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annotate fastq_filter.xml @ 3:ac4a365726a1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a
author devteam
date Sat, 30 Sep 2017 14:55:35 -0400
parents a30fc80df16c
children 283a55c8bcb7
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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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1 <tool id="fastq_filter" name="Filter FASTQ" version="1.1.1">
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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2 <description>reads by quality score and length</description>
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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3 <requirements>
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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4 <requirement type="package" version="1.1.1">galaxy_sequence_utils</requirement>
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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5 </requirements>
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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6 <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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7 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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8 ]]></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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9 <configfiles>
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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10 <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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11 def fastq_read_pass_filter(fastq_read):
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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12
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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13 def mean(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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14 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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15
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 if len(fastq_read) < $min_size:
0
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17 return False
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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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18 if $max_size > 0 and len(fastq_read) > $max_size:
0
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19 return False
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20 num_deviates = $max_num_deviants
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21 qual_scores = fastq_read.get_decimal_quality_scores()
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22 for qual_score in qual_scores:
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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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23 if qual_score < $min_quality or ($max_quality > 0 and qual_score > $max_quality):
0
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24 if num_deviates == 0:
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25 return False
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26 else:
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27 num_deviates -= 1
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28 #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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29 qual_scores_split = [qual_scores]
0
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30 #else:
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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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31 qual_scores_split = [qual_scores[0:int(len(qual_scores) / 2)], qual_scores[int(len(qual_scores) / 2): ]]
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32 #end if
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33 #for $fastq_filter in $fastq_filters:
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34 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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35 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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36 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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37 #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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38 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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39 right_column_offset = int(round(float(right_column_offset) / 100.0 * float(len(split_scores))))
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40 #end if
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41 if right_column_offset > 0:
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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 split_scores = split_scores[left_column_offset:-right_column_offset]
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43 else:
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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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44 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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45 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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46 if not (${fastq_filter['score_operation']}(split_scores) $fastq_filter['score_comparison'] $fastq_filter['score']):
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47 return False
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48 #end for
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49 return True
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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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50 ]]></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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51 </configfiles>
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 <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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53 <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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54 <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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55 <param name="max_size" type="integer" value="0" label="Maximum size" help="A maximum size less than 1 indicates no limit"/>
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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56 <param name="min_quality" type="float" value="0" label="Minimum quality"/>
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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57 <param name="max_quality" type="float" value="0" label="Maximum quality" help="A maximum quality less than 1 indicates no limit"/>
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 <param name="max_num_deviants" type="integer" min="0" value="0" label="Maximum number of bases allowed outside of quality 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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59 <param name="paired_end" type="boolean" truevalue="paired_end" falsevalue="single_end" checked="false" label="This is paired end data" />
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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60 <repeat name="fastq_filters" title="Quality Filter on a Range of Bases" help="The above settings do not apply to these filters">
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 <conditional name="offset_type">
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62 <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)">
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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63 <option value="offsets_absolute" selected="true">Absolute Values</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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64 <option value="offsets_percent">Percentage of Read Length</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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65 </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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66 <when value="offsets_absolute">
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67 <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" />
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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68 <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" />
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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69 </when>
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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70 <when value="offsets_percent">
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71 <param name="left_column_offset" type="float" min="0" max="100" value="0" label="Offset from 5' 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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72 <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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73 </when>
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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74 </conditional>
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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75 <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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76 <option value="min" selected="true">min 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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77 <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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78 <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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79 <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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80 </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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81 <param name="score_comparison" type="select" label="Keep read when aggregate score is">
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82 <option value="&gt;">&gt;</option>
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83 <option value="&gt;=" selected="true">&gt;=</option>
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84 <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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85 <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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86 <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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87 <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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88 </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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89 <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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90 </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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91 </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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92 <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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93 <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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94 </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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95 <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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96 <!-- 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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97 <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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98 <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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99 <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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100 <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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101 <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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102 <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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103 <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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104 <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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105 <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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106 <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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107 <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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108 <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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109 <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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110 <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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111 <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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112 </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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113 <!-- 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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114 <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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115 <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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116 <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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117 <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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118 <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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119 <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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120 <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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121 <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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122 <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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123 <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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124 <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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125 <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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126 <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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127 <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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128 <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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129 </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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130 <!-- 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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131 <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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132 <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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133 <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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134 <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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135 <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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136 <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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137 <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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138 <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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139 <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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140 <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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141 <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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142 <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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143 <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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144 <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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145 </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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146 <!-- 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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147 <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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148 <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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149 <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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150 <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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151 <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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152 <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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153 <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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154 <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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155 <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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156 <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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157 <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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158 <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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159 <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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160 <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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161 <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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162 </test>
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163 <!-- Remove all Filter -->
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164 <test>
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165 <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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166 <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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167 <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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168 <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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169 <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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170 <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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171 <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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172 <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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173 <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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174 <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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175 <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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176 <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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177 <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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178 <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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179 </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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180 <!-- crippled input types prevent this test <test>
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181 <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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182 <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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183 <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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184 <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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185 <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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186 <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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187 <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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188 <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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189 <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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190 <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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191 <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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192 <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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193 <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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194 <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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195 </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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196 <!-- 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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197 <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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198 <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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199 <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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200 <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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201 <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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202 <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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203 <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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204 <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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205 <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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206 <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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207 <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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208 <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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209 <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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210 <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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211 <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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212 </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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213 <!-- crippled input types prevent this test<test>
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214 <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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215 <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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216 <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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217 <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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218 <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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219 <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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220 <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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221 <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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222 <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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223 <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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224 <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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225 <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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226 <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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227 <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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228 </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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229 <!-- Filter inner range -->
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230 <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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231 <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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232 <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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233 <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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234 <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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235 <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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236 <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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237 <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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238 <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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239 <param name="left_column_offset" value="1"/>
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240 <param name="right_column_offset" value="1"/>
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241 <param name="score_operation" value="min"/>
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242 <param name="score_comparison" value="&gt;="/>
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243 <param name="score" value="1"/>
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244 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
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245 </test>
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246 <test>
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247 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger"/>
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248 <param name="min_size" value="0"/>
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249 <param name="max_size" value="0"/>
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250 <param name="min_quality" value="0"/>
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251 <param name="max_quality" value="0"/>
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252 <param name="max_num_deviants" value="0"/>
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253 <param name="paired_end" value="false"/>
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254 <param name="base_offset_type" value="offsets_absolute"/>
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255 <param name="left_column_offset" value="1"/>
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256 <param name="right_column_offset" value="1"/>
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257 <param name="score_operation" value="max"/>
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258 <param name="score_comparison" value="&lt;="/>
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259 <param name="score" value="92"/>
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260 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
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261 </test>
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262 <!-- percent based offsets -->
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263 <test>
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264 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger"/>
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265 <param name="min_size" value="0"/>
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266 <param name="max_size" value="0"/>
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267 <param name="min_quality" value="0"/>
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268 <param name="max_quality" value="0"/>
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269 <param name="max_num_deviants" value="0"/>
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270 <param name="paired_end" value="false"/>
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271 <param name="base_offset_type" value="offsets_percent"/>
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272 <param name="left_column_offset" value="1.075"/>
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273 <param name="right_column_offset" value="1.075"/>
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274 <param name="score_operation" value="min"/>
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275 <param name="score_comparison" value="&gt;="/>
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276 <param name="score" value="1"/>
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277 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
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278 </test>
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279 <test>
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280 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger"/>
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281 <param name="min_size" value="0"/>
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282 <param name="max_size" value="0"/>
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283 <param name="min_quality" value="0"/>
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284 <param name="max_quality" value="0"/>
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285 <param name="max_num_deviants" value="0"/>
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286 <param name="paired_end" value="true"/>
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287 <param name="base_offset_type" value="offsets_percent"/>
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288 <param name="left_column_offset" value="1"/>
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289 <param name="right_column_offset" value="1"/>
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290 <param name="score_operation" value="min"/>
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291 <param name="score_comparison" value="&gt;="/>
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292 <param name="score" value="1"/>
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293 <output name="output_file" file="empty_file.dat" ftype="fastqsanger" />
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294 </test>
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295 </tests>
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296 <help><![CDATA[
0
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297 This tool allows you to build complex filters to be applied to each read in a FASTQ file.
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298
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299 **Basic Options:**
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300 * You can specify a minimum and maximum read lengths.
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301 * 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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302 * 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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303
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304 **Advance Options:**
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305 * You can specify any number of advanced filters.
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306 * 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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307 * 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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308 * 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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309 * 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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310
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311 -----
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312
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313 .. class:: warningmark
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314
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315 Adapter bases in color space reads are excluded from filtering.
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316 ]]></help>
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317 <citations>
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318 <citation type="doi">10.1093/bioinformatics/btq281</citation>
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319 </citations>
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320 </tool>