comparison fastp.xml @ 4:7c82cb2a90c4 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 761a954744119f6317afe28eb50bd4f3fdea4984

3:e0b44bf2543e

<tool id="fastp" name="fastp" version="@WRAPPER_VERSION@.0">
    <description>- fast all-in-one preprocessing for FASTQ files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="@WRAPPER_VERSION@">fastp</requirement>
    </requirements>
    <version_command>fastp -v</version_command>
    <command detect_errors="exit_code"><![CDATA[
## Link input files

#if $in1.is_of_type('fastq.gz')
    #set ext = 'fastq.gz'
#else
    #set ext = 'fastq'
#end if

ln -s '$in1' input1.$ext &&

#if str($single_paired.single_paired_selector) == 'paired':
    ln -s '$in2' input2.$ext &&
#end if


## Set filename for output report

#import re
#set $filename = re.sub('[^\w\-\s]', '_', str($in1.element_identifier))


## Run fastp

fastp

--thread \${GALAXY_SLOTS:-1}
--report_title 'fastp report for $filename'

#if $in1.is_of_type('fastqillumina', 'fastqsolexa', 'fastqillumina.gz', 'fastqsolexa.gz'):
    --phred64
#end if

-i input1.$ext
-o first.$ext

#if str($single_paired.single_paired_selector) == 'paired':
    -I input2.$ext
    -O second.$ext
#end if


## Adapter Trimming Options

$read_mod_options.base_correction_options.correction

&&

mv first.$ext '${out1}'
#if str($single_paired.single_paired_selector) == 'paired':
    &&
    mv second.$ext '${out2}'
#end if
]]></command>
    <inputs>

        <conditional name="single_paired">

            </section>
        </section>

        <section name="output_options" title="Output Options" expanded="False">
            <param name="report_html" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Output HTML report" help="fastp provides a QC report for the data Before and After filtering within a single HTML page, which enables comparison of the quality statistics changed by the preprocessing step directly"/>
            <param name="report_json" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output JSON report" help="The JSON report contains all the data visualized in the HTML report. The format of the JSON report is manually optimized to be easily readable by humans"/>
        </section>
    </inputs>

    <outputs>
        <data name="out1" format_source="in1" label="${tool.name} on ${on_string}: Read 1 Output"/>

    * Processed reads

Optionally, under **Output Options** you can choose to output

    * HTML report (default is Yes)
    * JSON report

.. _fastp: https://github.com/OpenGene/fastp

]]></help>
    <citations>

4:7c82cb2a90c4

<tool id="fastp" name="fastp" version="@WRAPPER_VERSION@.1">
    <description>- fast all-in-one preprocessing for FASTQ files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="@WRAPPER_VERSION@">fastp</requirement>
    </requirements>
    <version_command>fastp -v</version_command>
    <command detect_errors="exit_code"><![CDATA[
#import re

## Link input files

#if $in1.is_of_type('fastq.gz')
    #set ext = '.fastq.gz'
#else
    #set ext = '.fastq'
#end if

#set $in1_name = re.sub('[^\w\-\s]', '_', str($in1.element_identifier)) + $ext
ln -s '$in1' $in1_name &&

#if str($single_paired.single_paired_selector) == 'paired':
    #set $in2_name = re.sub('[^\w\-\s]', '_', str($in2.element_identifier)) + $ext
    ln -s '$in2' $in2_name &&
#end if


## Run fastp

fastp

--thread \${GALAXY_SLOTS:-1}
--report_title 'fastp report for $in1_name'

#if $in1.is_of_type('fastqillumina', 'fastqsolexa', 'fastqillumina.gz', 'fastqsolexa.gz'):
    --phred64
#end if

-i $in1_name
-o first${ext}

#if str($single_paired.single_paired_selector) == 'paired':
    -I $in2_name
    -O second${ext}
#end if


## Adapter Trimming Options

$read_mod_options.base_correction_options.correction

&&

mv first${ext} '${out1}'
#if str($single_paired.single_paired_selector) == 'paired':
    &&
    mv second${ext} '${out2}'
#end if
]]></command>
    <inputs>

        <conditional name="single_paired">

            </section>
        </section>

        <section name="output_options" title="Output Options" expanded="False">
            <param name="report_html" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Output HTML report" help="fastp provides a QC report for the data Before and After filtering within a single HTML page, which enables comparison of the quality statistics changed by the preprocessing step directly"/>
            <param name="report_json" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output JSON report" help="The JSON report contains all the data visualized in the HTML report. The format of the JSON report is manually optimized to be easily readable by humans and is compatible with MultiQC"/>
        </section>
    </inputs>

    <outputs>
        <data name="out1" format_source="in1" label="${tool.name} on ${on_string}: Read 1 Output"/>

    * Processed reads

Optionally, under **Output Options** you can choose to output

    * HTML report (default is Yes)
    * JSON report (compatible with MultiQC)

.. _fastp: https://github.com/OpenGene/fastp

]]></help>
    <citations>