changeset 5:9aa9da228b8c draft default tip

planemo upload
author takakoron
date Mon, 11 Apr 2016 10:12:18 -0400
parents 2495b1506d06
children
files Visualize_Distrubution_of_polymorphism.loc.sample Visualize_distrubution_of_polymorphism_docker.xml
diffstat 2 files changed, 78 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Visualize_Distrubution_of_polymorphism.loc.sample	Mon Apr 11 10:12:18 2016 -0400
@@ -0,0 +1,35 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of BWA indexed sequences data files.  You will need
+#to create these data files and then create a bwa_index.loc file 
+#similar to this one (store it in this directory) that points to 
+#the directories in which those files are stored. The bwa_index.loc 
+#file has this format (white space characters are TAB characters):
+#
+#<build>	<file_base>
+#
+#So, for example, if you had phiX indexed stored in 
+#/depot/data2/galaxy/phiX/base/, 
+#then the bwa_index.loc entry would look like this:
+#
+#phiX	/depot/data2/galaxy/phiX/base/phiX.fa
+#
+#and your /depot/data2/galaxy/phiX/base/ directory
+#would contain phiX.fa.* files:
+#
+#-rw-r--r--  1 james    universe 830134 2005-09-13 10:12 phiX.fa.amb
+#-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 phiX.fa.ann
+#-rw-r--r--  1 james    universe 269808 2005-09-13 10:12 phiX.fa.bwt
+#...etc...
+#
+#Your bwa_index.loc file should include an entry per line for each
+#index set you have stored.  The "file" in the path does not actually
+#exist, but it is the prefix for the actual index files.  For example:
+#
+#phiX	/depot/data2/galaxy/phiX/base/phiX.fa
+#hg18	/depot/data2/galaxy/hg18/base/hg18.fa
+Oryza sativa(IRGSPbuild5)	/disk/reference/ddbj/distribution_of_polymorphism/o_sativa.build5.fa
+Oryza sativa(IRGSPbuild1.0)	/disk/reference/ddbj/distribution_of_polymorphism/o_sativa.build1.0.fa
+Arabidopsis thaliana(TAIR10)	/disk/reference/ddbj/distribution_of_polymorphism/TAIR10.fa
+Zea mays B73(RefGen_v2)	/disk/reference/ddbj/distribution_of_polymorphism/ZmB73.RefGen2.fa
+Sorghum bicolor(phytozome_v9.0_Sbicolor_v1.4)	/disk/reference/ddbj/distribution_of_polymorphism/Sorbi.Sbi1.4.fa
+Sorghum bicolor(phytozome_v9.0_Sbicolor_v2.1)	/disk/reference/ddbj/distribution_of_polymorphism/Sorbi.Sbi12.1.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Visualize_distrubution_of_polymorphism_docker.xml	Mon Apr 11 10:12:18 2016 -0400
@@ -0,0 +1,43 @@
+<tool id="Visualize_distrubution_of_polymorphism_docker" name="Visualize distribution of DNA polymorphism">
+	<requirements>
+	    <container type="docker">takakoron/distribution_of_dna_polymorphism</container>
+	</requirements>
+	<command interpreter="perl">
+
+		/usr/src/myapp/kick_distribution_polymorphism.pl
+		
+		'$annotation_data'
+		'$polymorphism'
+		'$output1'
+
+	</command>
+
+	<inputs>
+		<!--- input annotation data -->
+		<param name="annotation_data" type="select" label="Select an annotation data" help="If your annotation of interest is not listed, contact the P-GALAXY team">">
+			<options from_file="Visualize_Distrubution_of_polymorphism.loc">
+				<column name="value" index="1" />
+				<column name="name" index="0" />
+			</options>
+		</param>
+		<param name="polymorphism" type="data" label="Select DNA polymorphism file(format : samtools pileup or mpileup)" />
+	</inputs>
+
+	<outputs>
+		<data name="output1" format="html" />
+	</outputs>
+
+<!---
+   <help>
+
+.. class:: infomark
+**About data** 
+
+Distribution of chromosome is appeared in order of genome file.
+
+   </help>
+-->
+
+</tool>
+
+