diff makeWindowsBed.xml @ 34:dde39ba9c031 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95

--- a/makeWindowsBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/makeWindowsBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,39 +1,37 @@
-<tool id="bedtools_makewindowsbed" name="bedtools MakeWindowsBed" version="@WRAPPER_VERSION@">
+<tool id="bedtools_makewindowsbed" name="bedtools MakeWindowsBed" version="@TOOL_VERSION@">
     <description>make interval windows across a genome</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        bedtools makewindows
-        #if $type.type_select == 'genome':
-            @GENOME_FILE_MAKEWINDOWS@
-        #else:
-            -b '$type.input'
-        #end if
-        #if $action.action_select == 'windowsize':
-            -w $action.windowsize
-            #if $action.step_size.step_size_select == 'yes':
-                -s $action.step_size.step_size
-            #end if
-        #else:
-            -n $action.number
-            -s $action.step_size
-        #end if
-        $sourcename
-        > '$output'
-]]>
-    </command>
+    <command><![CDATA[
+bedtools makewindows
+#if $type.type_select == 'genome':
+    @GENOME_FILE_MAKEWINDOWS@
+#else:
+    -b '$type.input'
+#end if
+#if $action.action_select == 'windowsize':
+    -w $action.windowsize
+    #if $action.step_size.step_size_select == 'yes':
+        -s $action.step_size.step_size
+    #end if
+#else:
+    -n $action.number
+    -s $action.step_size
+#end if
+$sourcename
+> '$output'
+    ]]></command>
     <inputs>
          <conditional name="type">
             <param name="type_select" type="select" label="Work with">
-                <option value="bed" selected="True">Bed File</option>
+                <option value="bed" selected="true">Bed File</option>
                 <option value="genome">Genome File</option>
             </param>
             <when value="bed">
-                <param  name="input" format="@STD_BEDTOOLS_INPUTS@" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
+                <param name="input" argument="-b" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
             </when>
             <when value="genome">
                 <expand macro="input_conditional_genome_file" />
@@ -41,11 +39,11 @@
         </conditional>
         <conditional name="action">
             <param name="action_select" type="select" label="Work with">
-                <option value="windowsize" selected="True">Set WindowSize</option>
+                <option value="windowsize" selected="true">Set WindowSize</option>
                 <option value="number">Give Number of Windows</option>
             </param>
             <when value="windowsize">
-                <param name="windowsize" type="integer" value="1"
+                <param name="windowsize" argument="-w" type="integer" value="1"
                     label="Divide each input interval (either a chromosome or a BED interval) to fixed-sized windows"
                     help="i.e. same number of nucleotide in each window" />
                  <conditional name="step_size">
@@ -53,23 +51,23 @@
                         label="Specify Step size? i.e. how many base pairs to step before creating a new window"
                         help="Used to create 'sliding' windows. Defaults to window size (non-sliding windows).">
                         <option value="yes">Yes</option>
-                        <option value="no" selected="True">No</option>
+                        <option value="no" selected="true">No</option>
                     </param>
                     <when value="yes">
-                        <param name="step_size" type="integer" value="100" label="Specify it" />
+                        <param name="step_size" argument="-s" type="integer" value="100" label="Specify it" />
                     </when>
                     <when value="no" />
                  </conditional>
             </when>
             <when value="number">
-                <param name="number" type="integer" value="1"
+                <param name="number" argument="-n" type="integer" value="1"
                     label="Divide each input interval (either a chromosome or a BED interval) to fixed number of windows"
-                    help="i.e. same number of windows, with varying window sizes" />
-                <param name="step_size" type="integer" value="100" label="Specify it" />
+                    help="I.e. same number of windows, with varying window sizes" />
+                <param name="step_size" argument="-s" type="integer" value="100" label="Specify it" />
             </when>
         </conditional>
         <param name="sourcename" type="select" label="ID Naming Options">
-            <option value="" selected="True">Default</option>
+            <option value="" selected="true">Default</option>
             <option value="-i src">use the source interval's name</option>
             <option value="-i winnum">use the window number as the ID (e.g. 1,2,3,4...)</option>
             <option value="-i srcwinnum">use the source interval's name with the window number.</option>
@@ -115,14 +113,12 @@
             <output name="output" file="makeWindowBed_result4.bed" ftype="bed" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 Makes adjacent or sliding windows across a genome or BED file.
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>