comparison crispresso2.xml @ 2:eb5dbcfac76b draft default tip

Uploaded

1:3ed9b8271977

<tool id="crispresso2" name="CRISPResso2" version="0.1.0" python_template_version="3.5">
    <requirements>
        <requirement type="package" version="2.0.45">crispresso2</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        mkdir crispresso_out;

            --min_paired_end_reads_overlap $filtering_parameters.min_paired_end_reads_overlap
        #end if
        #if $filtering_parameters.max_paired_end_reads_overlap:
            --max_paired_end_reads_overlap $filtering_parameters.max_paired_end_reads_overlap
        #end if
        $filtering_parameters.stringent_flash_merging
        -o '${html_file.files_path}' > $output_log 
        && cp '${html_file.files_path}'/*\.html crispresso.html && cp '${html_file.files_path}'/CRISPResso_on_reads/CRISPResso_quantification_of_editing_frequency.txt $quant_editing_freq
    ]]></command>
    <inputs>

            <param argument="--min_bp_quality_or_N" type="integer" value="0" label="Bases with a quality score (phred33) less than this value will be set to 'N'"/>
            <param argument="--min_paired_end_reads_overlap" type="integer" value="10" label="Minimum overlap length between reads" help="Parameter for the FLASH read merging step. Minimum required overlap length between two reads to provide a confident overlap. (default: 10)" />
            <param argument="--max_paired_end_reads_overlap" type="integer" value="100" label="Maximum overlap length between reads" help="Parameter for the FLASH merging step. Maximum overlap length expected in approximately 90% of read pairs. Please see the FLASH manual for more information. (default: 100)"/>
            <param name="stringent_flash_merging" truevalue="--stringent_flash_merging" falsevalue="" type="boolean" default="False" label="Use stringent parameters for flash merging" help="In the case where flash could merge R1 and R2 reads ambiguously, the expected overlap is calculated as 2*average_read_length - amplicon_length. The flash parameters for --min-overlap and --max-overlap will be set to prefer merged reads with length within 10bp of the expected overlap. These values override the --min_paired_end_reads_overlap or --max_paired_end_reads_overlap CRISPResso parameters"/>
        </section>
        <!--<section name="window_parameters" expanded="false" title="Quantification window parameters">-->
        <!--</section>-->
    </inputs>
    <outputs>
        <data format="txt" name="output_log" label="${tool.name} on ${on_string}: log" from_work_dir="Log.final.out"/>
        <data name="html_file" format="html" from_work_dir="crispresso.html" label="WebPage report"/>
        <data format="txt" name="quant_editing_freq" label="CRISPResso_quantification_of_editing_frequency"/>

2:eb5dbcfac76b

<tool id="crispresso2" name="CRISPResso2" version="0.1.1" python_template_version="3.5">
    <requirements>
        <requirement type="package" version="2.0.45">crispresso2</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        mkdir crispresso_out;

            --min_paired_end_reads_overlap $filtering_parameters.min_paired_end_reads_overlap
        #end if
        #if $filtering_parameters.max_paired_end_reads_overlap:
            --max_paired_end_reads_overlap $filtering_parameters.max_paired_end_reads_overlap
        #end if
        #if $window_parameters.cleavage_offset:
            --cleavage_offset '$window_parameters.cleavage_offset'
        #end if
        #if $output_parameters.suppress_report:
            --suppress_report
        #end if
        $filtering_parameters.stringent_flash_merging
        -o '${html_file.files_path}' > $output_log 
        && cp '${html_file.files_path}'/*\.html crispresso.html && cp '${html_file.files_path}'/CRISPResso_on_reads/CRISPResso_quantification_of_editing_frequency.txt $quant_editing_freq
    ]]></command>
    <inputs>

            <param argument="--min_bp_quality_or_N" type="integer" value="0" label="Bases with a quality score (phred33) less than this value will be set to 'N'"/>
            <param argument="--min_paired_end_reads_overlap" type="integer" value="10" label="Minimum overlap length between reads" help="Parameter for the FLASH read merging step. Minimum required overlap length between two reads to provide a confident overlap. (default: 10)" />
            <param argument="--max_paired_end_reads_overlap" type="integer" value="100" label="Maximum overlap length between reads" help="Parameter for the FLASH merging step. Maximum overlap length expected in approximately 90% of read pairs. Please see the FLASH manual for more information. (default: 100)"/>
            <param name="stringent_flash_merging" truevalue="--stringent_flash_merging" falsevalue="" type="boolean" default="False" label="Use stringent parameters for flash merging" help="In the case where flash could merge R1 and R2 reads ambiguously, the expected overlap is calculated as 2*average_read_length - amplicon_length. The flash parameters for --min-overlap and --max-overlap will be set to prefer merged reads with length within 10bp of the expected overlap. These values override the --min_paired_end_reads_overlap or --max_paired_end_reads_overlap CRISPResso parameters"/>
        </section>
        <section name="window_parameters" expanded="false" title="Quantification window parameters">
            <param argument="cleavage_offset" type="integer" optional="True" default="-3" label="Center of quantification window to use within respect to the 3' end of the provided sgRNA sequence." help="-wc or --quantification_window_center or --cleavage_offset (default = -3)"/>
        </section>
        <section name="output_parameters" expanded="false" title="Output parameters">
            <param name="suppress_report" type="boolean" default="False" label="Suppress output report, plots output as .pdf only (not .png)" help="--suppress_report"/>
        </section>
    </inputs>
    <outputs>
        <data format="txt" name="output_log" label="${tool.name} on ${on_string}: log" from_work_dir="Log.final.out"/>
        <data name="html_file" format="html" from_work_dir="crispresso.html" label="WebPage report"/>
        <data format="txt" name="quant_editing_freq" label="CRISPResso_quantification_of_editing_frequency"/>