comparison fastp.xml @ 15:a626e8c0e1ba draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 17a0a67dfbc7541a7fe3618cfbbb71d814042889

14:ecb9f4854617

<tool id="fastp" name="fastp" version="@TOOL_VERSION@+galaxy0" profile="23.1">
    <description>fast all-in-one preprocessing for FASTQ files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="biotools" />

#set ext = '.fastqsanger'

#if $single_paired.single_paired_selector == 'paired_collection'
    #if $single_paired.paired_input.forward.is_of_type('fastqsanger.gz')
        #set ext = '.fastqsanger.gz'
    #elif $single_paired.paired_input.forward.is_of_type('fastqillumina.gz')
        #set ext = '.fastqillumina.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

    ln -sf '$in1' '$in1_name' &&
    ln -sf '$in2' '$in2_name' &&
#else
    #if $in1.is_of_type('fastqsanger.gz')
        #set ext = '.fastqsanger.gz'
    #elif $in1.is_of_type('fastqillumina.gz')
        #set ext = '.fastqillumina.gz'
    #end if

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

        #set $in2_name = re.sub('[^\w\-\s]', '_', str("%s_R2" % $in2.element_identifier)) + $ext
        ln -sf '$in2' '$in2_name' &&
    #end if
#end if

cp '$c1' galaxy.json &&

## 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'

## Merge reads

    mv first${ext} '${out1}'
    &&
    mv second${ext} '${out2}'
#end if
]]></command>
    <configfiles>
        <configfile name="c1">
            #set $ext1 = "fastqsanger"
            #set $ext2 = "fastqsanger"
            #if str($single_paired.single_paired_selector) == "single"
                #if $in1.ext.endswith("gz")
                    #set $ext1 = "fastqsanger.gz"
                #end if
            #elif str($single_paired.single_paired_selector) == "paired"
                #if $in1.ext.endswith("gz")
                    #set $ext1 = "fastqsanger.gz"
                #end if
                #if $in2.ext.endswith("gz")
                    #set $ext2 = "fastqsanger.gz"
                #end if
            #else
                #if $paired_input.forward.ext.endswith("gz")
                    #set $ext1 = "fastqsanger.gz"
                #end if
                #if $paired_input.reverse.ext.endswith("gz")
                    #set $ext2 = "fastqsanger.gz"
                #end if
            #end if
            {
                "out1": {"ext": "$ext1"},
                "out2": {"ext": "$ext2"},
                "merged_reads": {"ext": "$ext1"},
                "unmerged_out1": {"ext": "$ext1"},
                "unmerged_out2": {"ext": "$ext2"},
                "unpaired1": {"ext": "$ext1"},
                "unpaired2": {"ext": "$ext2"}
            }
        </configfile>
    </configfiles>
    <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>

                    <expand macro="detect_adapter_for_pe" />
                </expand>
                <expand macro="global_trimming_options_paired" />
            </when>
            <when value="paired_collection">
                <param name="paired_input" type="data_collection" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz" label="Select paired collection(s)" collection_type="paired"/>
                <expand macro="merge_reads" />
                <expand macro="adapter_trimming_options">
                    <expand macro="adapter_sequence" read_number="2"/>
                    <expand macro="detect_adapter_for_pe" />
                </expand>

            <param name="report_json" type="boolean" truevalue="True" falsevalue="False" checked="True" 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="auto" label="${tool.name} on ${on_string}: Read 1 output">
            <filter>single_paired['single_paired_selector'] in ["single", "paired"] and not single_paired['merge_reads']['merge']</filter>
        </data>
        <data name="out2" format="auto" label="${tool.name} on ${on_string}: Read 2 output">
            <filter>single_paired['single_paired_selector'] == "paired" and not single_paired['merge_reads']['merge']</filter>
        </data>
        <collection name="output_paired_coll" type="paired" format_source="paired_input['forward']" label="${tool.name} on ${on_string}: Paired-end output">
            <filter>single_paired['single_paired_selector'] == "paired_collection" and not single_paired['merge_reads']['merge']</filter>
        </collection>

            <filter>output_options['report_html'] is True</filter>
        </data>
        <data name="report_json" format="json" from_work_dir="fastp.json" label="${tool.name} on ${on_string}: JSON report">
            <filter>output_options['report_json'] is True</filter>
        </data>
        <data name="merged_reads" format="auto" label="${tool.name} on ${on_string}: Merged reads">
            <filter>single_paired['single_paired_selector'] in ["paired", "paired_collection"] and single_paired['merge_reads']['merge']</filter>
        </data>
        <data name="unmerged_out1" format="auto" label="${tool.name} on ${on_string}: Unmerged filtered reads1">
            <filter>single_paired['single_paired_selector'] in ["paired", "paired_collection"] and single_paired['merge_reads']['merge'] and not single_paired['merge_reads']['include_unmerged']</filter>
        </data>
        <data name="unmerged_out2" format="auto" label="${tool.name} on ${on_string}: Unmerged filtered reads2">
            <filter>single_paired['single_paired_selector'] in ["paired", "paired_collection"] and single_paired['merge_reads']['merge'] and not single_paired['merge_reads']['include_unmerged']</filter>
        </data>
        <data name="unpaired1" format="auto" label="${tool.name} on ${on_string}: Unmerged unfiltered reads1">
            <filter>single_paired['single_paired_selector'] in ["paired", "paired_collection"] and single_paired['merge_reads']['merge'] and not single_paired['merge_reads']['include_unmerged']</filter>
        </data>
        <data name="unpaired2" format="auto" label="${tool.name} on ${on_string}: Unmerged unfiltered reads2">
            <filter>single_paired['single_paired_selector'] in ["paired", "paired_collection"] and single_paired['merge_reads']['merge'] and not single_paired['merge_reads']['include_unmerged']</filter>
        </data>
    </outputs>

    <tests>
        <!-- 1. Ensure default output works -->

-----

**Inputs**

Single-end or Paired-end (compressed) fastqsagnger or fastqillumina files

-----

**Outputs**

15:a626e8c0e1ba

<tool id="fastp" name="fastp" version="@TOOL_VERSION@+galaxy3" profile="23.1">
    <description>fast all-in-one preprocessing for FASTQ files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="biotools" />

#set ext = '.fastqsanger'

#if $single_paired.single_paired_selector == 'paired_collection'
    #if $single_paired.paired_input.forward.is_of_type('fastqsanger.gz')
        #set ext = '.fastqsanger.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

    ln -sf '$in1' '$in1_name' &&
    ln -sf '$in2' '$in2_name' &&
#else
    #if $in1.is_of_type('fastqsanger.gz')
        #set ext = '.fastqsanger.gz'
    #end if

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

        #set $in2_name = re.sub('[^\w\-\s]', '_', str("%s_R2" % $in2.element_identifier)) + $ext
        ln -sf '$in2' '$in2_name' &&
    #end if
#end if

## Run fastp

fastp

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

-i '$in1_name'

## Merge reads

    mv first${ext} '${out1}'
    &&
    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>

                    <expand macro="detect_adapter_for_pe" />
                </expand>
                <expand macro="global_trimming_options_paired" />
            </when>
            <when value="paired_collection">
                <param name="paired_input" type="data_collection" format="fastqsanger,fastqsanger.gz" label="Select paired collection(s)" collection_type="paired"/>
                <expand macro="merge_reads" />
                <expand macro="adapter_trimming_options">
                    <expand macro="adapter_sequence" read_number="2"/>
                    <expand macro="detect_adapter_for_pe" />
                </expand>

            <param name="report_json" type="boolean" truevalue="True" falsevalue="False" checked="True" 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 ${on_string}: Read 1 output">
            <filter>single_paired['single_paired_selector'] in ["single", "paired"] and not single_paired['merge_reads']['merge']</filter>
        </data>
        <data name="out2" format_source="in2" label="${tool.name} on ${on_string}: Read 2 output">
            <filter>single_paired['single_paired_selector'] == "paired" and not single_paired['merge_reads']['merge']</filter>
        </data>
        <collection name="output_paired_coll" type="paired" format_source="paired_input['forward']" label="${tool.name} on ${on_string}: Paired-end output">
            <filter>single_paired['single_paired_selector'] == "paired_collection" and not single_paired['merge_reads']['merge']</filter>
        </collection>

            <filter>output_options['report_html'] is True</filter>
        </data>
        <data name="report_json" format="json" from_work_dir="fastp.json" label="${tool.name} on ${on_string}: JSON report">
            <filter>output_options['report_json'] is True</filter>
        </data>
        <data name="merged_reads" format_source="in1" label="${tool.name} on ${on_string}: Merged reads">
            <filter>single_paired['single_paired_selector'] in ["paired", "paired_collection"] and single_paired['merge_reads']['merge']</filter>
            <expand macro="format_actions" read_number="1" forward_reverse="forward" />
        </data>
        <data name="unmerged_out1" format_source="in1" label="${tool.name} on ${on_string}: Unmerged filtered reads1">
            <filter>single_paired['single_paired_selector'] in ["paired", "paired_collection"] and single_paired['merge_reads']['merge'] and not single_paired['merge_reads']['include_unmerged']</filter>
            <expand macro="format_actions" read_number="1" forward_reverse="forward" />
        </data>
        <data name="unmerged_out2" format_source="in2" label="${tool.name} on ${on_string}: Unmerged filtered reads2">
            <filter>single_paired['single_paired_selector'] in ["paired", "paired_collection"] and single_paired['merge_reads']['merge'] and not single_paired['merge_reads']['include_unmerged']</filter>
            <expand macro="format_actions" read_number="2" forward_reverse="reverse" />
        </data>
        <data name="unpaired1" format_source="in1" label="${tool.name} on ${on_string}: Unmerged unfiltered reads1">
            <filter>single_paired['single_paired_selector'] in ["paired", "paired_collection"] and single_paired['merge_reads']['merge'] and not single_paired['merge_reads']['include_unmerged']</filter>
            <expand macro="format_actions" read_number="1" forward_reverse="forward" />
        </data>
        <data name="unpaired2" format_source="in2" label="${tool.name} on ${on_string}: Unmerged unfiltered reads2">
            <filter>single_paired['single_paired_selector'] in ["paired", "paired_collection"] and single_paired['merge_reads']['merge'] and not single_paired['merge_reads']['include_unmerged']</filter>
            <expand macro="format_actions" read_number="2" forward_reverse="reverse" />
        </data>
    </outputs>

    <tests>
        <!-- 1. Ensure default output works -->

-----

**Inputs**

Single-end or Paired-end (compressed) fastqsanger files

-----

**Outputs**