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annotate fastq_groomer.xml @ 3:bbc72602f69f draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
author devteam
date Sat, 30 Sep 2017 14:55:55 -0400
parents 6b294cefd2ae
children dafabb4c2037
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bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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1 <tool id="fastq_groomer" name="FASTQ Groomer" version="1.1.1">
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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2 <description>convert between various FASTQ quality formats</description>
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3 <requirements>
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4 <requirement type="package" version="1.1.1">galaxy_sequence_utils</requirement>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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5 </requirements>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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6 <command><![CDATA[
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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7 gx-fastq-groomer '$input_file'
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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8 #if $input_file.extension.endswith(".gz"):
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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9 #set $suffix = ".gz"
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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10 #elif $input_file.extension.endswith(".bz2"):
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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11 #set $suffix = ".bz2"
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12 #else:
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bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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13 #set $suffix = ""
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14 #end if
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bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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15 $input_type$suffix '$output_file'
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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16 #if $options_type['options_type_selector'] == 'basic':
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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17 #if str($input_type) == 'cssanger':
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18 cssanger
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19 #else:
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20 sanger
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21 #end if
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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22 ascii summarize_input
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23 #else:
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24 ${options_type.output_type} ${options_type.force_quality_encoding} ${options_type.summarize_input}
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25 #end if
3
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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26 ]]></command>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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27 <inputs>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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28 <param name="input_file" type="data" format="fastq,fastq.gz,fastq.bz2" label="File to groom" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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29 <param name="input_type" type="select" label="Input FASTQ quality scores type">
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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30 <option value="solexa">Solexa</option>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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31 <option value="illumina">Illumina 1.3-1.7</option>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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32 <option value="sanger" selected="true">Sanger &amp; Illumina 1.8+</option>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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33 <option value="cssanger">Color Space Sanger</option>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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34 </param>
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35 <conditional name="options_type">
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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36 <param name="options_type_selector" type="select" label="Advanced Options">
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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37 <option value="basic" selected="true">Hide Advanced Options</option>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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38 <option value="advanced">Show Advanced Options</option>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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39 </param>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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40 <when value="basic" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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41 <when value="advanced">
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42 <param name="output_type" type="select" label="Output FASTQ quality scores type" help="Galaxy tools are designed to work with the Sanger Quality score format">
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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43 <option value="solexa">Solexa</option>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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44 <option value="illumina">Illumina 1.3-1.7</option>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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45 <option value="sanger" selected="true">Sanger</option>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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46 <option value="cssanger">Color Space Sanger</option>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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47 <option value="solexa.gz">Solexa (gz compressed)</option>
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48 <option value="illumina.gz">Illumina 1.3-1.7 (gz compressed)</option>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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49 <option value="sanger.gz">Sanger (gz compressed - recommended)</option>
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50 <option value="cssanger.gz">Color Space Sanger (gz compressed)</option>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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51 <option value="solexa.bz2">Solexa (bz2 compressed)</option>
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52 <option value="illumina.bz2">Illumina 1.3-1.7 (bz2 compressed)</option>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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53 <option value="sanger.bz2">Sanger (bz2 compressed)</option>
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54 <option value="cssanger.bz2">Color Space Sanger (bz2 compressed)</option>
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55 </param>
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56 <param name="force_quality_encoding" type="select" label="Force Quality Score encoding">
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57 <option value="None">Use Source Encoding</option>
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58 <option value="ascii" selected="true">ASCII</option>
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59 <option value="decimal">Decimal</option>
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60 </param>
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61 <param name="summarize_input" type="select" label="Summarize input data">
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62 <option value="summarize_input" selected="true">Summarize Input</option>
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63 <option value="dont_summarize_input">Do not Summarize Input (faster)</option>
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64 </param>
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65 </when>
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66 </conditional>
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67 </inputs>
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68 <outputs>
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69 <data name="output_file" format="fastqsanger">
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70 <change_format>
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71 <when input="input_type" value="cssanger" format="fastqcssanger" />
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72 <when input="options_type.output_type" value="solexa" format="fastqsolexa" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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73 <when input="options_type.output_type" value="illumina" format="fastqillumina" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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74 <when input="options_type.output_type" value="sanger" format="fastqsanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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75 <when input="options_type.output_type" value="cssanger" format="fastqcssanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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76 <when input="options_type.output_type" value="solexa.gz" format="fastqsolexa.gz" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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77 <when input="options_type.output_type" value="illumina.gz" format="fastqillumina.gz" />
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78 <when input="options_type.output_type" value="sanger.gz" format="fastqsanger.gz" />
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79 <when input="options_type.output_type" value="cssanger.gz" format="fastqcssanger.gz" />
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80 <when input="options_type.output_type" value="solexa.bz2" format="fastqsolexa.bz2" />
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81 <when input="options_type.output_type" value="illumina.bz2" format="fastqillumina.bz2" />
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82 <when input="options_type.output_type" value="sanger.bz2" format="fastqsanger.bz2" />
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83 <when input="options_type.output_type" value="cssanger.bz2" format="fastqcssanger.bz2" />
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84 </change_format>
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85 </data>
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86 </outputs>
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87 <tests>
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88 <!-- These tests include test files adapted from supplemental material in Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res. 2009 Dec 16. -->
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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89 <!-- Test basic options -->
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90 <test>
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91 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" />
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92 <param name="input_type" value="sanger" />
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93 <param name="options_type_selector" value="basic" />
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94 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
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95 </test>
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96 <test>
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97 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastq" />
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98 <param name="input_type" value="cssanger" />
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99 <param name="options_type_selector" value="basic" />
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100 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" />
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101 </test>
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102 <test>
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103 <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastq" />
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104 <param name="input_type" value="illumina" />
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105 <param name="options_type_selector" value="basic" />
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106 <output name="output_file" file="illumina_full_range_as_sanger.fastqsanger" />
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107 </test>
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108 <test>
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109 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" />
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110 <param name="input_type" value="solexa" />
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111 <param name="options_type_selector" value="basic" />
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112 <output name="output_file" file="solexa_full_range_as_sanger.fastqsanger" />
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113 </test>
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114 <test>
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115 <param name="input_file" value="sanger_full_range_as_illumina.fastqillumina" ftype="fastq" />
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116 <param name="input_type" value="sanger" />
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117 <param name="options_type_selector" value="basic" />
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118 <output name="output_file" file="sanger_full_range_as_illumina.fastqillumina" />
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119 </test>
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120 <!-- Test grooming from illumina -->
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121 <test>
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122 <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastq" />
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123 <param name="input_type" value="illumina" />
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124 <param name="options_type_selector" value="advanced" />
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125 <param name="output_type" value="illumina" />
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126 <param name="force_quality_encoding" value="None" />
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127 <param name="summarize_input" value="summarize_input" />
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128 <output name="output_file" file="illumina_full_range_original_illumina.fastqillumina" />
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129 </test>
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130 <test>
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131 <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastq" />
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132 <param name="input_type" value="illumina" />
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133 <param name="options_type_selector" value="advanced" />
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134 <param name="output_type" value="sanger" />
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135 <param name="force_quality_encoding" value="None" />
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136 <param name="summarize_input" value="summarize_input" />
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137 <output name="output_file" file="illumina_full_range_as_sanger.fastqsanger" />
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138 </test>
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139 <test>
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140 <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastq" />
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141 <param name="input_type" value="illumina" />
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142 <param name="options_type_selector" value="advanced" />
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143 <param name="output_type" value="solexa" />
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144 <param name="force_quality_encoding" value="None" />
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145 <param name="summarize_input" value="summarize_input" />
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146 <output name="output_file" file="illumina_full_range_as_solexa.fastqsolexa" />
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147 </test>
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148 <test>
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149 <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastq" />
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150 <param name="input_type" value="illumina" />
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151 <param name="options_type_selector" value="advanced" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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152 <param name="output_type" value="cssanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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153 <param name="force_quality_encoding" value="None" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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154 <param name="summarize_input" value="summarize_input" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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155 <output name="output_file" file="illumina_full_range_as_cssanger.fastqcssanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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156 </test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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157 <!-- Test grooming from sanger -->
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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158 <test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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159 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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160 <param name="input_type" value="sanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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161 <param name="options_type_selector" value="advanced" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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162 <param name="output_type" value="sanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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163 <param name="force_quality_encoding" value="None" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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164 <param name="summarize_input" value="summarize_input" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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165 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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166 </test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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167 <test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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168 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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169 <param name="input_type" value="sanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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170 <param name="options_type_selector" value="advanced" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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171 <param name="output_type" value="illumina" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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172 <param name="force_quality_encoding" value="None" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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173 <param name="summarize_input" value="summarize_input" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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174 <output name="output_file" file="sanger_full_range_as_illumina.fastqillumina" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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175 </test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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176 <test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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177 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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178 <param name="input_type" value="sanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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179 <param name="options_type_selector" value="advanced" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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180 <param name="output_type" value="solexa" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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181 <param name="force_quality_encoding" value="None" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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182 <param name="summarize_input" value="summarize_input" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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183 <output name="output_file" file="sanger_full_range_as_solexa.fastqsolexa" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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184 </test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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185 <test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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186 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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187 <param name="input_type" value="sanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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188 <param name="options_type_selector" value="advanced" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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189 <param name="output_type" value="cssanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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190 <param name="force_quality_encoding" value="None" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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191 <param name="summarize_input" value="summarize_input" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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192 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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193 </test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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194 <!-- Test grooming from solexa -->
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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195 <test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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196 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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197 <param name="input_type" value="solexa" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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198 <param name="options_type_selector" value="advanced" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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199 <param name="output_type" value="solexa" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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200 <param name="force_quality_encoding" value="None" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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201 <param name="summarize_input" value="summarize_input" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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202 <output name="output_file" file="solexa_full_range_original_solexa.fastqsolexa" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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203 </test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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204 <test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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205 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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206 <param name="input_type" value="solexa" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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207 <param name="options_type_selector" value="advanced" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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208 <param name="output_type" value="illumina" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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209 <param name="force_quality_encoding" value="None" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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210 <param name="summarize_input" value="summarize_input" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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211 <output name="output_file" file="solexa_full_range_as_illumina.fastqillumina" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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212 </test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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213 <test>
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214 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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215 <param name="input_type" value="solexa" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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216 <param name="options_type_selector" value="advanced" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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217 <param name="output_type" value="sanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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218 <param name="force_quality_encoding" value="None" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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219 <param name="summarize_input" value="summarize_input" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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220 <output name="output_file" file="solexa_full_range_as_sanger.fastqsanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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221 </test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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222 <test>
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223 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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224 <param name="input_type" value="solexa" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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225 <param name="options_type_selector" value="advanced" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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226 <param name="output_type" value="cssanger" />
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227 <param name="force_quality_encoding" value="None" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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228 <param name="summarize_input" value="summarize_input" />
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229 <output name="output_file" file="solexa_full_range_as_cssanger.fastqcssanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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230 </test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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231 <!-- Test grooming from cssanger -->
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232 <test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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233 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastq" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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234 <param name="input_type" value="cssanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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235 <param name="options_type_selector" value="advanced" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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236 <param name="output_type" value="cssanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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237 <param name="force_quality_encoding" value="None" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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238 <param name="summarize_input" value="summarize_input" />
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239 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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240 </test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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241 <test>
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242 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastq" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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243 <param name="input_type" value="cssanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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244 <param name="options_type_selector" value="advanced" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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245 <param name="output_type" value="sanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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246 <param name="force_quality_encoding" value="None" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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247 <param name="summarize_input" value="summarize_input" />
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248 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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249 </test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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250 <test>
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251 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastq" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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252 <param name="input_type" value="cssanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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253 <param name="options_type_selector" value="advanced" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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254 <param name="output_type" value="illumina" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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255 <param name="force_quality_encoding" value="None" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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256 <param name="summarize_input" value="summarize_input" />
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257 <output name="output_file" file="sanger_full_range_as_illumina.fastqillumina" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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258 </test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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259 <test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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260 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastq" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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261 <param name="input_type" value="cssanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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262 <param name="options_type_selector" value="advanced" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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263 <param name="output_type" value="solexa" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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264 <param name="force_quality_encoding" value="None" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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265 <param name="summarize_input" value="summarize_input" />
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266 <output name="output_file" file="sanger_full_range_as_solexa.fastqsolexa" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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267 </test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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268 <test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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269 <param name="input_file" value="sanger_full_range_as_cssanger_adapter_base_with_quality_score.fastqcssanger_fake_score" ftype="fastq" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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270 <param name="input_type" value="cssanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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271 <param name="options_type_selector" value="advanced" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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272 <param name="output_type" value="cssanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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273 <param name="force_quality_encoding" value="None" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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274 <param name="summarize_input" value="summarize_input" />
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275 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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276 </test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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277 <!-- Test fastq with line wrapping -->
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278 <test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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279 <param name="input_file" value="wrapping_original_sanger.fastqsanger" ftype="fastq" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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280 <param name="input_type" value="sanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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281 <param name="options_type_selector" value="advanced" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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282 <param name="output_type" value="sanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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283 <param name="force_quality_encoding" value="None" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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284 <param name="summarize_input" value="summarize_input" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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285 <output name="output_file" file="wrapping_as_sanger.fastqsanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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286 </test>
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287 <test>
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288 <param name="input_file" value="wrapping_original_sanger.fastqsanger" ftype="fastq" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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289 <param name="input_type" value="sanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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290 <param name="options_type_selector" value="advanced" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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291 <param name="output_type" value="illumina" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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292 <param name="force_quality_encoding" value="None" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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293 <param name="summarize_input" value="summarize_input" />
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294 <output name="output_file" file="wrapping_as_illumina.fastqillumina" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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295 </test>
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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296 <test>
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297 <param name="input_file" value="wrapping_original_sanger.fastqsanger" ftype="fastq" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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298 <param name="input_type" value="sanger" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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299 <param name="options_type_selector" value="advanced" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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300 <param name="output_type" value="solexa" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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301 <param name="force_quality_encoding" value="None" />
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302 <param name="summarize_input" value="summarize_input" />
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303 <output name="output_file" file="wrapping_as_solexa.fastqsolexa" />
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304 </test>
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305 <!-- Test forcing quality score encoding -->
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306 <!-- Sanger, range 0 - 93 -->
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307 <test>
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308 <param name="input_file" value="sanger_full_range_as_decimal_sanger.fastqsanger" ftype="fastq" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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309 <param name="input_type" value="sanger" />
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310 <param name="options_type_selector" value="advanced" />
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311 <param name="output_type" value="sanger" />
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312 <param name="force_quality_encoding" value="ascii" />
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313 <param name="summarize_input" value="summarize_input" />
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314 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
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315 </test>
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316 <test>
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317 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" />
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318 <param name="input_type" value="sanger" />
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319 <param name="options_type_selector" value="advanced" />
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320 <param name="output_type" value="sanger" />
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321 <param name="force_quality_encoding" value="decimal" />
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322 <param name="summarize_input" value="summarize_input" />
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323 <output name="output_file" file="sanger_full_range_as_decimal_sanger.fastqsanger" />
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324 </test>
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325 <test>
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326 <param name="input_file" value="sanger_full_range_as_tab_decimal_sanger.fastqsanger" ftype="fastq" />
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327 <param name="input_type" value="sanger" />
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328 <param name="options_type_selector" value="advanced" />
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329 <param name="output_type" value="sanger" />
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330 <param name="force_quality_encoding" value="ascii" />
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331 <param name="summarize_input" value="summarize_input" />
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332 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
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333 </test>
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334 <!-- Solexa, range -5 - 62 -->
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335 <test>
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336 <param name="input_file" value="solexa_full_range_as_decimal_solexa.fastqsolexa" ftype="fastq" />
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337 <param name="input_type" value="solexa" />
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338 <param name="options_type_selector" value="advanced" />
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339 <param name="output_type" value="solexa" />
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340 <param name="force_quality_encoding" value="ascii" />
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341 <param name="summarize_input" value="summarize_input" />
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342 <output name="output_file" file="solexa_full_range_original_solexa.fastqsolexa" />
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343 </test>
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344 <test>
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345 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" />
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346 <param name="input_type" value="solexa" />
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347 <param name="options_type_selector" value="advanced" />
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348 <param name="output_type" value="solexa" />
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349 <param name="force_quality_encoding" value="decimal" />
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350 <param name="summarize_input" value="summarize_input" />
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351 <output name="output_file" file="solexa_full_range_as_decimal_solexa.fastqsolexa" />
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352 </test>
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353 <!-- compressed formats -->
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354 <test>
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355 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger.gz" ftype="fastq.gz" />
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356 <param name="input_type" value="sanger" />
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357 <param name="options_type_selector" value="basic" />
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358 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" decompress="true" />
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359 </test>
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360 <test>
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361 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger.bz2" ftype="fastq.bz2" />
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362 <param name="input_type" value="cssanger" />
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363 <param name="options_type_selector" value="basic" />
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364 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" decompress="true" />
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365 </test>
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366 </tests>
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367 <help><![CDATA[
0
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368 **What it does**
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369
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370 This tool offers several conversions options relating to the FASTQ format.
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371
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372 When using *Basic* options, the output will be *sanger* formatted or *cssanger* formatted (when the input is Color Space Sanger).
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373
3
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374 When converting, if a quality score falls outside of the target score range, it will be coerced to the closest available value (i.e. the minimum or maximum).
0
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375
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376 When converting between Solexa and the other formats, quality scores are mapped between Solexa and PHRED scales using the equations found in `Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res. 2009 Dec 16.`_
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377
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378 When converting between color space (csSanger) and base/sequence space (Sanger, Illumina, Solexa) formats, adapter bases are lost or gained; if gained, the base 'G' is used as the adapter. You cannot convert a color space read to base space if there is no adapter present in the color space sequence. Any masked or ambiguous nucleotides in base space will be converted to 'N's when determining color space encoding.
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379
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380 -----
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381
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382 **Quality Score Comparison**
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383
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384 ::
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385
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386 SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
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387 ...............................IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
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388 ..........................XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
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389 !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
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390 | | | | | |
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391 33 59 64 73 104 126
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392
0
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393 S - Sanger Phred+33, 93 values (0, 93) (0 to 60 expected in raw reads)
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394 I - Illumina 1.3 Phred+64, 62 values (0, 62) (0 to 40 expected in raw reads)
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395 X - Solexa Solexa+64, 67 values (-5, 62) (-5 to 40 expected in raw reads)
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396
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397 Diagram adapted from http://en.wikipedia.org/wiki/FASTQ_format
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398
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399 .. class:: infomark
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400
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401 Output from Illumina 1.8+ pipelines are Sanger encoded.
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402
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403 ------
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404
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405 .. _Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res. 2009 Dec 16.: https://doi.org/10.1093/nar/gkp1137
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406 ]]></help>
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407 <citations>
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408 <citation type="doi">10.1093/bioinformatics/btq281</citation>
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409 </citations>
0
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410 </tool>