Mercurial > repos > mvdbeek > bam_readtagger

diff allow_dovetailing.xml @ 0:a38447a59412 draft

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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
author mvdbeek
date Fri, 17 Feb 2017 10:54:47 -0500
parents
children f69131f584e8
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/allow_dovetailing.xml	Fri Feb 17 10:54:47 2017 -0500
@@ -0,0 +1,34 @@
+<tool id="allow_dovetailing" name="Allow dovetailing" version="0.1.8">
+    <description>modifies proper_pair flag in bam files</description>
+    <requirements>
+        <requirement type="package" version="0.1.8">readtagger</requirement>
+    </requirements>
+    <command detect_errors="aggressive"><![CDATA[
+        allow_dovetailing -i '$input' -o '$output'
+    ]]></command>
+    <inputs>
+        <param name="input" argument="--input_path" type="data" format="bam"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="bam"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="not_a_proper_pair.bam" ftype="bam"/>
+            <output name="output" file="proper_pair.bam" ftype="bam" lines_diff="2"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+::
+usage: allow_dovetailing [-h] -i INPUT_PATH -o OUTPUT_PATH
+
+Allow dovetailing.
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -i INPUT_PATH, --input_path INPUT_PATH
+                        Input alignment file to manipulate
+  -o OUTPUT_PATH, --output_path OUTPUT_PATH
+                        Output alignment file
+    ]]></help>
+</tool>