Mercurial > repos > devteam > fastq_groomer

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
author iuc
date Sun, 23 Nov 2025 17:50:18 +0000
parents e9f8633db0a2
children
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e9f8633db0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit bb5df9e62585e12f08dfc0a9f86eec8e205b4845
iuc
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1 <tool id="fastq_groomer" name="FASTQ Groomer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2
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2 <description>convert between various FASTQ quality formats</description>
4
47e5dbc3e790 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
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3 <macros>
47e5dbc3e790 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
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4 <import>macros.xml</import>
47e5dbc3e790 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
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5 </macros>
3
8611b80a14d6 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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6 <edam_topics>
8611b80a14d6 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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7 <edam_topic>topic_0622</edam_topic>
8611b80a14d6 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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8 </edam_topics>
8611b80a14d6 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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9 <edam_operations>
8611b80a14d6 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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10 <edam_operation>operation_0233</edam_operation>
8611b80a14d6 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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11 </edam_operations>
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e9f8633db0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit bb5df9e62585e12f08dfc0a9f86eec8e205b4845
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12 <expand macro="requirements"/>
2
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13 <command><![CDATA[
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14 gx-fastq-groomer '$input_file'
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15 #if $input_file.extension.endswith(".gz"):
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16 #set $suffix = ".gz"
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17 #elif $input_file.extension.endswith(".bz2"):
71e5fa25b8a2 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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18 #set $suffix = ".bz2"
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19 #else:
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20 #set $suffix = ""
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21 #end if
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22 $input_type$suffix '$output_file'
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47e5dbc3e790 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
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23 #if $options_type.options_type_selector == 'basic':
2
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24 #if str($input_type) == 'cssanger':
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25 cssanger
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26 #else:
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27 sanger
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28 #end if
71e5fa25b8a2 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 ascii summarize_input
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30 #else:
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47e5dbc3e790 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
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31 ${options_type.output_type} ${options_type.force_quality_encoding} ${options_type.summarize_input} ${options_type.fix_id}
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32 #end if
2
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33 ]]></command>
71e5fa25b8a2 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 <inputs>
71e5fa25b8a2 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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35 <param name="input_file" type="data" format="fastq,fastq.gz,fastq.bz2" label="File to groom" />
71e5fa25b8a2 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="input_type" type="select" label="Input FASTQ quality scores type">
71e5fa25b8a2 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="solexa">Solexa</option>
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38 <option value="illumina">Illumina 1.3-1.7</option>
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39 <option value="sanger" selected="true">Sanger &amp; Illumina 1.8+</option>
71e5fa25b8a2 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 <option value="cssanger">Color Space Sanger</option>
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41 </param>
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42 <conditional name="options_type">
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43 <param name="options_type_selector" type="select" label="Advanced Options">
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44 <option value="basic" selected="true">Hide Advanced Options</option>
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45 <option value="advanced">Show Advanced Options</option>
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46 </param>
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47 <when value="basic" />
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48 <when value="advanced">
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49 <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">
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50 <option value="solexa">Solexa</option>
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51 <option value="illumina">Illumina 1.3-1.7</option>
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52 <option value="sanger" selected="true">Sanger</option>
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53 <option value="cssanger">Color Space Sanger</option>
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54 <option value="solexa.gz">Solexa (gz compressed)</option>
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55 <option value="illumina.gz">Illumina 1.3-1.7 (gz compressed)</option>
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56 <option value="sanger.gz">Sanger (gz compressed - recommended)</option>
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57 <option value="cssanger.gz">Color Space Sanger (gz compressed)</option>
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58 <option value="solexa.bz2">Solexa (bz2 compressed)</option>
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59 <option value="illumina.bz2">Illumina 1.3-1.7 (bz2 compressed)</option>
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60 <option value="sanger.bz2">Sanger (bz2 compressed)</option>
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61 <option value="cssanger.bz2">Color Space Sanger (bz2 compressed)</option>
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62 </param>
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63 <param name="force_quality_encoding" type="select" label="Force Quality Score encoding">
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64 <option value="None">Use Source Encoding</option>
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65 <option value="ascii" selected="true">ASCII</option>
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66 <option value="decimal">Decimal</option>
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67 </param>
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68 <param name="summarize_input" type="select" label="Summarize input data">
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69 <option value="summarize_input" selected="true">Summarize Input</option>
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70 <option value="dont_summarize_input">Do not Summarize Input (faster)</option>
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71 </param>
4
47e5dbc3e790 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
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72 <param name="fix_id" type="boolean" label="Fix inconsistent identifiers"
47e5dbc3e790 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
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73 truevalue="--fix-id" falsevalue="--no-fix-id" checked="true">
47e5dbc3e790 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
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74 </param>
2
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75 </when>
71e5fa25b8a2 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 </conditional>
71e5fa25b8a2 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 </inputs>
71e5fa25b8a2 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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78 <outputs>
71e5fa25b8a2 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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79 <data name="output_file" format="fastqsanger">
71e5fa25b8a2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
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80 <change_format>
71e5fa25b8a2 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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81 <when input="input_type" value="cssanger" format="fastqcssanger" />
71e5fa25b8a2 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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82 <when input="options_type.output_type" value="solexa" format="fastqsolexa" />
71e5fa25b8a2 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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83 <when input="options_type.output_type" value="illumina" format="fastqillumina" />
71e5fa25b8a2 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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84 <when input="options_type.output_type" value="sanger" format="fastqsanger" />
71e5fa25b8a2 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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85 <when input="options_type.output_type" value="cssanger" format="fastqcssanger" />
71e5fa25b8a2 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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86 <when input="options_type.output_type" value="solexa.gz" format="fastqsolexa.gz" />
71e5fa25b8a2 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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87 <when input="options_type.output_type" value="illumina.gz" format="fastqillumina.gz" />
71e5fa25b8a2 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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88 <when input="options_type.output_type" value="sanger.gz" format="fastqsanger.gz" />
71e5fa25b8a2 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 <when input="options_type.output_type" value="cssanger.gz" format="fastqcssanger.gz" />
71e5fa25b8a2 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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90 <when input="options_type.output_type" value="solexa.bz2" format="fastqsolexa.bz2" />
71e5fa25b8a2 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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91 <when input="options_type.output_type" value="illumina.bz2" format="fastqillumina.bz2" />
71e5fa25b8a2 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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92 <when input="options_type.output_type" value="sanger.bz2" format="fastqsanger.bz2" />
71e5fa25b8a2 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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93 <when input="options_type.output_type" value="cssanger.bz2" format="fastqcssanger.bz2" />
71e5fa25b8a2 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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94 </change_format>
71e5fa25b8a2 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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95 </data>
71e5fa25b8a2 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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96 </outputs>
71e5fa25b8a2 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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97 <tests>
4
47e5dbc3e790 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
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98 <!-- Test fix-id by default -->
47e5dbc3e790 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
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99 <test>
47e5dbc3e790 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
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100 <param name="input_file" value="fastq_invalid-line3" ftype="fastq" />
47e5dbc3e790 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
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101 <param name="input_type" value="sanger" />
6
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102 <conditional name="options_type">
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103 <param name="options_type_selector" value="basic" />
10d4df6a9d94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
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104 </conditional>
4
47e5dbc3e790 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
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105 <output name="output_file" file="fastq_invalid-line3_fixed" />
47e5dbc3e790 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
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106 </test>
47e5dbc3e790 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
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107 <!-- Test fix-id by setting the option -->
47e5dbc3e790 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
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108 <test>
47e5dbc3e790 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
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109 <param name="input_file" value="fastq_invalid-line3" ftype="fastq" />
47e5dbc3e790 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
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110 <param name="input_type" value="sanger" />
6
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111 <conditional name="options_type">
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112 <param name="options_type_selector" value="advanced" />
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113 <param name="fix_id" value="true" />
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114 </conditional>
4
47e5dbc3e790 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
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115 <output name="output_file" file="fastq_invalid-line3_fixed" />
47e5dbc3e790 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
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116 </test>
47e5dbc3e790 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
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117 <!-- Test fix-id / option not set; expect failure -->
47e5dbc3e790 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
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118 <test expect_failure="true">
47e5dbc3e790 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
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119 <param name="input_file" value="fastq_invalid-line3" ftype="fastq" />
47e5dbc3e790 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
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120 <param name="input_type" value="sanger" />
6
10d4df6a9d94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
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121 <conditional name="options_type">
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122 <param name="options_type_selector" value="advanced" />
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123 <param name="fix_id" value="false" />
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124 </conditional>
4
47e5dbc3e790 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
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125 </test>
2
71e5fa25b8a2 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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126 <!-- 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. -->
71e5fa25b8a2 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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127 <!-- Test basic options -->
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128 <test>
71e5fa25b8a2 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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129 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" />
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130 <param name="input_type" value="sanger" />
6
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131 <conditional name="options_type">
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132 <param name="options_type_selector" value="basic" />
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133 </conditional>
2
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134 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
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135 </test>
71e5fa25b8a2 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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136 <test>
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137 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastq" />
71e5fa25b8a2 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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138 <param name="input_type" value="cssanger" />
6
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139 <conditional name="options_type">
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140 <param name="options_type_selector" value="basic" />
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141 </conditional>
2
71e5fa25b8a2 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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142 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" />
71e5fa25b8a2 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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143 </test>
71e5fa25b8a2 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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144 <test>
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145 <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastq" />
71e5fa25b8a2 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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146 <param name="input_type" value="illumina" />
6
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147 <conditional name="options_type">
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148 <param name="options_type_selector" value="basic" />
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149 </conditional>
2
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150 <output name="output_file" file="illumina_full_range_as_sanger.fastqsanger" />
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151 </test>
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152 <test>
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153 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" />
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154 <param name="input_type" value="solexa" />
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155 <conditional name="options_type">
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156 <param name="options_type_selector" value="basic" />
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157 </conditional>
2
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158 <output name="output_file" file="solexa_full_range_as_sanger.fastqsanger" />
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159 </test>
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160 <test>
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161 <param name="input_file" value="sanger_full_range_as_illumina.fastqillumina" ftype="fastq" />
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162 <param name="input_type" value="sanger" />
6
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163 <conditional name="options_type">
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164 <param name="options_type_selector" value="basic" />
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165 </conditional>
2
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166 <output name="output_file" file="sanger_full_range_as_illumina.fastqillumina" />
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167 </test>
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168 <!-- Test grooming from illumina -->
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169 <test>
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170 <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastq" />
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171 <param name="input_type" value="illumina" />
6
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172 <conditional name="options_type">
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173 <param name="options_type_selector" value="advanced" />
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174 <param name="output_type" value="illumina" />
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175 <param name="force_quality_encoding" value="None" />
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176 <param name="summarize_input" value="summarize_input" />
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177 </conditional>
2
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178 <output name="output_file" file="illumina_full_range_original_illumina.fastqillumina" />
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179 </test>
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180 <test>
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181 <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastq" />
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182 <param name="input_type" value="illumina" />
6
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183 <conditional name="options_type">
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184 <param name="options_type_selector" value="advanced" />
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185 <param name="output_type" value="sanger" />
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186 <param name="force_quality_encoding" value="None" />
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187 <param name="summarize_input" value="summarize_input" />
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188 </conditional>
2
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189 <output name="output_file" file="illumina_full_range_as_sanger.fastqsanger" />
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190 </test>
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191 <test>
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192 <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastq" />
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193 <param name="input_type" value="illumina" />
6
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194 <conditional name="options_type">
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195 <param name="options_type_selector" value="advanced" />
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196 <param name="output_type" value="solexa" />
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197 <param name="force_quality_encoding" value="None" />
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198 <param name="summarize_input" value="summarize_input" />
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199 </conditional>
2
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200 <output name="output_file" file="illumina_full_range_as_solexa.fastqsolexa" />
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201 </test>
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202 <test>
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203 <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastq" />
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204 <param name="input_type" value="illumina" />
6
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205 <conditional name="options_type">
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206 <param name="options_type_selector" value="advanced" />
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207 <param name="output_type" value="cssanger" />
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208 <param name="force_quality_encoding" value="None" />
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209 <param name="summarize_input" value="summarize_input" />
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210 </conditional>
2
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211 <output name="output_file" file="illumina_full_range_as_cssanger.fastqcssanger" />
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212 </test>
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213 <!-- Test grooming from sanger -->
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214 <test>
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215 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" />
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216 <param name="input_type" value="sanger" />
6
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217 <conditional name="options_type">
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218 <param name="options_type_selector" value="advanced" />
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219 <param name="output_type" value="sanger" />
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220 <param name="force_quality_encoding" value="None" />
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221 <param name="summarize_input" value="summarize_input" />
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222 </conditional>
2
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223 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
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224 </test>
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225 <test>
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226 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" />
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227 <param name="input_type" value="sanger" />
6
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228 <conditional name="options_type">
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229 <param name="options_type_selector" value="advanced" />
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230 <param name="output_type" value="illumina" />
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231 <param name="force_quality_encoding" value="None" />
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232 <param name="summarize_input" value="summarize_input" />
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233 </conditional>
2
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234 <output name="output_file" file="sanger_full_range_as_illumina.fastqillumina" />
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235 </test>
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236 <test>
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237 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" />
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238 <param name="input_type" value="sanger" />
6
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239 <conditional name="options_type">
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240 <param name="options_type_selector" value="advanced" />
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241 <param name="output_type" value="solexa" />
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242 <param name="force_quality_encoding" value="None" />
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243 <param name="summarize_input" value="summarize_input" />
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244 </conditional>
2
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245 <output name="output_file" file="sanger_full_range_as_solexa.fastqsolexa" />
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246 </test>
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247 <test>
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248 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" />
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249 <param name="input_type" value="sanger" />
6
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250 <conditional name="options_type">
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251 <param name="options_type_selector" value="advanced" />
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252 <param name="output_type" value="cssanger" />
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253 <param name="force_quality_encoding" value="None" />
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254 <param name="summarize_input" value="summarize_input" />
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255 </conditional>
2
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256 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" />
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257 </test>
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258 <!-- Test grooming from solexa -->
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259 <test>
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260 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" />
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261 <param name="input_type" value="solexa" />
6
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262 <conditional name="options_type">
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263 <param name="options_type_selector" value="advanced" />
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264 <param name="output_type" value="solexa" />
10d4df6a9d94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
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265 <param name="force_quality_encoding" value="None" />
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266 <param name="summarize_input" value="summarize_input" />
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267 </conditional>
2
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268 <output name="output_file" file="solexa_full_range_original_solexa.fastqsolexa" />
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269 </test>
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270 <test>
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271 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" />
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272 <param name="input_type" value="solexa" />
6
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273 <conditional name="options_type">
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274 <param name="options_type_selector" value="advanced" />
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275 <param name="output_type" value="illumina" />
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276 <param name="force_quality_encoding" value="None" />
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277 <param name="summarize_input" value="summarize_input" />
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278 </conditional>
2
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279 <output name="output_file" file="solexa_full_range_as_illumina.fastqillumina" />
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280 </test>
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281 <test>
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282 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" />
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283 <param name="input_type" value="solexa" />
6
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284 <conditional name="options_type">
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285 <param name="options_type_selector" value="advanced" />
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286 <param name="output_type" value="sanger" />
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287 <param name="force_quality_encoding" value="None" />
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288 <param name="summarize_input" value="summarize_input" />
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289 </conditional>
2
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290 <output name="output_file" file="solexa_full_range_as_sanger.fastqsanger" />
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291 </test>
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292 <test>
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293 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" />
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294 <param name="input_type" value="solexa" />
6
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295 <conditional name="options_type">
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296 <param name="options_type_selector" value="advanced" />
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297 <param name="output_type" value="cssanger" />
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298 <param name="force_quality_encoding" value="None" />
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299 <param name="summarize_input" value="summarize_input" />
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300 </conditional>
2
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301 <output name="output_file" file="solexa_full_range_as_cssanger.fastqcssanger" />
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302 </test>
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303 <!-- Test grooming from cssanger -->
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304 <test>
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305 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastq" />
71e5fa25b8a2 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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306 <param name="input_type" value="cssanger" />
6
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307 <conditional name="options_type">
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308 <param name="options_type_selector" value="advanced" />
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309 <param name="output_type" value="cssanger" />
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310 <param name="force_quality_encoding" value="None" />
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311 <param name="summarize_input" value="summarize_input" />
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312 </conditional>
2
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313 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" />
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314 </test>
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315 <test>
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316 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastq" />
71e5fa25b8a2 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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317 <param name="input_type" value="cssanger" />
6
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318 <conditional name="options_type">
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319 <param name="options_type_selector" value="advanced" />
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320 <param name="output_type" value="sanger" />
10d4df6a9d94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
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321 <param name="force_quality_encoding" value="None" />
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322 <param name="summarize_input" value="summarize_input" />
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323 </conditional>
2
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324 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
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325 </test>
71e5fa25b8a2 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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326 <test>
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327 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastq" />
71e5fa25b8a2 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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328 <param name="input_type" value="cssanger" />
6
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329 <conditional name="options_type">
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330 <param name="options_type_selector" value="advanced" />
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331 <param name="output_type" value="illumina" />
10d4df6a9d94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
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332 <param name="force_quality_encoding" value="None" />
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333 <param name="summarize_input" value="summarize_input" />
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334 </conditional>
2
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335 <output name="output_file" file="sanger_full_range_as_illumina.fastqillumina" />
71e5fa25b8a2 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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336 </test>
71e5fa25b8a2 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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337 <test>
71e5fa25b8a2 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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338 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastq" />
71e5fa25b8a2 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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339 <param name="input_type" value="cssanger" />
6
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340 <conditional name="options_type">
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341 <param name="options_type_selector" value="advanced" />
10d4df6a9d94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
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342 <param name="output_type" value="solexa" />
10d4df6a9d94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
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343 <param name="force_quality_encoding" value="None" />
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344 <param name="summarize_input" value="summarize_input" />
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345 </conditional>
2
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346 <output name="output_file" file="sanger_full_range_as_solexa.fastqsolexa" />
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347 </test>
71e5fa25b8a2 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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348 <test>
71e5fa25b8a2 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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349 <param name="input_file" value="sanger_full_range_as_cssanger_adapter_base_with_quality_score.fastqcssanger_fake_score" ftype="fastq" />
71e5fa25b8a2 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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350 <param name="input_type" value="cssanger" />
6
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351 <conditional name="options_type">
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352 <param name="options_type_selector" value="advanced" />
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353 <param name="output_type" value="cssanger" />
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354 <param name="force_quality_encoding" value="None" />
10d4df6a9d94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
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355 <param name="summarize_input" value="summarize_input" />
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356 </conditional>
2
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357 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" />
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358 </test>
71e5fa25b8a2 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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359 <!-- Test fastq with line wrapping -->
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360 <test>
71e5fa25b8a2 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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361 <param name="input_file" value="wrapping_original_sanger.fastqsanger" ftype="fastq" />
71e5fa25b8a2 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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362 <param name="input_type" value="sanger" />
6
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363 <conditional name="options_type">
10d4df6a9d94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
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364 <param name="options_type_selector" value="advanced" />
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365 <param name="output_type" value="sanger" />
10d4df6a9d94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
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366 <param name="force_quality_encoding" value="None" />
10d4df6a9d94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
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367 <param name="summarize_input" value="summarize_input" />
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368 </conditional>
2
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369 <output name="output_file" file="wrapping_as_sanger.fastqsanger" />
71e5fa25b8a2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
370 </test>
71e5fa25b8a2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
371 <test>
71e5fa25b8a2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
372 <param name="input_file" value="wrapping_original_sanger.fastqsanger" ftype="fastq" />
71e5fa25b8a2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
373 <param name="input_type" value="sanger" />
6
10d4df6a9d94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 5
diff changeset
374 <conditional name="options_type">
10d4df6a9d94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 5
diff changeset
375 <param name="options_type_selector" value="advanced" />
10d4df6a9d94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 5
diff changeset
376 <param name="output_type" value="illumina" />
10d4df6a9d94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 5
diff changeset
377 <param name="force_quality_encoding" value="None" />
10d4df6a9d94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 5
diff changeset
378 <param name="summarize_input" value="summarize_input" />
10d4df6a9d94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 5
diff changeset
379 </conditional>
2
71e5fa25b8a2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
380 <output name="output_file" file="wrapping_as_illumina.fastqillumina" />
71e5fa25b8a2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
381 </test>
71e5fa25b8a2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
382 <test>
71e5fa25b8a2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
383 <param name="input_file" value="wrapping_original_sanger.fastqsanger" ftype="fastq" />
71e5fa25b8a2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
384 <param name="input_type" value="sanger" />
6
10d4df6a9d94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 5
diff changeset
385 <conditional name="options_type">
10d4df6a9d94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 5
diff changeset
386 <param name="options_type_selector" value="advanced" />
10d4df6a9d94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 5
diff changeset
387 <param name="output_type" value="solexa" />
10d4df6a9d94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 5
diff changeset
388 <param name="force_quality_encoding" value="None" />
10d4df6a9d94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 5
diff changeset
389 <param name="summarize_input" value="summarize_input" />
10d4df6a9d94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 5
diff changeset
390 </conditional>
2
71e5fa25b8a2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
391 <output name="output_file" file="wrapping_as_solexa.fastqsolexa" />
71e5fa25b8a2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
392 </test>
71e5fa25b8a2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
393 <!-- Test forcing quality score encoding -->
71e5fa25b8a2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
394 <!-- Sanger, range 0 - 93 -->
71e5fa25b8a2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
395 <test>
71e5fa25b8a2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
396 <param name="input_file" value="sanger_full_range_as_decimal_sanger.fastqsanger" ftype="fastq" />
71e5fa25b8a2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
397 <param name="input_type" value="sanger" />
6
10d4df6a9d94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 5
diff changeset
398 <conditional name="options_type">
10d4df6a9d94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 5
diff changeset
399 <param name="options_type_selector" value="advanced" />
10d4df6a9d94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 5
diff changeset
400 <param name="output_type" value="sanger" />
10d4df6a9d94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 5
diff changeset
401 <param name="force_quality_encoding" value="ascii" />
10d4df6a9d94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 5
diff changeset
402 <param name="summarize_input" value="summarize_input" />
10d4df6a9d94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 5
diff changeset
403 </conditional>
2
71e5fa25b8a2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
404 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
71e5fa25b8a2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
405 </test>
71e5fa25b8a2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
406 <test>
71e5fa25b8a2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
407 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" />
71e5fa25b8a2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
408 <param name="input_type" value="sanger" />
6
10d4df6a9d94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 5
diff changeset
409 <conditional name="options_type">
10d4df6a9d94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 5
diff changeset
410 <param name="options_type_selector" value="advanced" />
10d4df6a9d94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 5
diff changeset
411 <param name="output_type" value="sanger" />
10d4df6a9d94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 5
diff changeset
412 <param name="force_quality_encoding" value="decimal" />
10d4df6a9d94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 5
diff changeset
413 <param name="summarize_input" value="summarize_input" />
10d4df6a9d94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 5
diff changeset
414 </conditional>
2
71e5fa25b8a2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
415 <output name="output_file" file="sanger_full_range_as_decimal_sanger.fastqsanger" />
71e5fa25b8a2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
416 </test>
71e5fa25b8a2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
417 <test>
71e5fa25b8a2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
418 <param name="input_file" value="sanger_full_range_as_tab_decimal_sanger.fastqsanger" ftype="fastq" />
71e5fa25b8a2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
419 <param name="input_type" value="sanger" />
6
10d4df6a9d94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 5
diff changeset
420 <conditional name="options_type">
10d4df6a9d94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 5
diff changeset
421 <param name="options_type_selector" value="advanced" />
10d4df6a9d94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 5
diff changeset
422 <param name="output_type" value="sanger" />
10d4df6a9d94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 5
diff changeset
423 <param name="force_quality_encoding" value="ascii" />
10d4df6a9d94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 5
diff changeset
424 <param name="summarize_input" value="summarize_input" />
10d4df6a9d94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 5
diff changeset
425 </conditional>
2
71e5fa25b8a2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
426 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
71e5fa25b8a2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
427 </test>
71e5fa25b8a2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
428 <!-- Solexa, range -5 - 62 -->
71e5fa25b8a2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
429 <test>
71e5fa25b8a2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
430 <param name="input_file" value="solexa_full_range_as_decimal_solexa.fastqsolexa" ftype="fastq" />
71e5fa25b8a2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
431 <param name="input_type" value="solexa" />
6
10d4df6a9d94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 5
diff changeset
432 <conditional name="options_type">
10d4df6a9d94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 5
diff changeset
433 <param name="options_type_selector" value="advanced" />
10d4df6a9d94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 5
diff changeset
434 <param name="output_type" value="solexa" />
10d4df6a9d94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 5
diff changeset
435 <param name="force_quality_encoding" value="ascii" />
10d4df6a9d94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 5
diff changeset
436 <param name="summarize_input" value="summarize_input" />
10d4df6a9d94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 5
diff changeset
437 </conditional>
2
71e5fa25b8a2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
438 <output name="output_file" file="solexa_full_range_original_solexa.fastqsolexa" />
71e5fa25b8a2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
439 </test>
71e5fa25b8a2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
440 <test>
71e5fa25b8a2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
441 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" />
71e5fa25b8a2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
442 <param name="input_type" value="solexa" />
6
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443 <conditional name="options_type">
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444 <param name="options_type_selector" value="advanced" />
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445 <param name="output_type" value="solexa" />
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446 <param name="force_quality_encoding" value="decimal" />
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447 <param name="summarize_input" value="summarize_input" />
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448 </conditional>
2
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449 <output name="output_file" file="solexa_full_range_as_decimal_solexa.fastqsolexa" />
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450 </test>
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451 <!-- compressed formats -->
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452 <test>
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453 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger.gz" ftype="fastq.gz" />
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454 <param name="input_type" value="sanger" />
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455 <conditional name="options_type">
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456 <param name="options_type_selector" value="basic" />
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457 </conditional>
2
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458 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" decompress="true" />
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459 </test>
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460 <test>
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461 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger.bz2" ftype="fastq.bz2" />
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462 <param name="input_type" value="cssanger" />
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463 <conditional name="options_type">
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464 <param name="options_type_selector" value="basic" />
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465 </conditional>
2
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466 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" decompress="true" />
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467 </test>
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468 </tests>
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469 <help><![CDATA[
0
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470 **What it does**
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471
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472 This tool offers several conversions options relating to the FASTQ format.
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473
4
47e5dbc3e790 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
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474 When using *Basic* options, the output will be *sanger* formatted or *cssanger* formatted (when the input is Color Space Sanger). Inconsistent identifiers are fixed by default.
0
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475
2
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476 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).
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477
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478 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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479
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480 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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481
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482 -----
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483
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484 **Quality Score Comparison**
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485
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486 ::
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487
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488 SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
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489 ...............................IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
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490 ..........................XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
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491 !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
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492 | | | | | |
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493 33 59 64 73 104 126
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494
0
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495 S - Sanger Phred+33, 93 values (0, 93) (0 to 60 expected in raw reads)
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496 I - Illumina 1.3 Phred+64, 62 values (0, 62) (0 to 40 expected in raw reads)
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497 X - Solexa Solexa+64, 67 values (-5, 62) (-5 to 40 expected in raw reads)
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498
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499 Diagram adapted from http://en.wikipedia.org/wiki/FASTQ_format
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500
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501 .. class:: infomark
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502
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503 Output from Illumina 1.8+ pipelines are Sanger encoded.
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504
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505 ------
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506
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507 .. _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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508 ]]></help>
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509 <citations>
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510 <citation type="doi">10.1093/bioinformatics/btq281</citation>
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511 </citations>
0
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512 </tool>