diff makeWindowsBed.xml @ 1:82aac94b06c3 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/makeWindowsBed.xml	Thu Jan 08 14:25:51 2015 -0500
@@ -0,0 +1,125 @@
+<tool id="bedtools_makewindowsbed" name="MakeWindowsBed" version="@WRAPPER_VERSION@.0">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <command>
+<![CDATA[
+        bedtools makewindows
+        #if $type.type_select == 'genome':
+            -g $type.genome
+        #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="genome">Genome File</option>
+            </param>
+            <when value="bed">
+                <param  name="input" format="bed,vcf,gff,gff3" type="data" label="BED/VCF/GFF file"/>
+            </when>
+            <when value="genome">
+                <expand macro="genome" />
+            </when>
+        </conditional>
+        <conditional name="action">
+            <param name="action_select" type="select" label="Work with">
+                <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"
+                    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">
+                    <param name="step_size_select" type="select"
+                        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>
+                    </param>
+                    <when value="yes">
+                        <param name="step_size" type="integer" value="100" label="Specify it" />
+                    </when>
+                    <when value="no" />
+                 </conditional>
+            </when>
+            <when value="number">
+                <param name="number" 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" />
+            </when>
+        </conditional>
+        <param name="sourcename" type="select" label="ID Naming Options">
+            <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>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="bed" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="type_select" value="genome" />
+            <param name="genome" value="mm9_chr1.len" ftype="tabular" />
+            <param name="action_select" value="windowsize" />
+            <param name="windowsize" value="1000000" />
+            <output name="output" file="makeWindowBed_result1.bed" ftype="bed" />
+        </test>
+        <test>
+            <param name="type_select" value="genome" />
+            <param name="genome" value="mm9_chr1.len" ftype="tabular" />
+            <param name="action_select" value="windowsize" />
+            <param name="windowsize" value="1000000" />
+            <param name="step_size_select" value="yes" />
+            <param name="step_size" value="50000" />
+            <output name="output" file="makeWindowBed_result2.bed" ftype="bed" />
+        </test>
+        <test>
+            <param name="type_select" value="genome" />
+            <param name="genome" value="mm9_chr1.len" ftype="tabular" />
+            <param name="action_select" value="number" />
+            <param name="number" value="100" />
+            <param name="step_size" value="10000" />
+            <output name="output" file="makeWindowBed_result3.bed" ftype="bed" />
+        </test>
+        <test>
+            <param name="type_select" value="bed" />
+            <param name="input" value="makeWindowBed1.bed" ftype="bed" />
+            <param name="action_select" value="number" />
+            <param name="number" value="15" />
+            <param name="step_size" value="100" />
+            <output name="output" file="makeWindowBed_result4.bed" ftype="bed" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**What it does**
+
+Makes adjacent or sliding windows across a genome or BED file.
+
+@REFERENCES@
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>