diff complement.xml @ 4:38c8bb402872 draft

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

--- a/complement.xml	Wed Nov 11 12:47:38 2015 -0500
+++ b/complement.xml	Thu Jun 22 18:40:33 2017 -0400
@@ -1,55 +1,50 @@
 <tool id="gops_complement_1" name="Complement" version="1.0.0">
-  <description>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_complement.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -l ${chromInfo} $allchroms</command>
-  <inputs>
-    <param format="interval" name="input1" type="data">
-      <label>Complement regions of</label>
-    </param>
-    <param name="allchroms" type="boolean" truevalue="--all" falsevalue="" label="Genome-wide complement">
-    </param>
-   </inputs>
-  <outputs>
-    <data format="input" name="output" metadata_source="input1" />
-  </outputs>
-  <code file="operation_filter.py"/>
-  <tests>
-    <test>
-      <param name="input1" value="1.bed" dbkey="hg17" />
-      <param name="allchroms" value="true" />
-      <output name="output" file="gops_complement_out.bed" />
-    </test>
-    <test>
-      <param name="input1" value="2_mod.bed" ftype="interval" dbkey="hg17" />
-      <param name="allchroms" value="true" />
-      <output name="output" file="gops_complement_out_diffCols.dat" />
-    </test>
-    <test>
-      <param name="input1" value="gops_bigint.interval" dbkey="hg17" />
-      <param name="allchroms" value="true" />
-      <output name="output" file="gops_complement_out2.bed" />
-    </test>
-  </tests>
-  <help>
-
+    <description>intervals of a dataset</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <code file="operation_filter.py"/>
+    <command><![CDATA[
+python '$__tool_directory__/gops_complement.py'
+'$input1'
+'$output'
+-1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol}
+-l '${chromInfo}'
+$allchroms
+    ]]></command>
+    <inputs>
+        <param name="input1" type="data" format="interval" label="Complement regions of" />
+        <param name="allchroms" type="boolean" truevalue="--all" falsevalue="" label="Genome-wide complement" />
+    </inputs>
+    <outputs>
+        <data name="output" format_source="input1" metadata_source="input1" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="1.bed" dbkey="hg17" />
+            <param name="allchroms" value="true" />
+            <output name="output" file="gops_complement_out.bed" />
+        </test>
+        <test>
+            <param name="input1" value="2_mod.bed" ftype="interval" dbkey="hg17" />
+            <param name="allchroms" value="true" />
+            <output name="output" file="gops_complement_out_diffCols.dat" />
+        </test>
+        <test>
+            <param name="input1" value="gops_bigint.interval" dbkey="hg17" />
+            <param name="allchroms" value="true" />
+            <output name="output" file="gops_complement_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.
 
 This operation complements the regions of a set of intervals.  Regions are returned that represent the empty space in the input interval.
 
------
-
-**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@
 
 **Syntax**
 
@@ -60,6 +55,5 @@
 **Example**
 
 .. image:: gops_complement.gif
-
-</help>
+    ]]></help>
 </tool>