comparison rgFastQC.xml @ 15:2b0c9d9fc6ca draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997

14:f2e8552cf1d0

<tool id="fastqc" name="FastQC" version="0.69">
    <description>Read Quality reports</description>
    <requirements>
        <requirement type="package" version="0.11.5">fastqc</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #import re
        #set input_name = re.sub('[^\w\-\s]', '_', str($input_file.element_identifier))
        python '$__tool_directory__/rgFastQC.py'
            -i '$input_file'
            -d '$html_file.files_path'
            -o '$html_file'
            -t '$text_file'
            -f '$input_file.ext'
            -j '$input_name'
            #if $contaminants.dataset and str($contaminants) > ''
                -c '$contaminants'
            #end if
            #if $limits.dataset and str($limits) > ''
                -l '$limits'
            #end if
    ]]></command>
    <inputs>
        <param format="fastq,fastq.gz,fastq.bz2,bam,sam" name="input_file" type="data"
               label="Short read data from your current history" />
        <param name="contaminants" type="data" format="tabular" optional="true" label="Contaminant list"
               help="tab delimited file with 2 columns: name and sequence.  For example: Illumina Small RNA RT Primer CAAGCAGAAGACGGCATACGA" />
        <param name="limits" type="data" format="txt" optional="true" label="Submodule and Limit specifing file"
               help="a file that specifies which submodules are to be executed (default=all) and also specifies the thresholds for the each submodules warning parameter" />
    </inputs>
    <outputs>
        <data format="html" name="html_file" label="${tool.name} on ${on_string}: Webpage" />
        <data format="txt" name="text_file"  label="${tool.name} on ${on_string}: RawData" />
    </outputs>
    <tests>
        <test>
            <param name="input_file" value="1000gsample.fastq" />
            <param name="contaminants" value="fastqc_contaminants.txt" ftype="tabular" />
            <output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="100"/>
            <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="100"/>
        </test>
        <test>
            <param name="input_file" value="1000gsample.fastq" />
            <param name="limits" value="fastqc_customlimits.txt" ftype="txt" />
            <output name="html_file" file="fastqc_report2.html" ftype="html" compare="sim_size" delta="4096"/>
            <output name="text_file" file="fastqc_data2.txt" ftype="txt" compare="sim_size"/>
        </test>
        <test>
            <param name="input_file" value="1000gsample.fastq.gz" ftype="fastq.gz" />
            <param name="contaminants" value="fastqc_contaminants.txt" ftype="tabular" />
            <output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="100"/>
            <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="100"/>
        </test>
        <test>
            <param name="input_file" value="1000gsample.fastq.bz2" ftype="fastq.bz2" />
            <param name="contaminants" value="fastqc_contaminants.txt" ftype="tabular" />
            <output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="100"/>
            <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="100"/>
        </test>
    </tests>
    <help>
.. class:: infomark

15:2b0c9d9fc6ca

<tool id="fastqc" name="FastQC" version="0.70">
    <description>Read Quality reports</description>
    <requirements>
        <requirement type="package" version="0.11.5">fastqc</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #import re
        #set input_name = re.sub('[^\w\-\s]', '_', str($input_file.element_identifier))
        
        #if $input_file.ext.endswith('.gz'):
            #set input_file_sl = $input_name + '.gz'
        #elif $input_file.ext.endswith('.bz2'):
            #set input_file_sl = $input_name + '.bz2'
        #else
            #set input_file_sl = $input_name
        #end if

        #if 'bam' in $input_file.ext:
            #set format = 'bam'
        #elif 'sam' in $input_file.ext:
            #set format = 'sam'
        #else
            #set format = 'fastq'
        #end if


        ln -s '${input_file}' '${input_file_sl}' &&
        mkdir -p '${html_file.files_path}' &&
        fastqc
            --outdir '${html_file.files_path}'
            
            #if $contaminants.dataset and str($contaminants) > ''
                --contaminants '${contaminants}'
            #end if
            
            #if $limits.dataset and str($limits) > ''
                --limits '${limits}'
            #end if
            
            --quiet
            --extract
            -f '${format}'
            '${input_file_sl}'

        && cp '${html_file.files_path}'/*/fastqc_data.txt output.txt
        && cp '${html_file.files_path}'/*\.html output.html

    ]]></command>
    <inputs>
        <param format="fastq,fastq.gz,fastq.bz2,bam,sam" name="input_file" type="data"
               label="Short read data from your current history" />
        <param name="contaminants" type="data" format="tabular" optional="true" label="Contaminant list"
               help="tab delimited file with 2 columns: name and sequence.  For example: Illumina Small RNA RT Primer CAAGCAGAAGACGGCATACGA" />
        <param name="limits" type="data" format="txt" optional="true" label="Submodule and Limit specifing file"
               help="a file that specifies which submodules are to be executed (default=all) and also specifies the thresholds for the each submodules warning parameter" />
    </inputs>
    <outputs>
        <data format="html" name="html_file" from_work_dir="output.html" label="${tool.name} on ${on_string}: Webpage" />
        <data format="txt" name="text_file"  from_work_dir="output.txt" label="${tool.name} on ${on_string}: RawData" />
    </outputs>
    <tests>
        <test>
            <param name="input_file" value="1000gsample.fastq" />
            <param name="contaminants" value="fastqc_contaminants.txt" ftype="tabular" />
            <output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="100"/>
            <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="2"/>
        </test>
        <test>
            <param name="input_file" value="1000gsample.fastq" />
            <param name="limits" value="fastqc_customlimits.txt" ftype="txt" />
            <output name="html_file" file="fastqc_report2.html" ftype="html" compare="sim_size" delta="4096"/>
            <output name="text_file" file="fastqc_data2.txt" ftype="txt" lines_diff="2"/>
        </test>
        <test>
            <param name="input_file" value="1000gsample.fastq.gz" ftype="fastq.gz" />
            <param name="contaminants" value="fastqc_contaminants.txt" ftype="tabular" />
            <output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="100"/>
            <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="2"/>
        </test>
        <test>
            <param name="input_file" value="1000gsample.fastq.bz2" ftype="fastq.bz2" />
            <param name="contaminants" value="fastqc_contaminants.txt" ftype="tabular" />
            <output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="100"/>
            <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="2"/>
        </test>
        <test>
            <param name="input_file" value="hisat_output_1.bam" ftype="bam" />
            <output name="html_file" file="fastqc_report_hisat.html" ftype="html" lines_diff="100"/>
            <output name="text_file" file="fastqc_data_hisat.txt" ftype="txt" lines_diff="2"/>
        </test>
    </tests>
    <help>
.. class:: infomark