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comparison fastq_filter.xml @ 3:10b75444feae draft

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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter commit 31edb920789fbd080260f853bc856be72fa7cfa8"
author devteam
date Fri, 01 Nov 2019 13:23:29 -0400
parents 06934412f56d
children 81a9090d6df3
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2:06934412f56d 3:10b75444feae
1 <tool id="fastq_filter" name="Filter FASTQ" version="1.1.1"> 1 <tool id="fastq_filter" name="Filter FASTQ" version="1.1.1">
2 <description>reads by quality score and length</description> 2 <description>reads by quality score and length</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.1.1">galaxy_sequence_utils</requirement> 4 <requirement type="package" version="1.1.1">galaxy_sequence_utils</requirement>
5 </requirements> 5 </requirements>
6 <edam_topics>
7 <edam_topic>topic_0622</edam_topic>
8 </edam_topics>
9 <edam_operations>
10 <edam_operation>operation_3695</edam_operation>
11 </edam_operations>
6 <command><![CDATA[ 12 <command><![CDATA[
7 gx-fastq-filter '$input_file' '$fastq_filter_file' '$output_file' '$output_file.files_path' '${input_file.extension[len( 'fastq' ):]}' 13 gx-fastq-filter '$input_file' '$fastq_filter_file' '$output_file' '$output_file.files_path' '${input_file.extension[len( 'fastq' ):]}'
8 ]]></command> 14 ]]></command>
9 <configfiles> 15 <configfiles>
10 <configfile name="fastq_filter_file"><![CDATA[ 16 <configfile name="fastq_filter_file"><![CDATA[
239 <param name="left_column_offset" value="1"/> 245 <param name="left_column_offset" value="1"/>
240 <param name="right_column_offset" value="1"/> 246 <param name="right_column_offset" value="1"/>
241 <param name="score_operation" value="min"/> 247 <param name="score_operation" value="min"/>
242 <param name="score_comparison" value="&gt;="/> 248 <param name="score_comparison" value="&gt;="/>
243 <param name="score" value="1"/> 249 <param name="score" value="1"/>
244 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> 250 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
245 </test> 251 </test>
246 <test> 252 <test>
247 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger"/> 253 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger"/>
248 <param name="min_size" value="0"/> 254 <param name="min_size" value="0"/>
249 <param name="max_size" value="0"/> 255 <param name="max_size" value="0"/>