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1 <tool id="solid_to_fastq" name="SOLiD-to-FASTQ" version="1.0.0">
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2 <description>converts SOLiD data to FASTQ data</description>
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3 <command interpreter="python">
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4 solid_to_fastq.py
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5 --input1=$input1
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6 --input2=$input2
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7 #if $paired.pairedSingle == "single":
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8 --input3="None"
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9 --input4="None"
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10 #else:
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11 --input3=$input3
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12 --input4=$input4
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13 #end if
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14 --output1=$output1
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15 #if $paired.pairedSingle == "single":
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16 --output2="None"
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17 #else:
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18 --output2=$output2
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19 #end if
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20 </command>
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21 <inputs>
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22 <conditional name="paired">
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23 <param name="pairedSingle" type="select" label="Is this library mate-paired?">
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24 <option value="single">Single</option>
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25 <option value="paired">Paired</option>
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26 </param>
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27 <when value="single">
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28 <param name="input1" type="data" format="csfasta" label="F3 read file" />
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29 <param name="input2" type="data" format="qualsolid" label="F3 qual file" />
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30 </when>
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31 <when value="paired">
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32 <param name="input1" type="data" format="csfasta" label="F3 read file" />
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33 <param name="input2" type="data" format="qualsolid" label="F3 qual file" />
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34 <param name="input3" type="data" format="csfasta" label="R3 read file" />
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35 <param name="input4" type="data" format="qualsolid" label="R3 qual file" />
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36 </when>
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37 </conditional>
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38 </inputs>
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39 <outputs>
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40 <!-- Variable number of outputs. Either one (for single-end) or two (for paired-end) -->
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41 <data name="output1" format="fastqsanger"/>
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42 <data name="output2" format="fastqsanger">
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43 <filter>paired['pairedSingle'] == 'paired'</filter>
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44 </data>
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45 </outputs>
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46 <tests>
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47 <test>
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48 <param name="pairedSingle" value="single" />
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49 <param name="input1" value="s2fq_phiX.csfasta" ftype="csfasta" />
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50 <param name="input2" value="s2fq_phiX.qualsolid" ftype="qualsolid" />
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51 <output name="output1" file="s2fq_out1.fastqsanger" />
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52 </test>
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53 <test>
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54 <param name="pairedSingle" value="paired" />
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55 <param name="input1" value="s2fq_paired_F3.csfasta" ftype="csfasta" />
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56 <param name="input2" value="s2fq_paired_F3_QV.qualsolid" ftype="qualsolid" />
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57 <param name="input3" value="s2fq_paired_R3.csfasta" ftype="csfasta" />
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58 <param name="input4" value="s2fq_paired_R3_QV.qualsolid" ftype="qualsolid" />
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59 <output name="output1" file="s2fq_out2.fastqsanger" />
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60 <!-- testing framework does not deal with multiple outputs yet
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61 <output name="output2" file="s2fq_out3.fastqsanger" />
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62 -->
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63 </test>
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64 </tests>
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65 <help>
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66
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67 **What it does**
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68
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69 This tool takes reads and quality files and converts them to FASTQ data ( Sanger variant ). Any -1 qualities are converted to 1 before being converted to FASTQ. Note that it also converts sequences to base pairs.
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70
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71 -----
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72
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73 **Example**
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74
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75 - Converting the following sequences::
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76
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77 >1831_573_1004_F3
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78 T00030133312212111300011021310132222
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79 >1831_573_1567_F3
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80 T03330322230322112131010221102122113
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81
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82 - and quality scores::
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83
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84 >1831_573_1004_F3
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85 4 29 34 34 32 32 24 24 20 17 10 34 29 20 34 13 30 34 22 24 11 28 19 17 34 17 24 17 25 34 7 24 14 12 22
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86 >1831_573_1567_F3
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87 8 26 31 31 16 22 30 31 28 29 22 30 30 31 32 23 30 28 28 31 19 32 30 32 19 8 32 10 13 6 32 10 6 16 11
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88
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89 - will produce the following Sanger FASTQ data::
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90
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91 @1831_573_1004/1
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92 AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG
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93 +
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94 >CCAA9952+C>5C.?C79,=42C292:C(9/-7
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95 @1831_573_1567/1
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96 TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT
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97 +
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98 ;@@17?@=>7??@A8?==@4A?A4)A+.'A+'1,
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99
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100 </help>
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101 </tool>
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