diff merge.xml @ 4:381cd27bf67a draft

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

--- a/merge.xml	Wed Nov 11 12:49:11 2015 -0500
+++ b/merge.xml	Thu Jun 22 18:52:49 2017 -0400
@@ -1,62 +1,54 @@
 <tool id="gops_merge_1" name="Merge" version="1.0.0">
-  <description>the overlapping intervals of a dataset</description>
-  <requirements>
-    <requirement type="package" version="0.7.1">bx-python</requirement>
-    <requirement type="package" version="1.0.0">galaxy-ops</requirement>
-  </requirements>
-  <command interpreter="python">gops_merge.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} $returntype</command>
-  <inputs>
-    <param format="interval" name="input1" type="data">
-      <label>Merge overlaping regions of</label>
-    </param>
-    <param name="returntype" type="boolean" truevalue="-3" falsevalue="">
-      <label>Output 3 column bed</label>
-    </param>
-   </inputs>
-  <outputs>
-    <data format="input" name="output" metadata_source="input1" />
-  </outputs>
-  <code file="operation_filter.py">
-    <hook exec_after_process="exec_after_merge" />
-  </code>
-  <tests>
-    <test>
-      <param name="input1" value="1.bed" />
-      <output name="output" file="gops-merge.dat" />
-      <param name="returntype" value="true" />
-    </test>
-    <test>
-      <param name="input1" value="2_mod.bed" ftype="interval"/>
-      <output name="output" file="gops_merge_diffCols.dat" />
-      <param name="returntype" value="true" />
-    </test>
-    <test>
-      <param name="input1" value="gops_bigint.interval" />
-      <output name="output" file="gops_merge_out2.bed" />
-      <param name="returntype" value="true" />
-    </test>
-  </tests>
-  <help>
-
+    <description>the overlapping intervals of a dataset</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <code file="operation_filter.py">
+        <hook exec_after_process="exec_after_merge" />
+    </code>
+    <command><![CDATA[
+python '$__tool_directory__/gops_merge.py'
+'$input1'
+'$output'
+-1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol}
+$returntype
+    ]]></command>
+    <inputs>
+        <param name="input1" type="data" format="interval" label="Merge overlapping regions of" />
+        <param name="returntype" type="boolean" truevalue="-3" falsevalue="" label="Output 3 column bed" />
+    </inputs>
+    <outputs>
+        <data name="output" format_source="input1" metadata_source="input1" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="1.bed" />
+            <param name="returntype" value="true" />
+            <output name="output" file="gops-merge.dat" />
+        </test>
+        <test>
+            <param name="input1" value="2_mod.bed" ftype="interval"/>
+            <param name="returntype" value="true" />
+            <output name="output" file="gops_merge_diffCols.dat" />
+        </test>
+        <test>
+            <param name="input1" value="gops_bigint.interval" />
+            <param name="returntype" value="true" />
+            <output name="output" file="gops_merge_out2.bed" />
+        </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.
 
------
-
-**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@
 
 This operation merges all overlapping intervals into single intervals.
 
 **Example**
 
 .. image:: gops_merge.gif
-
-</help>
-</tool>
\ No newline at end of file
+    ]]></help>
+</tool>