diff subtract.xml @ 5:0145969324c4 draft

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

--- a/subtract.xml	Thu Feb 11 12:11:59 2016 -0500
+++ b/subtract.xml	Thu Jun 22 18:53:03 2017 -0400
@@ -1,110 +1,95 @@
 <tool id="gops_subtract_1" name="Subtract" version="1.0.0">
-  <description>the intervals of two datasets</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_subtract.py 
-      $input1 $input2 $output
-
-      #if isinstance( $input1.datatype, $__app__.datatypes_registry.get_datatype_by_extension('gff').__class__):
-        -1 1,4,5,7 --gff1
-      #else:
-        -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol}
-      #end if
+    <description>the intervals of two datasets</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <code file="operation_filter.py"/>
+    <command><![CDATA[
+python '$__tool_directory__/gops_subtract.py'
+'$input1'
+'$input2'
+'$output'
 
-      #if isinstance( $input2.datatype, $__app__.datatypes_registry.get_datatype_by_extension('gff').__class__):
-        -2 1,4,5,7 --gff2
-      #else:
-          -2 ${input2.metadata.chromCol},${input2.metadata.startCol},${input2.metadata.endCol},${input2.metadata.strandCol} 
-      #end if
+#if $input1.is_of_type('gff')
+    -1 1,4,5,7 --gff1
+#else:
+    -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol}
+#end if
 
-      -m $min $returntype
-  </command>
-  <inputs>
-    <param format="interval,gff" name="input2" type="data" help="Second dataset">
-      <label>Subtract</label>
-    </param>
-
-    <param format="interval,gff" name="input1" type="data" help="First dataset">
-      <label>from</label>
-    </param>
+#if $input2.is_of_type('gff')
+    -2 1,4,5,7 --gff2
+#else:
+    -2 ${input2.metadata.chromCol},${input2.metadata.startCol},${input2.metadata.endCol},${input2.metadata.strandCol}
+#end if
 
-    <param name="returntype" type="select" label="Return" help="of the first dataset (see figure below)">
-      <option value="">Intervals with no overlap</option>
-      <option value="-p">Non-overlapping pieces of intervals</option>
-    </param>
-    
-    <param name="min" type="integer" value="1" min="1" help="(bp)">
-      <label>where minimal overlap is</label>
-    </param>
-   </inputs>
-  <outputs>
-    <data format="input" name="output" metadata_source="input1"/>
-  </outputs>
-  <code file="operation_filter.py"/>
-  <trackster_conf/>
-  <tests>
-    <test>
-      <param name="input1" value="1.bed" />
-      <param name="input2" value="2.bed" />
-      <param name="min" value="1" />
-      <param name="returntype" value="" />
-      <output name="output" file="gops-subtract.dat" />
-    </test>
-    <test>
-      <param name="input1" value="1.bed" />
-      <param name="input2" value="2_mod.bed" ftype="interval"/>
-      <param name="min" value="1" />
-      <param name="returntype" value="" />
-      <output name="output" file="gops_subtract_diffCols.dat" />
-    </test>
-    <test>
-      <param name="input1" value="gops_subtract_bigint.bed" />
-      <param name="input2" value="2.bed" />
-      <param name="min" value="1" />
-      <param name="returntype" value="" />
-      <output name="output" file="gops-subtract.dat" />
-    </test>
-    <test>
-      <param name="input1" value="1.bed" />
-      <param name="input2" value="2.bed" />
-      <param name="min" value="10" />
-      <param name="returntype" value="Non-overlapping pieces of intervals" />
-      <output name="output" file="gops-subtract-p.dat" />     
-    </test>
-    <!-- Subtract two GFF files. -->
-    <test>
-        <param name="input1" value="gops_subtract_in1.gff" />
-        <param name="input2" value="gops_subtract_in2.gff" />
-        <param name="min" value="1" />
-        <param name="returntype" value="" />
-        <output name="output" file="gops_subtract_out1.gff" />
-    </test>
-    <!-- Subtract BED file from GFF file. -->
-    <test>
-        <param name="input1" value="gops_subtract_in1.gff" />
-        <param name="input2" value="gops_subtract_in2.bed" />
-        <param name="min" value="1" />
-        <param name="returntype" value="" />
-        <output name="output" file="gops_subtract_out1.gff" />
-    </test>
-  </tests>
-  <help>
-
+-m $min
+$returntype
+    ]]></command>
+    <inputs>
+        <param name="input2" type="data" format="interval,gff" label="Subtract" help="Second dataset" />
+        <param name="input1" type="data" format="interval,gff" label="from" help="First dataset" />
+        <param name="returntype" type="select" label="Return" help="of the first dataset (see figure below)">
+            <option value="">Intervals with no overlap</option>
+            <option value="-p">Non-overlapping pieces of intervals</option>
+        </param>
+        <param name="min" type="integer" value="1" min="1" label="where minimal overlap is" help="(bp)" />
+    </inputs>
+    <outputs>
+        <data name="output" format_source="input1" metadata_source="input1"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="1.bed" />
+            <param name="input2" value="2.bed" />
+            <param name="min" value="1" />
+            <param name="returntype" value="" />
+            <output name="output" file="gops-subtract.dat" />
+        </test>
+        <test>
+            <param name="input1" value="1.bed" />
+            <param name="input2" value="2_mod.bed" ftype="interval"/>
+            <param name="min" value="1" />
+            <param name="returntype" value="" />
+            <output name="output" file="gops_subtract_diffCols.dat" />
+        </test>
+        <test>
+            <param name="input1" value="gops_subtract_bigint.bed" />
+            <param name="input2" value="2.bed" />
+            <param name="min" value="1" />
+            <param name="returntype" value="" />
+            <output name="output" file="gops-subtract.dat" />
+        </test>
+        <test>
+            <param name="input1" value="1.bed" />
+            <param name="input2" value="2.bed" />
+            <param name="min" value="10" />
+            <param name="returntype" value="Non-overlapping pieces of intervals" />
+            <output name="output" file="gops-subtract-p.dat" />
+        </test>
+        <!-- Subtract two GFF files. -->
+        <test>
+            <param name="input1" value="gops_subtract_in1.gff" />
+            <param name="input2" value="gops_subtract_in2.gff" />
+            <param name="min" value="1" />
+            <param name="returntype" value="" />
+            <output name="output" file="gops_subtract_out1.gff" />
+        </test>
+        <!-- Subtract BED file from GFF file. -->
+        <test>
+            <param name="input1" value="gops_subtract_in1.gff" />
+            <param name="input2" value="gops_subtract_in2.bed" />
+            <param name="min" value="1" />
+            <param name="returntype" value="" />
+            <output name="output" file="gops_subtract_out1.gff" />
+        </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@
 
 **Syntax**
 
@@ -123,6 +108,5 @@
 Non-overlapping pieces of intervals:
 
 .. image:: gops_subtractOverlappingPieces.gif
-
-</help>
+    ]]></help>
 </tool>