changeset 0:04d416dd3b59 draft default tip

Uploaded

Binary file tar_align/tar has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tar_align/tar.sh	Wed Apr 18 02:52:38 2018 -0400
@@ -0,0 +1,20 @@
+#!/bin/bash 
+if [ "$#" -ne 2 ]; then echo "[usage:] tar.sh  read_R1.fastq  read_R2.fastq"
+ exit 1;
+fi
+
+FASTQ_1=$1
+FASTQ_2=$2
+FASTQ_1_lnk="sample_R1.fastq"
+FASTQ_2_lnk="sample_R2.fastq"
+
+ln -s $FASTQ_1 ./$FASTQ_1_lnk
+ln -s $FASTQ_2 ./$FASTQ_2_lnk
+
+OUT_TAR_GZ=$3.tar.gz
+
+OUTPUT=./out
+mkdir $OUTPUT
+
+$GALAXY_HOME/package/DAUMSOFT/RNA-seq/TAR/tar czlf $OUTPUT/sample.tar.gz  $FASTQ_1_lnk $FASTQ_2_lnk
+          

Binary file tar_align/tar_align/tar has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tar_align/tar_align/tar.sh	Wed Apr 18 02:52:38 2018 -0400
@@ -0,0 +1,20 @@
+#!/bin/bash 
+if [ "$#" -ne 2 ]; then echo "[usage:] tar.sh  read_R1.fastq  read_R2.fastq"
+ exit 1;
+fi
+
+FASTQ_1=$1
+FASTQ_2=$2
+FASTQ_1_lnk="sample_R1.fastq"
+FASTQ_2_lnk="sample_R2.fastq"
+
+ln -s $FASTQ_1 ./$FASTQ_1_lnk
+ln -s $FASTQ_2 ./$FASTQ_2_lnk
+
+OUT_TAR_GZ=$3.tar.gz
+
+OUTPUT=./out
+mkdir $OUTPUT
+
+$GALAXY_HOME/package/DAUMSOFT/RNA-seq/TAR/tar czlf $OUTPUT/sample.tar.gz  $FASTQ_1_lnk $FASTQ_2_lnk
+          

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tar_align/tar_gz.xml	Wed Apr 18 02:52:38 2018 -0400
@@ -0,0 +1,33 @@
+<tool id="daumsoft_wts_tar_gz" name="TAR_GZ" version="tar (GNU tar) 1.23">
+	<description></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/TAR/tar.sh $read1 $read2 
+
+	</command>
+    
+	<inputs>
+	 <param format="fastq" name="read1" type="data" label="input fastq read1" help="" />
+	 <param format="fastq" name="read2" type="data" label="input fastq read2" help="" />
+	</inputs>
+	<outputs>
+	 <data format="gz" name="tar_gz" label="${tool.name} on ${on_string}: fastq files in TAR-GZ" from_work_dir="out/sample.tar.gz"/>
+	</outputs>
+        <tests><test><output name="tar_gz"/></test></tests>
+        <help>
+tar (GNU tar) 1.23
+Copyright (C) 2010 Free Software Foundation, Inc.
+License GPLv3+: GNU GPL version 3 or later http://gnu.org/licenses/gpl.html.
+This is free software: you are free to change and redistribute it.
+There is NO WARRANTY, to the extent permitted by law.
+
+Written by John Gilmore and Jay Fenlason.
+	</help>
+        <citations></citations>
+</tool>