diff star_alignment/icgc_star2_wrapper.xml @ 0:8922a3be8490 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/star_alignment/icgc_star2_wrapper.xml	Mon Jun 04 02:38:49 2018 -0400
@@ -0,0 +1,36 @@
+<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>