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comparison fastq_trimmer.xml @ 5:b63b2bfb3ea3 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
author iuc
date Wed, 19 Feb 2020 12:35:44 -0500
parents 33794bdb7fe0
children f0b18efb97f1
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4:33794bdb7fe0 5:b63b2bfb3ea3
1 <tool id="fastq_trimmer" name="FASTQ Trimmer" version="1.1.1"> 1 <tool id="fastq_trimmer" name="FASTQ Trimmer" version="@TOOL_VERSION@">
2 <description>by column</description> 2 <description>by column</description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="1.1.1">galaxy_sequence_utils</requirement> 4 <import>macros.xml</import>
5 </requirements> 5 </macros>
6 <expand macro="requirements"/>
6 <edam_topics> 7 <edam_topics>
7 <edam_topic>topic_0622</edam_topic> 8 <edam_topic>topic_0622</edam_topic>
8 </edam_topics> 9 </edam_topics>
9 <edam_operations> 10 <edam_operations>
10 <edam_operation>operation_3192</edam_operation> 11 <edam_operation>operation_3192</edam_operation>
11 </edam_operations> 12 </edam_operations>
12 <command><![CDATA[ 13 <command><![CDATA[
13 gx-fastq-trimmer '$input_file' '$output_file' ${offset_type['left_column_offset']} ${offset_type['right_column_offset']} ${offset_type['base_offset_type']} '${input_file.extension[len('fastq'):]}' $keep_zero_length 14 gx-fastq-trimmer '$input_file' '$output_file' ${offset_type.left_column_offset} ${offset_type.right_column_offset} ${offset_type.base_offset_type} '${input_file.extension[len('fastq'):]}' $keep_zero_length
14 ]]></command> 15 ]]></command>
15 <inputs> 16 <inputs>
16 <param name="input_file" type="data" format="fastqsanger,fastqcssanger,fastqsanger.gz,fastqcssanger.gz,fastqsanger.bz2,fastqcssanger.bz2" label="FASTQ file"/> 17 <param name="input_file" type="data" format="fastqsanger,fastqcssanger,fastqsanger.gz,fastqcssanger.gz,fastqsanger.bz2,fastqcssanger.bz2" label="FASTQ file"/>
17 <conditional name="offset_type"> 18 <conditional name="offset_type">
18 <param name="base_offset_type" type="select" label="Define Base Offsets as" help="Use Absolute for fixed length reads (Illumina, SOLiD)&lt;br&gt;Use Percentage for variable length reads (Roche/454)"> 19 <param name="base_offset_type" type="select" label="Define Base Offsets as" help="Use Absolute for fixed length reads (Illumina, SOLiD)&lt;br&gt;Use Percentage for variable length reads (Roche/454)">