diff bedToIgv.xml @ 34:dde39ba9c031 draft

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

--- a/bedToIgv.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/bedToIgv.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,26 +1,24 @@
-<tool id="bedtools_bedtoigv" name="bedtools BED to IGV" version="@WRAPPER_VERSION@">
+<tool id="bedtools_bedtoigv" name="bedtools BED to IGV" version="@TOOL_VERSION@">
     <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>
+    <command><![CDATA[
+bedToIgv
+-i '$input'
+#if $sort:
+    -sort $sort
+#end if
+$clps
+$name
+-slop $slop
+-img $img
+> '$output'
+    ]]></command>
     <inputs>
-        <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="Create IGV batch script for this @STD_BEDTOOLS_INPUT_LABEL@ file"/>
+        <param name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="Create IGV batch script for this @STD_BEDTOOLS_INPUT_LABEL@ 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>
@@ -30,17 +28,17 @@
             <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 argument="-clps" type="boolean" truevalue="-clps" falsevalue="" label="Collapse the aligned reads prior to taking a snapshot?"/>
+        <param argument="-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 argument="-slop" type="integer" min="0" value="0" label="Number of flanking base pairs on the left and right of the image."/>
+        <param argument="-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}"/>
+        <data name="output" format="txt" metadata_source="input" label="BED to IGV on ${input.name}"/>
     </outputs>
     <tests>
         <test>
@@ -48,8 +46,7 @@
             <output name="output" file="igv_bed_script.txt" ftype="txt" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 Creates a batch script to create IGV images at each interval defined in a @STD_BEDTOOLS_INPUT_LABEL@ file.
@@ -60,7 +57,6 @@
 (2)  It is assumed that prior to running the script, you've loaded the proper genome and tracks.
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>