Mercurial > repos > iracooke > make_protein_decoys

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README	Fri Jun 13 18:02:27 2014 -0400
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+Requirements:
+This package uses protk which must be installed separately.
+
+For instructions please see: https://github.com/iracooke/protk/#galaxy-integration
\ No newline at end of file
--- a/README.md	Tue Mar 18 20:50:51 2014 -0400
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-# Make decoys from a protein database
-
-
--- a/make_decoy.xml	Tue Mar 18 20:50:51 2014 -0400
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@@ -1,46 +0,0 @@
-<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>
--- a/repository_dependencies.xml	Tue Mar 18 20:50:51 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-<?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>
--- a/tool_dependencies.xml	Tue Mar 18 20:50:51 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?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>