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 17:48:36 +0000
parents 3213285ee5d2
children
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3213285ee5d2 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@">
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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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2 <description>convert between various FASTQ quality formats</description>
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4fda2184efa5 "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>
4fda2184efa5 "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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4 <import>macros.xml</import>
4fda2184efa5 "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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5 </macros>
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dafabb4c2037 "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>
dafabb4c2037 "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>
dafabb4c2037 "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>
dafabb4c2037 "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>
dafabb4c2037 "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>
dafabb4c2037 "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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3213285ee5d2 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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12 <expand macro="requirements"/>
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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 <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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14 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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15 #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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16 #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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17 #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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18 #set $suffix = ".bz2"
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19 #else:
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4fda2184efa5 "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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20 #set $suffix = ""
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21 #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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22 $input_type$suffix '$output_file'
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4fda2184efa5 "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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23 #if $options_type.options_type_selector == 'basic':
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bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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24 #if str($input_type) == '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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25 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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26 #else:
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 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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28 #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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29 ascii summarize_input
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30 #else:
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4fda2184efa5 "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
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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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33 ]]></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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34 <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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35 <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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36 <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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37 <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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38 <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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39 <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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40 <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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41 </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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42 <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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43 <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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44 <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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45 <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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46 </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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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">
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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50 <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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51 <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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52 <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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53 <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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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>
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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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>
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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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>
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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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>
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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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>
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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67 </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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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>
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4fda2184efa5 "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"
4fda2184efa5 "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">
4fda2184efa5 "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>
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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75 </when>
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 </conditional>
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 </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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78 <outputs>
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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79 <data name="output_file" 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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80 <change_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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81 <when input="input_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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82 <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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83 <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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84 <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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85 <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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86 <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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87 <when input="options_type.output_type" value="illumina.gz" format="fastqillumina.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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88 <when input="options_type.output_type" value="sanger.gz" format="fastqsanger.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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89 <when input="options_type.output_type" value="cssanger.gz" format="fastqcssanger.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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90 <when input="options_type.output_type" value="solexa.bz2" format="fastqsolexa.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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91 <when input="options_type.output_type" value="illumina.bz2" format="fastqillumina.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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92 <when input="options_type.output_type" value="sanger.bz2" format="fastqsanger.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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93 <when input="options_type.output_type" value="cssanger.bz2" format="fastqcssanger.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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94 </change_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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95 </data>
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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96 </outputs>
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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97 <tests>
5
4fda2184efa5 "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 -->
4fda2184efa5 "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>
4fda2184efa5 "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" />
4fda2184efa5 "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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101 <param name="input_type" value="sanger" />
7
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102 <conditional name="options_type">
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103 <param name="options_type_selector" value="basic" />
b8144dbbc1ba 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>
5
4fda2184efa5 "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" />
4fda2184efa5 "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>
4fda2184efa5 "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 -->
4fda2184efa5 "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>
4fda2184efa5 "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" />
4fda2184efa5 "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" />
7
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111 <conditional name="options_type">
b8144dbbc1ba 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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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>
5
4fda2184efa5 "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" />
4fda2184efa5 "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>
4fda2184efa5 "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 -->
4fda2184efa5 "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">
4fda2184efa5 "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" />
4fda2184efa5 "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" />
7
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iuc
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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" />
b8144dbbc1ba 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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124 </conditional>
5
4fda2184efa5 "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>
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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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. -->
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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127 <!-- Test basic 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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128 <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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129 <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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130 <param name="input_type" value="sanger" />
7
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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>
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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134 <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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135 </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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136 <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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137 <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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138 <param name="input_type" value="cssanger" />
7
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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>
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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142 <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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143 </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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144 <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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145 <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" 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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146 <param name="input_type" value="illumina" />
7
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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>
3
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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" />
7
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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>
3
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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" />
7
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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>
3
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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" />
7
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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>
3
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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" />
7
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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>
3
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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" />
7
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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>
3
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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" />
7
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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>
3
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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" />
7
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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>
3
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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" />
7
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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>
3
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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" />
7
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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>
3
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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" />
7
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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>
3
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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" />
7
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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" />
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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>
3
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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" />
7
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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>
3
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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" />
7
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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>
3
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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" />
7
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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>
3
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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" />
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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306 <param name="input_type" value="cssanger" />
7
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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>
3
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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" />
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317 <param name="input_type" value="cssanger" />
7
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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" />
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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>
3
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324 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
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325 </test>
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326 <test>
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327 <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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328 <param name="input_type" value="cssanger" />
7
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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" />
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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>
3
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335 <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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336 </test>
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337 <test>
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338 <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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339 <param name="input_type" value="cssanger" />
7
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340 <conditional name="options_type">
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341 <param name="options_type_selector" value="advanced" />
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342 <param name="output_type" value="solexa" />
b8144dbbc1ba 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>
3
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346 <output name="output_file" file="sanger_full_range_as_solexa.fastqsolexa" />
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347 </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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348 <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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349 <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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350 <param name="input_type" value="cssanger" />
7
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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" />
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355 <param name="summarize_input" value="summarize_input" />
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356 </conditional>
3
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357 <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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358 </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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359 <!-- Test fastq with line wrapping -->
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360 <test>
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361 <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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362 <param name="input_type" value="sanger" />
7
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363 <conditional name="options_type">
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364 <param name="options_type_selector" value="advanced" />
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365 <param name="output_type" value="sanger" />
b8144dbbc1ba 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" />
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367 <param name="summarize_input" value="summarize_input" />
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368 </conditional>
3
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369 <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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370 </test>
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371 <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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372 <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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373 <param name="input_type" value="sanger" />
7
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374 <conditional name="options_type">
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375 <param name="options_type_selector" value="advanced" />
b8144dbbc1ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 6
diff changeset
376 <param name="output_type" value="illumina" />
b8144dbbc1ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 6
diff changeset
377 <param name="force_quality_encoding" value="None" />
b8144dbbc1ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 6
diff changeset
378 <param name="summarize_input" value="summarize_input" />
b8144dbbc1ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
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diff changeset
379 </conditional>
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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parents: 1
diff changeset
380 <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
devteam
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381 </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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parents: 1
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382 <test>
bbc72602f69f 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" />
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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parents: 1
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384 <param name="input_type" value="sanger" />
7
b8144dbbc1ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 6
diff changeset
385 <conditional name="options_type">
b8144dbbc1ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 6
diff changeset
386 <param name="options_type_selector" value="advanced" />
b8144dbbc1ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 6
diff changeset
387 <param name="output_type" value="solexa" />
b8144dbbc1ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 6
diff changeset
388 <param name="force_quality_encoding" value="None" />
b8144dbbc1ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 6
diff changeset
389 <param name="summarize_input" value="summarize_input" />
b8144dbbc1ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 6
diff changeset
390 </conditional>
3
bbc72602f69f 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" />
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
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392 </test>
bbc72602f69f 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 -->
bbc72602f69f 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 -->
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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parents: 1
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395 <test>
bbc72602f69f 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" />
bbc72602f69f 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" />
7
b8144dbbc1ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 6
diff changeset
398 <conditional name="options_type">
b8144dbbc1ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 6
diff changeset
399 <param name="options_type_selector" value="advanced" />
b8144dbbc1ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 6
diff changeset
400 <param name="output_type" value="sanger" />
b8144dbbc1ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 6
diff changeset
401 <param name="force_quality_encoding" value="ascii" />
b8144dbbc1ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 6
diff changeset
402 <param name="summarize_input" value="summarize_input" />
b8144dbbc1ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 6
diff changeset
403 </conditional>
3
bbc72602f69f 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" />
bbc72602f69f 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>
bbc72602f69f 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>
bbc72602f69f 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" />
bbc72602f69f 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" />
7
b8144dbbc1ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 6
diff changeset
409 <conditional name="options_type">
b8144dbbc1ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 6
diff changeset
410 <param name="options_type_selector" value="advanced" />
b8144dbbc1ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 6
diff changeset
411 <param name="output_type" value="sanger" />
b8144dbbc1ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 6
diff changeset
412 <param name="force_quality_encoding" value="decimal" />
b8144dbbc1ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 6
diff changeset
413 <param name="summarize_input" value="summarize_input" />
b8144dbbc1ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 6
diff changeset
414 </conditional>
3
bbc72602f69f 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" />
bbc72602f69f 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>
bbc72602f69f 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>
bbc72602f69f 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" />
bbc72602f69f 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" />
7
b8144dbbc1ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 6
diff changeset
420 <conditional name="options_type">
b8144dbbc1ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 6
diff changeset
421 <param name="options_type_selector" value="advanced" />
b8144dbbc1ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 6
diff changeset
422 <param name="output_type" value="sanger" />
b8144dbbc1ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 6
diff changeset
423 <param name="force_quality_encoding" value="ascii" />
b8144dbbc1ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 6
diff changeset
424 <param name="summarize_input" value="summarize_input" />
b8144dbbc1ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 6
diff changeset
425 </conditional>
3
bbc72602f69f 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" />
bbc72602f69f 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>
bbc72602f69f 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 -->
bbc72602f69f 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>
bbc72602f69f 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" />
bbc72602f69f 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" />
7
b8144dbbc1ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 6
diff changeset
432 <conditional name="options_type">
b8144dbbc1ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 6
diff changeset
433 <param name="options_type_selector" value="advanced" />
b8144dbbc1ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 6
diff changeset
434 <param name="output_type" value="solexa" />
b8144dbbc1ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 6
diff changeset
435 <param name="force_quality_encoding" value="ascii" />
b8144dbbc1ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 6
diff changeset
436 <param name="summarize_input" value="summarize_input" />
b8144dbbc1ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 6
diff changeset
437 </conditional>
3
bbc72602f69f 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" />
bbc72602f69f 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>
bbc72602f69f 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>
bbc72602f69f 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" />
bbc72602f69f 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" />
7
b8144dbbc1ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 6
diff changeset
443 <conditional name="options_type">
b8144dbbc1ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 6
diff changeset
444 <param name="options_type_selector" value="advanced" />
b8144dbbc1ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 6
diff changeset
445 <param name="output_type" value="solexa" />
b8144dbbc1ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 6
diff changeset
446 <param name="force_quality_encoding" value="decimal" />
b8144dbbc1ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 6
diff changeset
447 <param name="summarize_input" value="summarize_input" />
b8144dbbc1ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
iuc
parents: 6
diff changeset
448 </conditional>
3
bbc72602f69f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
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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>
3
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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>
3
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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
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4fda2184efa5 "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
3
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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>