comparison fastp.xml @ 9:e9f30696da0e draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit a64eb7904f80e90a5faff04ea3fb797ee1e07d36"

8:1eb1895ab19c

<tool id="fastp" name="fastp" version="@WRAPPER_VERSION@+galaxy1">
    <description>- fast all-in-one preprocessing for FASTQ files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>

$filter_options.length_filtering_options.disable_length_filtering

#if str($filter_options.length_filtering_options.length_required):
    -l $filter_options.length_filtering_options.length_required
#end if

## Low complexity filtering options

$filter_options.low_complexity_filter.enable_low_complexity_filter

            </section>

            <section name="length_filtering_options" title="Length filtering options" expanded="True">
                <param name="disable_length_filtering" argument="-L" type="boolean" truevalue="-L" falsevalue="" checked="false" label="Disable length filtering" help="Length filtering is enabled by default. If this option is specified, length filtering is disabled."/>
                <param name="length_required" argument="-l" type="integer" optional="true" label="Length required" help="Reads shorter than this value will be discarded. Default is 15."/>
            </section>

            <section name="low_complexity_filter" title="Low complexity filtering options" expanded="True">
                <param name="enable_low_complexity_filter" argument="-y" type="boolean" truevalue="-y" falsevalue="" checked="false" label="Enable low complexity filter" help="The complexity is defined as the percentage of base that is different from its next base, default is No"/>
                <param name="complexity_threshold" argument="-Y" type="integer" optional="true" label="Complexity threshold" help="Threshold for low complexity filter (0~100). Default is 30, which means 30% complexity is required."/>

9:e9f30696da0e

<tool id="fastp" name="fastp" version="@WRAPPER_VERSION@+galaxy0">
    <description>- fast all-in-one preprocessing for FASTQ files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>

$filter_options.length_filtering_options.disable_length_filtering

#if str($filter_options.length_filtering_options.length_required):
    -l $filter_options.length_filtering_options.length_required
#end if

#if str($filter_options.length_filtering_options.length_limit):
    --length_limit $filter_options.length_filtering_options.length_limit
#end if

## Low complexity filtering options

$filter_options.low_complexity_filter.enable_low_complexity_filter

            </section>

            <section name="length_filtering_options" title="Length filtering options" expanded="True">
                <param name="disable_length_filtering" argument="-L" type="boolean" truevalue="-L" falsevalue="" checked="false" label="Disable length filtering" help="Length filtering is enabled by default. If this option is specified, length filtering is disabled."/>
                <param name="length_required" argument="-l" type="integer" optional="true" label="Length required" help="Reads shorter than this value will be discarded. Default is 15."/>
                <param name="length_limit" argument="--length_limit" type="integer" optional="true" label="Maximum length" help="Reads longer than this value will be discarded. Default is 0 and means no limitation."/>
            </section>

            <section name="low_complexity_filter" title="Low complexity filtering options" expanded="True">
                <param name="enable_low_complexity_filter" argument="-y" type="boolean" truevalue="-y" falsevalue="" checked="false" label="Enable low complexity filter" help="The complexity is defined as the percentage of base that is different from its next base, default is No"/>
                <param name="complexity_threshold" argument="-Y" type="integer" optional="true" label="Complexity threshold" help="Threshold for low complexity filter (0~100). Default is 30, which means 30% complexity is required."/>