Mercurial > repos > devteam > fastq_quality_converter

annotate fastq_quality_converter.xml @ 2:54053ea6c77e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
author iuc
date Tue, 08 May 2018 13:26:24 -0400
parents 74db4cffab1f
children 045f0e1043f7
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54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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1 <tool id="cshl_fastq_quality_converter" name="Quality format converter" version="1.0.1">
1
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2 <description>(ASCII-Numeric)</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 @CATS@ fastq_quality_converter
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9 $QUAL_FORMAT
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10 -o '$output'
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11 @FQQUAL@
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12 ]]></command>
1
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13 <inputs>
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14 <expand macro="fastq_input" />
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15
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16 <param name="QUAL_FORMAT" type="select" label="Desired output format">
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17 <option value="-a">ASCII (letters) quality scores</option>
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18 <option value="-n">Numeric quality scores</option>
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19 </param>
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20 </inputs>
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21 <outputs>
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22 <data name="output" format="fastq" metadata_source="input" />
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23 </outputs>
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24 <tests>
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25 <test>
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26 <!-- ASCII to NUMERIC -->
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27 <param name="input" ftype="fastqillumina" value="fastq_qual_conv1.fastq" />
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28 <param name="QUAL_FORMAT" value="Numeric quality scores" />
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29 <output name="output" file="fastq_qual_conv1.out" />
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30 </test>
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31 <test>
2
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32 <!-- ASCII to ASCII (should basically copy the input to the output unchanged) -->
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33 <param name="input" ftype="fastqillumina" value="fastq_qual_conv1.fastq" />
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34 <param name="QUAL_FORMAT" value="ASCII (letters) quality scores" />
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35 <output name="output" file="fastq_qual_conv1a.out" />
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36 </test>
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37 <test>
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38 <!-- NUMERIC to ASCII -->
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39 <param name="input" ftype="fastqillumina" value="fastq_qual_conv2.fastq" />
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40 <param name="QUAL_FORMAT" value="ASCII (letters) quality scores" />
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41 <output name="output" file="fastq_qual_conv2.out" />
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42 </test>
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43 <test>
2
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44 <!-- NUMERIC to NUMERIC (should basically copy the input to the output unchanged) -->
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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45 <param name="input" ftype="fastqillumina" value="fastq_qual_conv2.fastq" />
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46 <param name="QUAL_FORMAT" value="Numeric quality scores" />
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47 <output name="output" file="fastq_qual_conv2n.out" />
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48 </test>
2
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49 <test>
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50 <!-- ASCII to NUMERIC -->
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51 <param name="input" ftype="fastqsanger" value="fastq_quality_converter-in5.fastq" />
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52 <param name="QUAL_FORMAT" value="Numeric quality scores" />
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53 <output name="output" file="fastq_quality_converter-out5.fastq" />
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54 </test>
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55 <test>
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56 <!-- ASCII to ASCII (should basically copy the input to the output unchanged) -->
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57 <param name="input" ftype="fastqsanger" value="fastq_quality_converter-in6.fastq" />
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58 <param name="QUAL_FORMAT" value="ASCII (letters) quality scores" />
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59 <output name="output" file="fastq_quality_converter-out6.fastq" />
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60 </test>
1
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61 </tests>
2
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62 <help><![CDATA[
0
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63 **What it does**
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64
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65 Converts a Solexa FASTQ file to/from numeric or ASCII quality format.
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66
1
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67 .. class:: warningmark
0
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68
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69 Re-scaling is **not** performed. (e.g. conversion from Phred scale to Solexa scale).
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70
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71 -----
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72
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73 FASTQ with Numeric quality scores::
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74
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75 @CSHL__2_FC042AGWWWXX:8:1:120:202
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76 ACGATAGATCGGAAGAGCTAGTATGCCGTTTTCTGC
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77 +CSHL__2_FC042AGWWWXX:8:1:120:202
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78 40 40 40 40 20 40 40 40 40 6 40 40 28 40 40 25 40 20 40 -1 30 40 14 27 40 8 1 3 7 -1 11 10 -1 21 10 8
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79 @CSHL__2_FC042AGWWWXX:8:1:103:1185
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80 ATCACGATAGATCGGCAGAGCTCGTTTACCGTCTTC
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81 +CSHL__2_FC042AGWWWXX:8:1:103:1185
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82 40 40 40 40 40 35 33 31 40 40 40 32 30 22 40 -0 9 22 17 14 8 36 15 34 22 12 23 3 10 -0 8 2 4 25 30 2
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83
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84
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85 FASTQ with ASCII quality scores::
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86
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87 @CSHL__2_FC042AGWWWXX:8:1:120:202
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88 ACGATAGATCGGAAGAGCTAGTATGCCGTTTTCTGC
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89 +CSHL__2_FC042AGWWWXX:8:1:120:202
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90 hhhhThhhhFhh\hhYhTh?^hN[hHACG?KJ?UJH
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91 @CSHL__2_FC042AGWWWXX:8:1:103:1185
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92 ATCACGATAGATCGGCAGAGCTCGTTTACCGTCTTC
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93 +CSHL__2_FC042AGWWWXX:8:1:103:1185
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94 hhhhhca_hhh`^Vh@IVQNHdObVLWCJ@HBDY^B
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95
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96 ------
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97
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98 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
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99
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100 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
2
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101 ]]></help>
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102 <expand macro="citations" />
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103 <!-- FASTQ-Quality-Converter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
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104 </tool>