == "on":
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16 -a $screening_options.screening_threshold
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17 #end if
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18
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19 -m $matching_threshold
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20
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21 </command>
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22 <inputs>
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23 <param name="input_file" type="data" format="fastqsanger" label="FASTQ input file"/>
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24
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25 <param name="read_length" type="integer" label="Read length [35, 1000]" value="75">
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26 <validator type="in_range" min="35" max="1000" message="Must be between 35 and 1000 (inclusive)"/>
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27 </param>
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28
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29 <param name="type_reads" type="select" label="Type of input reads">
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30 <option value="d">Direct</option>
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31 <option value="r">Reverse</option>
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32 </param>
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33
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34 <param name="more_details" type="select" label="Level of processing output detail"
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35 help="If set on, processing details are output to the job's STDOUT, including
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36 number of processed reads and number of spacer sequences found">
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37 <option value="on">High</option>
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38 <option value="off">Normal</option>
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39 </param>
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40
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41 <conditional name="screening_options">
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42 <param name="stop_screening" type="select" label="Read screening"
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43 help="Used to end read processing when Screening Threshold is reached">
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44 <option value="on">Perform read screening</option>
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45 <option value="off">Do not perform read screening</option>
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46 </param>
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47 <when value="on">
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48 <param name="screening_threshold" type="integer" label="Screening threshold" value="50"
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49 help="Average number of spacer occurrences used to stop screening">
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50 <validator type="in_range" min="0" max="inf" message="Must be at least 0"/>
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51 </param>
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52 </when>
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53 <when value="off"/>
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54 </conditional>
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55
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56 <param name="matching_threshold" type="integer" label="Matching threshold" value="4"
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57 help="Minimum number of spacer occurrences below which spacer absence is assigned">
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58 <validator type="in_range" min="1" max="inf" message="Must be at least 1"/>
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59 </param>
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60
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61 </inputs>
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62 <outputs>
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63 <data name="outfile" format="tabular" from_work_dir="output.txt"/>
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64 </outputs>
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65
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66 <tests>
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67 <test>
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68 <param/>
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69 <output/>
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70 </test>
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71 </tests>
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72
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73 <help>
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74 **Frequently Asked Questions**
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75
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76 **SpolPred only accepts one FASTQ file, what if I have got paired-end reads?**
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77
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78 Forward and reverse read files can be merged into one by making use of the Perl script
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79 shuffleSequences_fastq.pl provided in Velvet software suite. SpolPred run will therefore take longer
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80 than using only forward or reverse reads. In our dataset (read Methods for more details), the forward file
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81 had enough reads to find all present spacers and infer the octal code for 49 out of 51 samples. That
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82 decision will have to be made depending on the sample coverage depth.
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83
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84
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85
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86 **What if I have a FASTA file?**
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87
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88 SpolPred has been particularly designed to process raw reads and therefore only supports sequence
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89 files in FASTQ format.
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90
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91
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92
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93 **What is the point of stopping the read screening?**
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94
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95 By default, all reads in the FASTQ file will be processed. Nevertheless, we have observed that a point is
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96 reached when no more reads are needed to infer the octal code, in other words, the number of spacer
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97 occurrences is high enough and steady to assume that all present spacers have already been found.
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98 Therefore, stopping the program at this point would save time and computer resources. If low coverage
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99 is the case, stopping the scanning is not advisable.
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100
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101
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102
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103 **How do I choose the Screening threshold?**
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104
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105 If you have decided to scan the whole input file there is no need to set such threshold. The Screening
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106 threshold is used to let the program know when the screening should stop. Such value will depend on
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107 read coverage. Running the software and looking at the number of times all spacers are detected will
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108 provide insight into both the coverage and the most appropriate threshold value.
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109
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110
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111
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112 **Why is a Matching threshold required? Are spacers not supposed to occur uniquely?**
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113
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114 The number of times each spacer is found is tracked during the screening and absence assigned when
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115 such number does not reach a user-defined threshold (4 times by default). This threshold, here called
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116 Matching threshold, has had to be implemented because for some absent spacers, a few spurious
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117 matches were found. Those false positives are likely to be related with bad-quality issues, like
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118 sequencing errors. In our data set, no more than 3 false matches were detected for absent spacers, in
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119 contrast to 50-150 found per present spacer.
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120
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121
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122
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123 **Should I be worried then about false positive matches?**
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124
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125 As long as proper pre-filtering steps are carried out to the raw reads, no important issues are expected
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126 to come up.
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127
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128
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129
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130 **Can I change the number of allowed SNPs when querying the spacers?**
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131
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132 This option has not been implemented. Spacer sequences are conserved and only one SNP has been
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133 reported to occur at the most.
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134
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135
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136
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137 **Why are exact matches output as well?**
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138
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139 The number of read-spacer exact matches, i.e. without allowing SNPs, will enable the easily
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140 identification of SNPs on spacer sequences. When inferring the octal code, exact matches are not
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141 employed.
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142
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143 Wrapper Author: Mark Iskander
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144 </help>
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145 <citations>
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146 <citation type="doi">10.1093/bioinformatics/bts544</citation>
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147 </citations>
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148 </tool>