fastq_filter: fastq_filter.xml annotate

annotate fastq_filter.xml @ 7:8afe4308ef8e draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9

author	iuc
date	Sun, 23 Nov 2025 17:48:16 +0000
parents	2acc5fd82ea2
children

rev	line source
6 2acc5fd82ea2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit bb5df9e62585e12f08dfc0a9f86eec8e205b4845 iuc parents: 5 diff changeset	1 <tool id="fastq_filter" name="Filter FASTQ" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
3 ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	2 <description>reads by quality score and length</description>
5 31685bacc9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit d4ced60a941c4c4a2fe95de9c09a10086810b387" iuc parents: 4 diff changeset	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 parents: 4 diff changeset	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 parents: 4 diff changeset	5 </macros>
4 283a55c8bcb7 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit 31edb920789fbd080260f853bc856be72fa7cfa8" devteam parents: 3 diff changeset	6 <edam_topics>
283a55c8bcb7 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit 31edb920789fbd080260f853bc856be72fa7cfa8" devteam parents: 3 diff changeset	7 <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" devteam parents: 3 diff changeset	8 </edam_topics>
283a55c8bcb7 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit 31edb920789fbd080260f853bc856be72fa7cfa8" devteam parents: 3 diff changeset	9 <edam_operations>
283a55c8bcb7 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit 31edb920789fbd080260f853bc856be72fa7cfa8" devteam parents: 3 diff changeset	10 <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" devteam parents: 3 diff changeset	11 </edam_operations>
6 2acc5fd82ea2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit bb5df9e62585e12f08dfc0a9f86eec8e205b4845 iuc parents: 5 diff changeset	12 <expand macro="requirements"/>
3 ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	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 devteam parents: 1 diff changeset	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 devteam parents: 1 diff changeset	15 ]]></command>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	16 <configfiles>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	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 devteam parents: 1 diff changeset	18 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 devteam parents: 1 diff changeset	19
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	20 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 devteam parents: 1 diff changeset	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 devteam parents: 1 diff changeset	22
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	23 if len(fastq_read) < $min_size:
0 0017fa63af6c Imported from capsule None devteam parents: diff changeset	24 return False
3 ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	25 if $max_size > 0 and len(fastq_read) > $max_size:
0 0017fa63af6c Imported from capsule None devteam parents: diff changeset	26 return False
0017fa63af6c Imported from capsule None devteam parents: diff changeset	27 num_deviates = $max_num_deviants
0017fa63af6c Imported from capsule None devteam parents: diff changeset	28 qual_scores = fastq_read.get_decimal_quality_scores()
0017fa63af6c Imported from capsule None devteam parents: diff changeset	29 for qual_score in qual_scores:
3 ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	30 if qual_score < $min_quality or ($max_quality > 0 and qual_score > $max_quality):
0 0017fa63af6c Imported from capsule None devteam parents: diff changeset	31 if num_deviates == 0:
0017fa63af6c Imported from capsule None devteam parents: diff changeset	32 return False
0017fa63af6c Imported from capsule None devteam parents: diff changeset	33 else:
0017fa63af6c Imported from capsule None devteam parents: diff changeset	34 num_deviates -= 1
0017fa63af6c Imported from capsule None devteam parents: diff changeset	35 #if not $paired_end:
3 ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	36 qual_scores_split = [qual_scores]
0 0017fa63af6c Imported from capsule None devteam parents: diff changeset	37 #else:
3 ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	38 qual_scores_split = [qual_scores[0:int(len(qual_scores) / 2)], qual_scores[int(len(qual_scores) / 2): ]]
0 0017fa63af6c Imported from capsule None devteam parents: diff changeset	39 #end if
0017fa63af6c Imported from capsule None devteam parents: diff changeset	40 #for $fastq_filter in $fastq_filters:
0017fa63af6c Imported from capsule None devteam parents: diff changeset	41 for split_scores in qual_scores_split:
3 ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	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 devteam parents: 1 diff changeset	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 devteam parents: 1 diff changeset	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 devteam parents: 1 diff changeset	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 devteam parents: 1 diff changeset	46 right_column_offset = int(round(float(right_column_offset) / 100.0 * float(len(split_scores))))
0 0017fa63af6c Imported from capsule None devteam parents: diff changeset	47 #end if
0017fa63af6c Imported from capsule None devteam parents: diff changeset	48 if right_column_offset > 0:
3 ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	49 split_scores = split_scores[left_column_offset:-right_column_offset]
0 0017fa63af6c Imported from capsule None devteam parents: diff changeset	50 else:
3 ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	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 devteam parents: 1 diff changeset	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 devteam parents: 1 diff changeset	53 if not (${fastq_filter['score_operation']}(split_scores) $fastq_filter['score_comparison'] $fastq_filter['score']):
0 0017fa63af6c Imported from capsule None devteam parents: diff changeset	54 return False
0017fa63af6c Imported from capsule None devteam parents: diff changeset	55 #end for
0017fa63af6c Imported from capsule None devteam parents: diff changeset	56 return True
3 ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	57 ]]></configfile>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	58 </configfiles>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	59 <inputs>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	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 devteam parents: 1 diff changeset	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 devteam parents: 1 diff changeset	62 <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 devteam parents: 1 diff changeset	63 <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 devteam parents: 1 diff changeset	64 <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 devteam parents: 1 diff changeset	65 <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 devteam parents: 1 diff changeset	66 <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 devteam parents: 1 diff changeset	67 <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 devteam parents: 1 diff changeset	68 <conditional name="offset_type">
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	69 <param name="base_offset_type" type="select" label="Define Base Offsets as" help="Use Absolute for fixed length reads (Illumina, SOLiD)<br>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 devteam parents: 1 diff changeset	70 <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 devteam parents: 1 diff changeset	71 <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 devteam parents: 1 diff changeset	72 </param>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	73 <when 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 devteam parents: 1 diff changeset	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" />
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	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" />
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	76 </when>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	77 <when value="offsets_percent">
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	78 <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 devteam parents: 1 diff changeset	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 devteam parents: 1 diff changeset	80 </when>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	81 </conditional>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	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 devteam parents: 1 diff changeset	83 <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 devteam parents: 1 diff changeset	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 devteam parents: 1 diff changeset	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 devteam parents: 1 diff changeset	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 devteam parents: 1 diff changeset	87 </param>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	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 devteam parents: 1 diff changeset	89 <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 devteam parents: 1 diff changeset	90 <option value=">=" selected="true">>=</option>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	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 devteam parents: 1 diff changeset	92 <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 devteam parents: 1 diff changeset	93 <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 devteam parents: 1 diff changeset	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 devteam parents: 1 diff changeset	95 </param>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	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 devteam parents: 1 diff changeset	97 </repeat>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	98 </inputs>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	99 <outputs>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	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 devteam parents: 1 diff changeset	101 </outputs>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	102 <tests>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	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 devteam parents: 1 diff changeset	104 <test>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	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 devteam parents: 1 diff changeset	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 devteam parents: 1 diff changeset	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 devteam parents: 1 diff changeset	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 devteam parents: 1 diff changeset	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 devteam parents: 1 diff changeset	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 devteam parents: 1 diff changeset	111 <param name="paired_end" value="false"/>
7 8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	112 <repeat name="fastq_filters">
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	113 <conditional name="offset_type">
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	114 <param name="base_offset_type" value="offsets_absolute"/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	115 <param name="left_column_offset" value="0"/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	116 <param name="right_column_offset" value="0"/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	117 </conditional>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	118 <param name="score_operation" value="min"/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	119 <param name="score_comparison" value=">="/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	120 <param name="score" value="0"/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	121 </repeat>
3 ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	122 <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 devteam parents: 1 diff changeset	123 </test>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	124 <!-- 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 devteam parents: 1 diff changeset	125 <test>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	126 <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 devteam parents: 1 diff changeset	127 <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 devteam parents: 1 diff changeset	128 <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 devteam parents: 1 diff changeset	129 <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 devteam parents: 1 diff changeset	130 <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 devteam parents: 1 diff changeset	131 <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 devteam parents: 1 diff changeset	132 <param name="paired_end" value="false"/>
7 8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	133 <repeat name="fastq_filters">
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	134 <conditional name="offset_type">
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	135 <param name="base_offset_type" value="offsets_absolute"/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	136 <param name="left_column_offset" value="0"/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	137 <param name="right_column_offset" value="0"/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	138 </conditional>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	139 <param name="score_operation" value="min"/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	140 <param name="score_comparison" value=">="/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	141 <param name="score" value="0"/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	142 </repeat>
3 ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	143 <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 devteam parents: 1 diff changeset	144 </test>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	145 <!-- 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 devteam parents: 1 diff changeset	146 <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 devteam parents: 1 diff changeset	147 <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 devteam parents: 1 diff changeset	148 <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 devteam parents: 1 diff changeset	149 <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 devteam parents: 1 diff changeset	150 <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 devteam parents: 1 diff changeset	151 <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 devteam parents: 1 diff changeset	152 <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 devteam parents: 1 diff changeset	153 <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 devteam parents: 1 diff changeset	154 <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 devteam parents: 1 diff changeset	155 <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 devteam parents: 1 diff changeset	156 <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 devteam parents: 1 diff changeset	157 <param name="score_comparison" value=">="/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	158 <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 devteam parents: 1 diff changeset	159 <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 devteam parents: 1 diff changeset	160 </test> -->
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	161 <!-- 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 devteam parents: 1 diff changeset	162 <test>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	163 <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 devteam parents: 1 diff changeset	164 <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 devteam parents: 1 diff changeset	165 <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 devteam parents: 1 diff changeset	166 <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 devteam parents: 1 diff changeset	167 <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 devteam parents: 1 diff changeset	168 <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 devteam parents: 1 diff changeset	169 <param name="paired_end" value="false"/>
7 8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	170 <repeat name="fastq_filters">
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	171 <conditional name="offset_type">
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	172 <param name="base_offset_type" value="offsets_absolute"/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	173 <param name="left_column_offset" value="0"/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	174 <param name="right_column_offset" value="0"/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	175 </conditional>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	176 <param name="score_operation" value="min"/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	177 <param name="score_comparison" value=">="/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	178 <param name="score" value="0"/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	179 </repeat>
3 ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	180 <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 devteam parents: 1 diff changeset	181 </test>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	182 <!-- Remove all Filter -->
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	183 <test>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	184 <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 devteam parents: 1 diff changeset	185 <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 devteam parents: 1 diff changeset	186 <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 devteam parents: 1 diff changeset	187 <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 devteam parents: 1 diff changeset	188 <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 devteam parents: 1 diff changeset	189 <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 devteam parents: 1 diff changeset	190 <param name="paired_end" value="false"/>
7 8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	191 <repeat name="fastq_filters">
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	192 <conditional name="offset_type">
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	193 <param name="base_offset_type" value="offsets_absolute"/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	194 <param name="left_column_offset" value="0"/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	195 <param name="right_column_offset" value="0"/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	196 </conditional>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	197 <param name="score_operation" value="min"/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	198 <param name="score_comparison" value=">="/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	199 <param name="score" value="0"/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	200 </repeat>
3 ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	201 <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 devteam parents: 1 diff changeset	202 </test>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	203 <!-- 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 devteam parents: 1 diff changeset	204 <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 devteam parents: 1 diff changeset	205 <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 devteam parents: 1 diff changeset	206 <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 devteam parents: 1 diff changeset	207 <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 devteam parents: 1 diff changeset	208 <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 devteam parents: 1 diff changeset	209 <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 devteam parents: 1 diff changeset	210 <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 devteam parents: 1 diff changeset	211 <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 devteam parents: 1 diff changeset	212 <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 devteam parents: 1 diff changeset	213 <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 devteam parents: 1 diff changeset	214 <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 devteam parents: 1 diff changeset	215 <param name="score_comparison" value=">="/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	216 <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 devteam parents: 1 diff changeset	217 <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 devteam parents: 1 diff changeset	218 </test> -->
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	219 <!-- 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 devteam parents: 1 diff changeset	220 <test>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	221 <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 devteam parents: 1 diff changeset	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 devteam parents: 1 diff changeset	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 devteam parents: 1 diff changeset	224 <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 devteam parents: 1 diff changeset	225 <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 devteam parents: 1 diff changeset	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 devteam parents: 1 diff changeset	227 <param name="paired_end" value="false"/>
7 8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	228 <repeat name="fastq_filters">
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	229 <conditional name="offset_type">
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	230 <param name="base_offset_type" value="offsets_absolute"/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	231 <param name="left_column_offset" value="0"/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	232 <param name="right_column_offset" value="0"/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	233 </conditional>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	234 <param name="score_operation" value="min"/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	235 <param name="score_comparison" value=">="/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	236 <param name="score" value="0"/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	237 </repeat>
3 ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	238 <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 devteam parents: 1 diff changeset	239 </test>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	240 <!-- 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 devteam parents: 1 diff changeset	241 <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 devteam parents: 1 diff changeset	242 <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 devteam parents: 1 diff changeset	243 <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 devteam parents: 1 diff changeset	244 <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 devteam parents: 1 diff changeset	245 <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 devteam parents: 1 diff changeset	246 <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 devteam parents: 1 diff changeset	247 <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 devteam parents: 1 diff changeset	248 <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 devteam parents: 1 diff changeset	249 <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 devteam parents: 1 diff changeset	250 <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 devteam parents: 1 diff changeset	251 <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 devteam parents: 1 diff changeset	252 <param name="score_comparison" value=">="/>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	253 <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 devteam parents: 1 diff changeset	254 <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 devteam parents: 1 diff changeset	255 </test> -->
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	256 <!-- Filter inner range -->
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	257 <test>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	258 <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 devteam parents: 1 diff changeset	259 <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 devteam parents: 1 diff changeset	260 <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 devteam parents: 1 diff changeset	261 <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 devteam parents: 1 diff changeset	262 <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 devteam parents: 1 diff changeset	263 <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 devteam parents: 1 diff changeset	264 <param name="paired_end" value="false"/>
7 8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	265 <repeat name="fastq_filters">
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	266 <conditional name="offset_type">
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	267 <param name="base_offset_type" value="offsets_absolute"/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	268 <param name="left_column_offset" value="1"/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	269 <param name="right_column_offset" value="1"/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	270 </conditional>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	271 <param name="score_operation" value="min"/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	272 <param name="score_comparison" value=">="/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	273 <param name="score" value="1"/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	274 </repeat>
4 283a55c8bcb7 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit 31edb920789fbd080260f853bc856be72fa7cfa8" devteam parents: 3 diff changeset	275 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
3 ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	276 </test>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	277 <test>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	278 <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 devteam parents: 1 diff changeset	279 <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 devteam parents: 1 diff changeset	280 <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 devteam parents: 1 diff changeset	281 <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 devteam parents: 1 diff changeset	282 <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 devteam parents: 1 diff changeset	283 <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 devteam parents: 1 diff changeset	284 <param name="paired_end" value="false"/>
7 8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	285 <repeat name="fastq_filters">
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	286 <conditional name="offset_type">
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	287 <param name="base_offset_type" value="offsets_absolute"/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	288 <param name="left_column_offset" value="1"/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	289 <param name="right_column_offset" value="1"/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	290 </conditional>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	291 <param name="score_operation" value="max"/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	292 <param name="score_comparison" value="<="/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	293 <param name="score" value="92"/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	294 </repeat>
3 ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	295 <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 devteam parents: 1 diff changeset	296 </test>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	297 <!-- percent based offsets -->
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	298 <test>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	299 <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 devteam parents: 1 diff changeset	300 <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 devteam parents: 1 diff changeset	301 <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 devteam parents: 1 diff changeset	302 <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 devteam parents: 1 diff changeset	303 <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 devteam parents: 1 diff changeset	304 <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 devteam parents: 1 diff changeset	305 <param name="paired_end" value="false"/>
7 8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	306 <repeat name="fastq_filters">
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	307 <conditional name="offset_type">
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	308 <param name="base_offset_type" value="offsets_percent"/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	309 <param name="left_column_offset" value="1.075"/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	310 <param name="right_column_offset" value="1.075"/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	311 </conditional>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	312 <param name="score_operation" value="min"/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	313 <param name="score_comparison" value=">="/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	314 <param name="score" value="1"/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	315 </repeat>
3 ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	316 <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 devteam parents: 1 diff changeset	317 </test>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	318 <test>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	319 <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 devteam parents: 1 diff changeset	320 <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 devteam parents: 1 diff changeset	321 <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 devteam parents: 1 diff changeset	322 <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 devteam parents: 1 diff changeset	323 <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 devteam parents: 1 diff changeset	324 <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 devteam parents: 1 diff changeset	325 <param name="paired_end" value="true"/>
7 8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	326 <repeat name="fastq_filters">
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	327 <conditional name="offset_type">
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	328 <param name="base_offset_type" value="offsets_percent"/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	329 <param name="left_column_offset" value="1"/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	330 <param name="right_column_offset" value="1"/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	331 </conditional>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	332 <param name="score_operation" value="min"/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	333 <param name="score_comparison" value=">="/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	334 <param name="score" value="1"/>
8afe4308ef8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 iuc parents: 6 diff changeset	335 </repeat>
3 ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	336 <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 devteam parents: 1 diff changeset	337 </test>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	338 </tests>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	339 <help><![CDATA[
0 0017fa63af6c Imported from capsule None devteam parents: diff changeset	340 This tool allows you to build complex filters to be applied to each read in a FASTQ file.
0017fa63af6c Imported from capsule None devteam parents: diff changeset	341
0017fa63af6c Imported from capsule None devteam parents: diff changeset	342 Basic Options:
0017fa63af6c Imported from capsule None devteam parents: diff changeset	343 * You can specify a minimum and maximum read lengths.
0017fa63af6c Imported from capsule None devteam parents: diff changeset	344 * 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).
0017fa63af6c Imported from capsule None devteam parents: diff changeset	345 * 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.
0017fa63af6c Imported from capsule None devteam parents: diff changeset	346
0017fa63af6c Imported from capsule None devteam parents: diff changeset	347 Advance Options:
3 ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	348 * You can specify any number of advanced filters.
0 0017fa63af6c Imported from capsule None devteam parents: diff changeset	349 * 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".
0017fa63af6c Imported from capsule None devteam parents: diff changeset	350 * 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.
0017fa63af6c Imported from capsule None devteam parents: diff changeset	351 * 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.
0017fa63af6c Imported from capsule None devteam parents: diff changeset	352 * 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.
0017fa63af6c Imported from capsule None devteam parents: diff changeset	353
0017fa63af6c Imported from capsule None devteam parents: diff changeset	354 -----
0017fa63af6c Imported from capsule None devteam parents: diff changeset	355
0017fa63af6c Imported from capsule None devteam parents: diff changeset	356 .. class:: warningmark
0017fa63af6c Imported from capsule None devteam parents: diff changeset	357
0017fa63af6c Imported from capsule None devteam parents: diff changeset	358 Adapter bases in color space reads are excluded from filtering.
3 ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	359 ]]></help>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	360 <citations>
ac4a365726a1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit f2582539542b33240234e8ea6093e25d0aee9b6a devteam parents: 1 diff changeset	361 <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 devteam parents: 1 diff changeset	362 </citations>
0 0017fa63af6c Imported from capsule None devteam parents: diff changeset	363 </tool>

Mercurial > repos > devteam > fastq_filter

annotate fastq_filter.xml @ 7:8afe4308ef8e draft default tip