comparison fastp.xml @ 5:3e2551a37201 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498

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>

    <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

#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

#if str($single_paired.adapter_trimming_options.adapter_sequence1):
    --adapter_sequence '$single_paired.adapter_trimming_options.adapter_sequence1'
#end if

#if str($single_paired.single_paired_selector) == 'paired':
    #if str($single_paired.adapter_trimming_options.adapter_sequence2):
        --adapter_sequence_r2 '$single_paired.adapter_trimming_options.adapter_sequence2'
    #end if
#end if

#if str($single_paired.global_trimming_options.trim_tail1):
    -t $single_paired.global_trimming_options.trim_tail1
#end if

#if str($single_paired.single_paired_selector) == 'paired':
    #if str($single_paired.global_trimming_options.trim_front2):
        -F $single_paired.global_trimming_options.trim_front2
    #end if
    #if str($single_paired.global_trimming_options.trim_tail2):
        -T $single_paired.global_trimming_options.trim_tail2

$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">
            <param name="single_paired_selector" type="select" label="Single-end or paired reads">
                <option value="single" selected="true">Single-end</option>
                <option value="paired">Paired</option>
            </param>
            <when value="single">
                <expand macro="in1" />
                <section name="adapter_trimming_options" title="Adapter Trimming Options" expanded="False">
                    <param name="disable_adapter_trimming" argument="-A" type="boolean" truevalue="-A" falsevalue="" checked="false" label="Disable adapter trimming" help="Adapter trimming is enabled by default. If this option is specified, adapter trimming is disabled."/>
                    <expand macro="adapter_sequence1" />
                </section>
                <section name="global_trimming_options" title="Global Trimming Options" expanded="False">
                    <param name="trim_front1" argument="-f" type="integer" optional="true" label="Trim front for input 1" help="Trimming how many bases in front for read1, default is 0."/>
                    <param name="trim_tail1" argument="-t" type="integer" optional="true" label="Trim tail for input 1" help="Trimming how many bases in tail for read1, default is 0."/>
                </section>
            </when>
            <when value="paired">
                <expand macro="in1" />
                <param name="in2" argument="-I" type="data" format="fastq,fastq.gz" optional="true" label="Input 2" help="Input FASTQ file #2."/>
                <section name="adapter_trimming_options" title="Adapter trimming options" expanded="False">
                    <param name="disable_adapter_trimming" argument="-A" type="boolean" truevalue="-A" falsevalue="" checked="false" label="Disable adapter trimming" help="Adapter trimming is enabled by default. If this option is specified, adapter trimming is disabled."/>
                    <expand macro="adapter_sequence1" />
                    <param name="adapter_sequence2" argument="--adapter_sequence_r2" type="text" optional="true" label="Adapter sequence for input 2" help="The adapter for read2 (PE data only). This is used if R1/R2 are found not overlapped. If not specified, it will be the same as adapter sequence value for input 1.">
                        <sanitizer>
                            <valid>
                                <add value="A"/>
                                <add value="T"/>
                                <add value="C"/>
                                <add value="G"/>
                            </valid>
                        </sanitizer>
                    </param>
                </section>
                <section name="global_trimming_options" title="Global trimming options" expanded="False">
                    <param name="trim_front1" argument="-f" type="integer" optional="true" label="Trim front for input 1" help="Trimming how many bases in front for read1, default is 0."/>
                    <param name="trim_tail1" argument="-t" type="integer" optional="true" label="Trim tail for input 1" help="Trimming how many bases in tail for read1, default is 0."/>
                    <param name="trim_front2" argument="-F" type="integer" optional="true" label="Trim front for input 2" help="Trimming how many bases in front for read2. If it's not specified, it will follow read1's settings."/>
                    <param name="trim_tail2" argument="-T" type="integer" optional="true" label="Trim tail for input 2" help="Trimming how many bases in tail for read2. If it's not specified, it will follow read1's settings."/>
                </section>
            </when>
        </conditional>

        <section name="overrepresented_sequence_analysis" title="Overrepresented Sequence Analysis" expanded="False">
            <param name="overrepresentation_analysis" argument="-p" type="boolean" truevalue="-p" falsevalue="" checked="false" label="Enable overrepresented analysis" help="Enable overrepresented sequence analysis."/>

            <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 ${on_string}: Read 1 Output"/>
        <data name="out2" format_source="in2" label="${tool.name} on ${on_string}: Read 2 Output">
            <filter>single_paired['single_paired_selector'] == "paired"</filter>
        </data>
        <data name="report_html" format="html" from_work_dir="fastp.html" label="${tool.name} on ${on_string}: HTML Report">
            <filter>output_options['report_html'] is True</filter>
        </data>
        <data name="report_json" format="json" from_work_dir="fastp.json" label="${tool.name} on ${on_string}: JSON Report">
            <filter>output_options['report_json'] is True</filter>

            <output name="report_html">
                <assert_contents>
                    <has_text text="fastp report"/>
                </assert_contents>
            </output>
        </test>
        <!-- Ensure custom adapter works -->
        <test expect_num_outputs="2">
            <param name="in1" ftype="fastq" value="R1.fq"/>
            <param name="single_paired_selector" value="single"/>

5:3e2551a37201

<tool id="fastp" name="fastp" version="@WRAPPER_VERSION@.2">
    <description>- fast all-in-one preprocessing for FASTQ files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>

    <command detect_errors="exit_code"><![CDATA[
#import re

## Link input files

#set ext = '.fastq'

#if $single_paired.single_paired_selector == 'paired_collection':
    #if $single_paired.paired_input.forward.is_of_type('fastq.gz'):
        #set ext = '.fastq.gz'
    #end if
    #set $in1 = $single_paired.paired_input.forward
    #set $in2 = $single_paired.paired_input.reverse
    #set $in1_name = re.sub('[^\w\-\s]', '_', str($single_paired.paired_input.name)) + $ext
    #set $in2_name = re.sub('[^\w\-\s]', '_', str("%s_%s" % ($single_paired.paired_input.name, "R2"))) + $ext
    #set out1 = $output_paired_coll.forward
    #set out2 = $output_paired_coll.reverse
    ln -s '$in1' '$in1_name' &&
    ln -s '$in2' '$in2_name' &&
#else
    #if $in1.is_of_type('fastq.gz')
        #set ext = '.fastq.gz'
    #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("%s_R2" % $in2.element_identifier)) + $ext
        ln -s '$in2' '$in2_name' &&
    #end if
#end if


## Run fastp

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

-i '$in1_name'
-o first${ext}

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


## Adapter Trimming Options

#if str($single_paired.adapter_trimming_options.adapter_sequence1):
    --adapter_sequence '$single_paired.adapter_trimming_options.adapter_sequence1'
#end if

#if str($single_paired.single_paired_selector).startswith('paired'):
    #if str($single_paired.adapter_trimming_options.adapter_sequence2):
        --adapter_sequence_r2 '$single_paired.adapter_trimming_options.adapter_sequence2'
    #end if
#end if

#if str($single_paired.global_trimming_options.trim_tail1):
    -t $single_paired.global_trimming_options.trim_tail1
#end if

#if str($single_paired.single_paired_selector).startswith('paired'):
    #if str($single_paired.global_trimming_options.trim_front2):
        -F $single_paired.global_trimming_options.trim_front2
    #end if
    #if str($single_paired.global_trimming_options.trim_tail2):
        -T $single_paired.global_trimming_options.trim_tail2

$read_mod_options.base_correction_options.correction

&&

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

        <conditional name="single_paired">
            <param name="single_paired_selector" type="select" label="Single-end or paired reads">
                <option value="single" selected="true">Single-end</option>
                <option value="paired">Paired</option>
                <option value="paired_collection">Paired Collection</option>
            </param>
            <when value="single">
                <expand macro="in" />
                <expand macro="adapter_trimming_options" />
                <expand macro="global_trimming_options" />
            </when>
            <when value="paired">
                <expand macro="in" read_number="1" argument="-i"/>
                <expand macro="in" read_number="2" argument="-I"/>
                <expand macro="adapter_trimming_options">
                    <expand macro="adapter_sequence" read_number="2"/>
                </expand>
                <expand macro="global_trimming_options_paired" />
            </when>
        <when value="paired_collection">
                <param name="paired_input" type="data_collection" collection_type="paired" format="fastq,fastq.gz" label="Select paired collection(s)"/>
                <expand macro="adapter_trimming_options">
                    <expand macro="adapter_sequence" read_number="2"/>
                </expand>
                <expand macro="global_trimming_options_paired" />
            </when>
        </conditional>

        <section name="overrepresented_sequence_analysis" title="Overrepresented Sequence Analysis" expanded="False">
            <param name="overrepresentation_analysis" argument="-p" type="boolean" truevalue="-p" falsevalue="" checked="false" label="Enable overrepresented analysis" help="Enable overrepresented sequence analysis."/>

            <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 ${on_string}: Read 1 Output">
            <filter>single_paired['single_paired_selector'] in ["single", "paired"]</filter>
        </data>
        <data name="out2" format_source="in2" label="${tool.name} on ${on_string}: Read 2 Output">
            <filter>single_paired['single_paired_selector'] == "paired"</filter>
        </data>
        <collection name="output_paired_coll" type="paired" structured_like="paired_input" inherit_format="true" label="Paired-end output of ${tool.name} on ${on_string}">
            <filter>single_paired['single_paired_selector'] == "paired_collection"</filter>
        </collection>
        <data name="report_html" format="html" from_work_dir="fastp.html" label="${tool.name} on ${on_string}: HTML Report">
            <filter>output_options['report_html'] is True</filter>
        </data>
        <data name="report_json" format="json" from_work_dir="fastp.json" label="${tool.name} on ${on_string}: JSON Report">
            <filter>output_options['report_json'] is True</filter>

            <output name="report_html">
                <assert_contents>
                    <has_text text="fastp report"/>
                </assert_contents>
            </output>
        </test>
        <!-- Ensure paired collection works -->
        <test expect_num_outputs="3">
            <param name="single_paired_selector" value="paired_collection"/>
            <param name="paired_input">
                <collection type="paired">
                    <element name="forward" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
                    <element name="reverse" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
                </collection>
            </param>
            <output name="report_html">
                <assert_contents>
                    <has_text text="fastp report"/>
                </assert_contents>
            </output>
            <output_collection name="output_paired_coll" type="paired">
                <element name="forward" value="out_bwa1.fq" ftype="fastqsanger"/>
                <element name="reverse" value="out_bwa2.fq" ftype="fastqsanger"/>
            </output_collection>
        </test>
        <!-- Ensure custom adapter works -->
        <test expect_num_outputs="2">
            <param name="in1" ftype="fastq" value="R1.fq"/>
            <param name="single_paired_selector" value="single"/>