diff basecoverage.xml @ 5:37652c34b3bf draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689

--- a/basecoverage.xml	Fri Dec 18 19:36:36 2015 -0500
+++ b/basecoverage.xml	Thu Jun 22 18:37:49 2017 -0400
@@ -1,49 +1,43 @@
 <tool id="gops_basecoverage_1" name="Base Coverage" version="1.0.0">
-  <description>of all intervals</description>
-  <command interpreter="python">gops_basecoverage.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol}</command>
-  <requirements>
-    <requirement type="package" version="0.7.1">bx-python</requirement>
-    <requirement type="package" version="1.0.0">galaxy-ops</requirement>
-  </requirements>
-  <inputs>
-    <param format="interval" name="input1" type="data">
-      <label>Compute coverage for</label>
-    </param>
-   </inputs>
-  <outputs>
-    <data format="txt" name="output" />
-  </outputs>
-  <code file="operation_filter.py"/>
-  <tests>
-    <test>
-      <param name="input1" value="1.bed" />
-      <output name="output" file="gops_basecoverage_out.txt" />     
-    </test>
-    <test>
-      <param name="input1" value="gops_bigint.interval" />
-      <output name="output" file="gops_basecoverage_out2.txt" />     
-    </test>
-  </tests>
-  <help>
-
+    <description>of all intervals</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <code file="operation_filter.py"/>
+    <command><![CDATA[
+python '$__tool_directory__/gops_basecoverage.py'
+'$input1'
+'$output'
+-1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol}
+    ]]></command>
+    <inputs>
+        <param name="input1" type="data" format="interval" label="Compute coverage for" />
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="1.bed" />
+            <output name="output" file="gops_basecoverage_out.txt" />
+        </test>
+        <test>
+            <param name="input1" value="gops_bigint.interval" />
+            <output name="output" file="gops_basecoverage_out2.txt" />
+        </test>
+    </tests>
+    <help><![CDATA[
 .. class:: infomark
 
 **TIP:** If your dataset does not appear in the pulldown menu, it means that it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns.
 
 This operation counts the total bases covered by a set of intervals.  Bases that are covered by more than one interval are **not** counted more than once towards the total.
 
------
-
-**Screencasts!**
-
-See Galaxy Interval Operation Screencasts_ (right click to open this link in another window).
-
-.. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations
+@SCREENCASTS@
 
 **Example**
 
 .. image:: gops_baseCoverage.gif
-
-
-</help>
+    ]]></help>
 </tool>