Mercurial > repos > devteam > fastq_filter

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
author iuc
date Wed, 19 Feb 2020 16:49:00 +0000
parents 283a55c8bcb7
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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31685bacc9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
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1 <tool id="fastq_filter" name="Filter FASTQ" version="@TOOL_VERSION@">
3
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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2 <description>reads by quality score and length</description>
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31685bacc9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
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3 <macros>
31685bacc9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
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4 <import>macros.xml</import>
31685bacc9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
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5 </macros>
31685bacc9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
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6 <expand macro="requirements"/>
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283a55c8bcb7 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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7 <edam_topics>
283a55c8bcb7 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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8 <edam_topic>topic_0622</edam_topic>
283a55c8bcb7 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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9 </edam_topics>
283a55c8bcb7 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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10 <edam_operations>
283a55c8bcb7 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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11 <edam_operation>operation_3695</edam_operation>
283a55c8bcb7 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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12 </edam_operations>
3
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13 <command><![CDATA[
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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14 gx-fastq-filter '$input_file' '$fastq_filter_file' '$output_file' '$output_file.files_path' '${input_file.extension[len( 'fastq' ):]}'
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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15 ]]></command>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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16 <configfiles>
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17 <configfile name="fastq_filter_file"><![CDATA[
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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18 def fastq_read_pass_filter(fastq_read):
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19
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20 def mean(score_list):
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21 return float(sum(score_list)) / float(len(score_list))
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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22
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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23 if len(fastq_read) < $min_size:
0
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24 return False
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25 if $max_size > 0 and len(fastq_read) > $max_size:
0
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26 return False
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27 num_deviates = $max_num_deviants
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28 qual_scores = fastq_read.get_decimal_quality_scores()
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29 for qual_score in qual_scores:
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30 if qual_score < $min_quality or ($max_quality > 0 and qual_score > $max_quality):
0
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31 if num_deviates == 0:
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32 return False
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33 else:
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34 num_deviates -= 1
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35 #if not $paired_end:
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ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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36 qual_scores_split = [qual_scores]
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37 #else:
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38 qual_scores_split = [qual_scores[0:int(len(qual_scores) / 2)], qual_scores[int(len(qual_scores) / 2): ]]
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39 #end if
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40 #for $fastq_filter in $fastq_filters:
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41 for split_scores in qual_scores_split:
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ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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42 left_column_offset = $fastq_filter['offset_type']['left_column_offset']
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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43 right_column_offset = $fastq_filter['offset_type']['right_column_offset']
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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44 #if $fastq_filter['offset_type']['base_offset_type'] == 'offsets_percent':
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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45 left_column_offset = int(round(float(left_column_offset) / 100.0 * float(len(split_scores))))
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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46 right_column_offset = int(round(float(right_column_offset) / 100.0 * float(len(split_scores))))
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47 #end if
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48 if right_column_offset > 0:
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49 split_scores = split_scores[left_column_offset:-right_column_offset]
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50 else:
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51 split_scores = split_scores[left_column_offset:]
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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52 if split_scores: ##if a read doesn't have enough columns, it passes by default
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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53 if not (${fastq_filter['score_operation']}(split_scores) $fastq_filter['score_comparison'] $fastq_filter['score']):
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54 return False
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55 #end for
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56 return True
3
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57 ]]></configfile>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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58 </configfiles>
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59 <inputs>
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60 <param name="input_file" type="data" format="fastqsanger,fastqcssanger,fastqsanger.gz,fastqcssanger.gz,fastqsanger.bz2,fastqcssanger.bz2" label="FASTQ File" help="Requires groomed data: if your data does not appear here try using the FASTQ groomer"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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61 <param name="min_size" type="integer" min="0" value="0" label="Minimum size" />
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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62 <param name="max_size" type="integer" value="0" label="Maximum size" help="A maximum size less than 1 indicates no limit"/>
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63 <param name="min_quality" type="float" value="0" label="Minimum quality"/>
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64 <param name="max_quality" type="float" value="0" label="Maximum quality" help="A maximum quality less than 1 indicates no limit"/>
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65 <param name="max_num_deviants" type="integer" min="0" value="0" label="Maximum number of bases allowed outside of quality range" />
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66 <param name="paired_end" type="boolean" truevalue="paired_end" falsevalue="single_end" checked="false" label="This is paired end data" />
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67 <repeat name="fastq_filters" title="Quality Filter on a Range of Bases" help="The above settings do not apply to these filters">
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68 <conditional name="offset_type">
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69 <param name="base_offset_type" type="select" label="Define Base Offsets as" help="Use Absolute for fixed length reads (Illumina, SOLiD)&lt;br&gt;Use Percentage for variable length reads (Roche/454)">
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70 <option value="offsets_absolute" selected="true">Absolute Values</option>
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71 <option value="offsets_percent">Percentage of Read Length</option>
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72 </param>
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73 <when value="offsets_absolute">
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74 <param name="left_column_offset" type="integer" min="0" value="0" label="Offset from 5' end" help="Values start at 0, increasing from the left" />
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75 <param name="right_column_offset" type="integer" min="0" value="0" label="Offset from 3' end" help="Values start at 0, increasing from the right" />
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76 </when>
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77 <when value="offsets_percent">
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78 <param name="left_column_offset" type="float" min="0" max="100" value="0" label="Offset from 5' end" />
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79 <param name="right_column_offset" type="float" min="0" max="100" value="0" label="Offset from 3' end" />
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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80 </when>
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81 </conditional>
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82 <param name="score_operation" type="select" label="Aggregate read score for specified range">
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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83 <option value="min" selected="true">min score</option>
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84 <option value="max">max score</option>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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85 <option value="sum">sum of scores</option>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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86 <option value="mean">mean of scores</option>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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87 </param>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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88 <param name="score_comparison" type="select" label="Keep read when aggregate score is">
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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89 <option value="&gt;">&gt;</option>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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90 <option value="&gt;=" selected="true">&gt;=</option>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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91 <option value="==">==</option>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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92 <option value="&lt;">&lt;</option>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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93 <option value="&lt;=">&lt;=</option>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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94 <sanitizer sanitize="false"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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95 </param>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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96 <param name="score" type="float" value="0" label="Quality score" />
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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97 </repeat>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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98 </inputs>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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99 <outputs>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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100 <data name="output_file" format_source="input_file" />
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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101 </outputs>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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102 <tests>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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103 <!-- Do nothing filter -->
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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104 <test>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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105 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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106 <param name="min_size" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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107 <param name="max_size" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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108 <param name="min_quality" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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109 <param name="max_quality" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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110 <param name="max_num_deviants" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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111 <param name="paired_end" value="false"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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112 <param name="base_offset_type" value="offsets_absolute"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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113 <param name="left_column_offset" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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114 <param name="right_column_offset" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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115 <param name="score_operation" value="min"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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116 <param name="score_comparison" value="&gt;="/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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117 <param name="score" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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118 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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119 </test>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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120 <!-- Do nothing filter compressed -->
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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121 <test>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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122 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger.gz" ftype="fastqsanger.gz"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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123 <param name="min_size" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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124 <param name="max_size" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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125 <param name="min_quality" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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126 <param name="max_quality" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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127 <param name="max_num_deviants" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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128 <param name="paired_end" value="false"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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129 <param name="base_offset_type" value="offsets_absolute"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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130 <param name="left_column_offset" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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131 <param name="right_column_offset" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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132 <param name="score_operation" value="min"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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133 <param name="score_comparison" value="&gt;="/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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134 <param name="score" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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135 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger.gz" ftype="fastqsanger.gz" decompress="true"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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136 </test>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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137 <!-- crippled input types prevent this test <test>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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138 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastqsolexa"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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139 <param name="min_size" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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140 <param name="max_size" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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141 <param name="min_quality" value="-5"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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142 <param name="max_quality" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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143 <param name="max_num_deviants" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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144 <param name="paired_end" value="false"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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145 <param name="base_offset_type" value="offsets_absolute"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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146 <param name="left_column_offset" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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147 <param name="right_column_offset" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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148 <param name="score_operation" value="min"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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149 <param name="score_comparison" value="&gt;="/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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150 <param name="score" value="-5"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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151 <output name="output_file" file="solexa_full_range_original_solexa.fastqsolexa" ftype="fastqsolexa"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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152 </test> -->
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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153 <!-- No trim, so does not remove Adapter from cssanger -->
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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154 <test>
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155 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastqcssanger"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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156 <param name="min_size" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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157 <param name="max_size" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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158 <param name="min_quality" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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159 <param name="max_quality" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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160 <param name="max_num_deviants" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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161 <param name="paired_end" value="false"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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162 <param name="base_offset_type" value="offsets_absolute"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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163 <param name="left_column_offset" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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164 <param name="right_column_offset" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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165 <param name="score_operation" value="min"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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166 <param name="score_comparison" value="&gt;="/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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167 <param name="score" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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168 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastqcssanger" />
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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169 </test>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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170 <!-- Remove all Filter -->
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171 <test>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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172 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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173 <param name="min_size" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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174 <param name="max_size" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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175 <param name="min_quality" value="1"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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176 <param name="max_quality" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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177 <param name="max_num_deviants" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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178 <param name="paired_end" value="false"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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179 <param name="base_offset_type" value="offsets_absolute"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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180 <param name="left_column_offset" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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181 <param name="right_column_offset" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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182 <param name="score_operation" value="min"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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183 <param name="score_comparison" value="&gt;="/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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184 <param name="score" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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185 <output name="output_file" file="empty_file.dat" ftype="fastqsanger" />
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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186 </test>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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187 <!-- crippled input types prevent this test <test>
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188 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastqsolexa"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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189 <param name="min_size" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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190 <param name="max_size" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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191 <param name="min_quality" value="-4"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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192 <param name="max_quality" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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193 <param name="max_num_deviants" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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194 <param name="paired_end" value="false"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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195 <param name="base_offset_type" value="offsets_absolute"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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196 <param name="left_column_offset" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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197 <param name="right_column_offset" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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198 <param name="score_operation" value="min"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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199 <param name="score_comparison" value="&gt;="/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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200 <param name="score" value="-5"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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201 <output name="output_file" file="empty_file.dat" ftype="fastqsolexa" />
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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202 </test> -->
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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203 <!-- Keep all by allowing 1 deviant -->
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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204 <test>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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205 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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206 <param name="min_size" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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207 <param name="max_size" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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208 <param name="min_quality" value="1"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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209 <param name="max_quality" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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210 <param name="max_num_deviants" value="1"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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211 <param name="paired_end" value="false"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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212 <param name="base_offset_type" value="offsets_absolute"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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213 <param name="left_column_offset" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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214 <param name="right_column_offset" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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215 <param name="score_operation" value="min"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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216 <param name="score_comparison" value="&gt;="/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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217 <param name="score" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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218 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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219 </test>
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220 <!-- crippled input types prevent this test<test>
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221 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastqsolexa"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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222 <param name="min_size" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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223 <param name="max_size" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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224 <param name="min_quality" value="-5"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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225 <param name="max_quality" value="61"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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226 <param name="max_num_deviants" value="1"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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227 <param name="paired_end" value="false"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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228 <param name="base_offset_type" value="offsets_absolute"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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229 <param name="left_column_offset" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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230 <param name="right_column_offset" value="0"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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231 <param name="score_operation" value="min"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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232 <param name="score_comparison" value="&gt;="/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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233 <param name="score" value="-5"/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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234 <output name="output_file" file="solexa_full_range_original_solexa.fastqsolexa" ftype="fastqsolexa" />
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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235 </test> -->
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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236 <!-- Filter inner range -->
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237 <test>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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238 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger"/>
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239 <param name="min_size" value="0"/>
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240 <param name="max_size" value="0"/>
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241 <param name="min_quality" value="0"/>
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242 <param name="max_quality" value="0"/>
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243 <param name="max_num_deviants" value="0"/>
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244 <param name="paired_end" value="false"/>
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245 <param name="base_offset_type" value="offsets_absolute"/>
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246 <param name="left_column_offset" value="1"/>
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247 <param name="right_column_offset" value="1"/>
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248 <param name="score_operation" value="min"/>
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249 <param name="score_comparison" value="&gt;="/>
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250 <param name="score" value="1"/>
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251 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
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252 </test>
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253 <test>
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254 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger"/>
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255 <param name="min_size" value="0"/>
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256 <param name="max_size" value="0"/>
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257 <param name="min_quality" value="0"/>
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258 <param name="max_quality" value="0"/>
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259 <param name="max_num_deviants" value="0"/>
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260 <param name="paired_end" value="false"/>
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261 <param name="base_offset_type" value="offsets_absolute"/>
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262 <param name="left_column_offset" value="1"/>
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263 <param name="right_column_offset" value="1"/>
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264 <param name="score_operation" value="max"/>
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265 <param name="score_comparison" value="&lt;="/>
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266 <param name="score" value="92"/>
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267 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
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268 </test>
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269 <!-- percent based offsets -->
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270 <test>
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271 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger"/>
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272 <param name="min_size" value="0"/>
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273 <param name="max_size" value="0"/>
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274 <param name="min_quality" value="0"/>
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275 <param name="max_quality" value="0"/>
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276 <param name="max_num_deviants" value="0"/>
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277 <param name="paired_end" value="false"/>
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278 <param name="base_offset_type" value="offsets_percent"/>
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279 <param name="left_column_offset" value="1.075"/>
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280 <param name="right_column_offset" value="1.075"/>
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281 <param name="score_operation" value="min"/>
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282 <param name="score_comparison" value="&gt;="/>
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283 <param name="score" value="1"/>
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284 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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285 </test>
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286 <test>
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287 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger"/>
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288 <param name="min_size" value="0"/>
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289 <param name="max_size" value="0"/>
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290 <param name="min_quality" value="0"/>
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291 <param name="max_quality" value="0"/>
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292 <param name="max_num_deviants" value="0"/>
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293 <param name="paired_end" value="true"/>
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294 <param name="base_offset_type" value="offsets_percent"/>
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295 <param name="left_column_offset" value="1"/>
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296 <param name="right_column_offset" value="1"/>
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297 <param name="score_operation" value="min"/>
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298 <param name="score_comparison" value="&gt;="/>
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299 <param name="score" value="1"/>
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300 <output name="output_file" file="empty_file.dat" ftype="fastqsanger" />
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301 </test>
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302 </tests>
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303 <help><![CDATA[
0
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304 This tool allows you to build complex filters to be applied to each read in a FASTQ file.
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305
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306 **Basic Options:**
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307 * You can specify a minimum and maximum read lengths.
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308 * You can specify minimum and maximum per base quality scores, with optionally specifying the number of bases that are allowed to deviate from this range (default of 0 deviant bases).
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309 * If your data is paired-end, select the proper checkbox; this will cause each read to be internally split down the middle and filters applied to each half using the offsets specified.
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310
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311 **Advance Options:**
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312 * You can specify any number of advanced filters.
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313 * 5' and 3' offsets are defined, starting at zero, increasing from the respective end of the reads. For example, a quality string of "ABCDEFG", with 5' and 3' offsets of 1 and 1, respectively, specified will yield "BCDEF".
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314 * You can specify either absolute offset values, or percentage offset values. *Absolute Values* based offsets are useful for fixed length reads (e.g. Illumina or SOLiD data). *Percentage of Read Length* based offsets are useful for variable length reads (e.g. 454 data). When using the percent-based method, offsets are rounded to the nearest integer.
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315 * The user specifies the aggregating action (min, max, sum, mean) to perform on the quality score values found between the specified offsets to be used with the user defined comparison operation and comparison value.
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316 * If a set of offsets is specified that causes the remaining quality score list to be of length zero, then the read will **pass** the quality filter unless the size range filter is used to remove these reads.
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317
0017fa63af6c Imported from capsule None
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318 -----
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319
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320 .. class:: warningmark
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321
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322 Adapter bases in color space reads are excluded from filtering.
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323 ]]></help>
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324 <citations>
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325 <citation type="doi">10.1093/bioinformatics/btq281</citation>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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326 </citations>
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327 </tool>