changeset 12:7b3aaff0d78c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5664837d1ea4575f87a9e963f5d4e18a82d51d5

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bedToIgv.xml	Fri Oct 28 12:54:40 2016 -0400
@@ -0,0 +1,66 @@
+<tool id="bedtools_bedtoigv" name="BED to IGV" version="@WRAPPER_VERSION@.0">
+    <description>create batch script for taking IGV screenshots</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <command>
+<![CDATA[
+        bedToIgv
+        -i '$input'
+        #if $sort:
+            -sort $sort
+        #end if
+        $clps
+        $name
+        -slop $slop
+        -img $img
+        > '$output'
+]]>
+    </command>
+    <inputs>
+        <param format="bed,gff,gff3,vcf" name="input" type="data" label="Create IGV batch script the following BED file"/>
+        <param name="sort" type="select" label="Sort BAM file by" help="The type of BAM sorting you would like to apply to each image.">
+            <option value="">No sorting at all (default)</option>
+            <option value="base">base</option>
+            <option value="position">position</option>
+            <option value="strand">strand</option>
+            <option value="quality">quality</option>
+            <option value="sample">sample</option>
+            <option value="readGroup">readGroup</option>
+        </param>
+        <param name="clps" type="boolean" truevalue="-clps" falsevalue="" label="Collapse the aligned reads prior to taking a snapshot?"/>
+        <param name="name" type="boolean" truevalue="-name" falsevalue="" label="Use the name field (column 4) for each image's filename." help="Default is to use chr:start-pos."/>
+        <param name="slop" type="integer" min="0" value="0" label="Number of flanking base pairs on the left and right of the image."/>
+        <param name="img" type="select" label="Select the type of image to be created.">
+            <option value="png">png</option>
+            <option value="eps">eps</option>
+            <option value="svg">svg</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data format="txt" name="output" metadata_source="input" label="BED to IGV on ${input.name}"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="bed12.bed" ftype="bed" />
+            <output name="output" file="igv_bed_script.txt" ftype="txt" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**What it does**
+
+Creates a batch script to create IGV images at each interval defined in a BED/GFF/VCF file.
+
+**Notes**
+
+(1)  The resulting script is meant to be run from within IGV.
+(2)  It is assumed that prior to running the script, you've loaded the proper genome and tracks.
+
+@REFERENCES@
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/igv_bed_script.txt	Fri Oct 28 12:54:40 2016 -0400
@@ -0,0 +1,7 @@
+snapshotDirectory ./
+goto chr1:14756-15038
+snapshot chr1_14756_15038.png
+goto chr1:14969-15836
+snapshot chr1_14969_15836.png
+goto chr1:15905-16677
+snapshot chr1_15905_16677.png