comparison htseq_count.xml @ 5:aacd5f53ac99 draft

v2.0.0

4:0fdb0d5f53ce

<tool id="aurora_htseq" name="Aurora htseq" version="1.0.0">
    <description>Counting reads in features.</description>
    <requirements>
        <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
        <requirement type="package" version="1.20.0">r-getopt</requirement>
        <requirement type="package" version="1.6">r-rmarkdown</requirement>

    </requirements>
    <stdio>
        <regex match="XXX" source="stderr" level="warning"
               description="Check the warnings_and_errors.txt file for more details."/>
    </stdio>
    <command><![CDATA[Rscript '${__tool_directory__}/htseq_count_render.R'

			-e $echo
			-o $report
			-d $report.files_path
			-s $sink_message
			-t '${__tool_directory__}'
			
			-A '$alignment_files'
			-B '$sample_names'
			-G $gff
			-f $format
			-r $order

			-a $minaqual
			-T $feature_type
			-i $idattr
			-m $mode
			-c $count
			-O $count_rdata]]></command>
    <inputs>
        <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false"
               label="Display analysis code in report?"/>
        <param type="data" name="alignment_files" label="Alignment file (SAM/BAM)" optional="False" format="sam,bam"
               multiple="True"/>
        <param type="text" name="sample_names" label="Sample names"
               help="sample names for each input SAM/BAM file. Use comma to separate multiple names, for example, sample_1, sample_2, sample_3. The number of sample names should be the same as the number of input SAM/BAM files."
               optional="False" size="5x25"/>

            <option value="intersection-strict" selected="false">Intersection (strict)</option>
            <option value="intersection-nonempty" selected="false">Intersection (nonempty)</option>
        </param>
    </inputs>
    <outputs>
        <data name="report" format="html" label="Aurora htseq on ${on_string}" hidden="false"/>
        <data format="txt" name="sink_message" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt"/>
        <data name="count" format="txt" label="Aurora htseq-count on ${on_string}" hidden="false"/>
        <data name="count_rdata" format="rdata" hidden="false"/>
    </outputs>
    <citations>
        <citation type="bibtex"><![CDATA[
            @article{allaire2016rmarkdown,
            title={rmarkdown: Dynamic Documents for R, 2016},

5:aacd5f53ac99

<tool id="aurora_htseq" name="aurora_htseq" version="2.0.0">
    <description>Counting reads in features.</description>
    <requirements>
        <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
        <requirement type="package" version="1.20.0">r-getopt</requirement>
        <requirement type="package" version="1.6">r-rmarkdown</requirement>

    </requirements>
    <stdio>
        <regex match="XXX" source="stderr" level="warning"
               description="Check the warnings_and_errors.txt file for more details."/>
    </stdio>
    <command><![CDATA[

        ######### each aurora tool generates a html file and have an files path directory associated with it.
        mkdir -p $report.files_path &&

        ######### three important paths:
        #########   1. path to tool installation directory
        #########   2. path to report html
        #########   3. path to files_path directory associated with the report output.
        export TOOL_INSTALL_DIR='${__tool_directory__}' &&
        export REPORT='$report' &&
        export REPORT_FILES_PATH='$report.files_path' &&

        ############ create a hidden file to store r markdown rendering log
        echo '------ Rmd rendering log -------\n' > $report.files_path/.r_rendering.log.txt &&

    echo echo 'R markdown rendering started.' &&

    Rscript '${__tool_directory__}/htseq_count_render.R'

			-o $report
			-d $report.files_path

			-A '$alignment_files'
			-B '$sample_names'
			-G $gff
			-f $format
			-r $order

			-a $minaqual
			-T $feature_type
			-i $idattr
			-m $mode
			-c $count
			-O $count_rdata &&

	echo 'R markdown rendering finished.'

    ]]></command>
    <inputs>
        <param type="data" name="alignment_files" label="Alignment file (SAM/BAM)" optional="False" format="sam,bam"
               multiple="True"/>
        <param type="text" name="sample_names" label="Sample names"
               help="sample names for each input SAM/BAM file. Use comma to separate multiple names, for example, sample_1, sample_2, sample_3. The number of sample names should be the same as the number of input SAM/BAM files."
               optional="False" size="5x25"/>

            <option value="intersection-strict" selected="false">Intersection (strict)</option>
            <option value="intersection-nonempty" selected="false">Intersection (nonempty)</option>
        </param>
    </inputs>
    <outputs>
        <data name="report" format="html" label="${tool.name} report on ${on_string}" hidden="false"/>
        <data name="count" format="txt" label="Aurora htseq-count on ${on_string}" hidden="false"/>
        <data name="count_rdata" format="rdata" label="${tool.name} count data on ${on_string}"/>
    </outputs>
    <citations>
        <citation type="bibtex"><![CDATA[
            @article{allaire2016rmarkdown,
            title={rmarkdown: Dynamic Documents for R, 2016},