annotate ICGC_STAR_ALIGNMENT_PIPELINE/icgc_star2_wrapper.xml @ 0:be0f5f54462d draft default tip

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<tool id="daumsoft_wts_star" name="ICGC_STAR_PIPELINE" version="2.4.2A">
	<description>STAR Alignment/ICGC Method</description>
        <stdio>
                <regex match="Exception|Error" source="both" level="fatal" description="Tool execution failed"/>
        </stdio>
	<version_command></version_command>
	<command>
         
          \$GALAXY_HOME/package/DAUMSOFT/RNA-seq/ICGC_STAR_ALIGNMENT_PIPELINE/ICGC_pipeline_RUN.sh 
           ${tar_gz}

	</command>
	<inputs>
		<param name="tar_gz" format="gz" type="data" label="RNA-Seq FASTQ file In TAR.GZ(GRCh38)/hg38" help="" />
	</inputs>
	<outputs>
		<data format="bam" name="alignment" label="${tool.name} on ${on_string}: Alignments BAM" from_work_dir="out/Aligned.sortedByCoord.out.bam"/>
	</outputs>
        <tests><test><output name="alignment"/></test></tests>
        <help>
          
For more detailed manual, please visit The GDC mRNA quantification analysis pipeline website:

https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline

The mRNA Analysis pipeline begins with the Alignment Workflow, which is performed using a two-pass method with STAR. 
STAR aligns each read group separately and then merges the resulting alignments into one.
Following the methods used by the International Cancer Genome Consortium ICGC, 
the two-pass method includes a splice junction detection step, which is used to generate the final alignment. 

This workflow outputs a BAM file, which contains both aligned and unaligned reads. 
Quality assessment is performed pre-alignment with  FASTQC and post-alignment with RNA-SeQC and   Picard Tools.

	</help>
        <citations></citations>
</tool>