Mercurial > repos > iracooke > make_protein_decoys

changeset 0:45dee11aa2bf draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author iracooke
date Tue, 18 Mar 2014 20:50:51 -0400
parents
children 1de17a5e8058
files README.md make_decoy.xml repository_dependencies.xml tool_dependencies.xml
diffstat 4 files changed, 59 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Tue Mar 18 20:50:51 2014 -0400
@@ -0,0 +1,3 @@
+# Make decoys from a protein database
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/make_decoy.xml	Tue Mar 18 20:50:51 2014 -0400
@@ -0,0 +1,46 @@
+<tool id="make_decoy" name="Generate protein decoy sequences" version="1.0.0">
+	<requirements>
+	    <requirement type="package" version="1.2.6">protk</requirement>
+   </requirements>
+
+	<description>Generate random protein sequences with the same AA composition and input sequences</description>
+
+	<command>
+		make_decoy.rb $fasta_file -o $output
+		-P $prefix_string
+		$append
+
+	</command>
+
+
+
+
+	<stdio>
+		<exit_code range="1:"   level="fatal"   description="Failure" />
+	</stdio>
+
+	<inputs>	
+		<param name="fasta_file" type="data" format="fasta" label="Fasta file contain protein sequences" />
+		<param name="prefix_string" help="Prefix String to use for Decoys" type="text" value="decoy_" label="Prefix String" size="20"/>		
+		<param name="append" type="boolean" label="Append input sequences to the generated sequences" help="" truevalue="--append" falsevalue="" />
+	</inputs>
+
+	<outputs>
+		<data format="fasta" name="output" />
+	</outputs>
+
+
+  <help>
+
+**What it does**
+
+Generates random protein sequences based on a given set of input sequences. To be used for decoy proteomics searches
+
+----
+
+**References**
+
+
+  </help>
+
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml	Tue Mar 18 20:50:51 2014 -0400
@@ -0,0 +1,4 @@
+<?xml version="1.0"?>
+<repositories description="Proteomics datatypes">
+    <repository changeset_revision="25f42af5b73d" name="proteomics_datatypes" owner="iracooke" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+ </repositories>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Mar 18 20:50:51 2014 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+	<package name="protk" version="1.2.6">
+         <repository changeset_revision="1b21ba7de3e7" name="package_protk_1_2_6" owner="iracooke" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>