comparison fastq_trimmer.xml @ 5:b63b2bfb3ea3 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"

4:33794bdb7fe0

<tool id="fastq_trimmer" name="FASTQ Trimmer" version="1.1.1">
    <description>by column</description>
    <requirements>
        <requirement type="package" version="1.1.1">galaxy_sequence_utils</requirement>
    </requirements>
    <edam_topics>
        <edam_topic>topic_0622</edam_topic>
    </edam_topics>
    <edam_operations>
        <edam_operation>operation_3192</edam_operation>
    </edam_operations>
    <command><![CDATA[
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
    ]]></command>
    <inputs>
        <param name="input_file" type="data" format="fastqsanger,fastqcssanger,fastqsanger.gz,fastqcssanger.gz,fastqsanger.bz2,fastqcssanger.bz2" label="FASTQ file"/>
        <conditional name="offset_type">
            <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)">

5:b63b2bfb3ea3

<tool id="fastq_trimmer" name="FASTQ Trimmer" version="@TOOL_VERSION@">
    <description>by column</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <edam_topics>
        <edam_topic>topic_0622</edam_topic>
    </edam_topics>
    <edam_operations>
        <edam_operation>operation_3192</edam_operation>
    </edam_operations>
    <command><![CDATA[
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
    ]]></command>
    <inputs>
        <param name="input_file" type="data" format="fastqsanger,fastqcssanger,fastqsanger.gz,fastqcssanger.gz,fastqsanger.bz2,fastqcssanger.bz2" label="FASTQ file"/>
        <conditional name="offset_type">
            <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)">