changeset 17:b28b80eb4b78

Deleted selected files
author mrvollger
date Fri, 12 Dec 2014 22:45:11 -0500
parents 08bbc7ba8f21
children d5427122db05
files tool_depensencies.xml trtr.xml
diffstat 2 files changed, 0 insertions(+), 49 deletions(-) [+]
line wrap: on
line diff
--- a/tool_depensencies.xml	Fri Dec 12 17:55:32 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-	<package name="trtr" version="1.0">
-		        <repository name="package_trtr_0_1" owner="mrvollger"/>
-	</package>
-</tool_dependency>
--- a/trtr.xml	Fri Dec 12 17:55:32 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,43 +0,0 @@
-<tool id="trtr" name="TRTR">
-	<requirements>
-		    <requirement type="package" version="1.0">trtr</requirement>
-	</requirements>
-
-	<description>Trim Reads of Tandem Repeat in a fastq file. </description>
-	
-	<command>
-		trtr $input $max_repeat $aggressive > $output
-	</command>
-	
-	<inputs>
-		<param format="fastq" name="input" type="data" label="Source file"/>
-		<param name="max_repeat" type="integer" value="10" label="Maximum repeat length" />
-		<param name="aggressive" type="integer" value="1" label="Aggressive? See description."/>
-	</inputs>
-	
-	<outputs>
-		<data format="fastq" name="output" />
-	</outputs>
-
-  <tests>
-    <test>
-      <param name="input" value="small.fastq"/>
-      <output name="output" file="smallTrimmed.fastq"/>
-    </test>
-    <test>
-      <param name="input" value="medium.fastq"/>
-      <output name="output" file="mediumTrimmed.fastq"/>
-    </test>
-  </tests>
-
-  <help>
-This tool removes tandem repeats from ends of unaligned sequencing reads (leaving one copy). This prevents reads that don't span the repeated region from overlapping and leading to innaccurate SNPs calls.
-
-The maximimum repeat length is adjustable (use 1 to trim only homopolymers).
-
-The "aggressive" option should not be touched in general. Setting to 0 will prevent the program from trimming to exactly 1 copy of the repeat, instead leaving between 1 and 2 copies.
-
-This could also be a useful first step before assembly. More testing needs to be done.
-  </help>
-
-</tool>