diff slopBed.xml @ 34:dde39ba9c031 draft

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

--- a/slopBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/slopBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,41 +1,39 @@
-<tool id="bedtools_slopbed" name="bedtools SlopBed" version="@WRAPPER_VERSION@">
+<tool id="bedtools_slopbed" name="bedtools SlopBed" version="@TOOL_VERSION@">
     <description>adjust the size of intervals</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        bedtools slop
-        $pct
-        $strand
-        -g @GENOME_FILE@
-        -i '$inputA'
-        #if $addition.addition_select == 'b':
-            -b $addition.b
-        #else:
-            -l $addition.l
-            -r $addition.r
-        #end if
-        $header
-        > '$output'
-]]>
-    </command>
+    <command><![CDATA[
+bedtools slop
+$pct
+$strand
+-g @GENOME_FILE@
+-i '$inputA'
+#if $addition.addition_select == 'b':
+    -b $addition.b
+#else:
+    -l $addition.l
+    -r $addition.r
+#end if
+$header
+> '$output'
+    ]]></command>
     <inputs>
-        <param format="@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
+        <param name="inputA" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
         <expand macro="input_conditional_genome_file" />
-        <param name="pct" type="boolean" checked="false" truevalue="-pct" falsevalue=""
+        <param argument="-pct" type="boolean" truevalue="-pct" falsevalue="" checked="false"
             label="Define -l and -r as a fraction of the feature’s length"
             help="E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp “upstream”" />
-        <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue=""
+        <param name="strand" argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false"
             label="Define -l and -r based on strand"
             help="If used, -l 500 for a negative-stranded feature, it will add 500 bp to the end coordinate" />
         <expand macro="addition" />
         <expand macro="print_header" />
     </inputs>
     <outputs>
-        <data format="bed" name="output"/>
+        <data name="output" format="bed" />
     </outputs>
     <tests>
         <test>
@@ -56,8 +54,7 @@
             <output name="output" file="slopBed_result2.bed" ftype="bed" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 bedtools slop will increase the size of each feature in a feature file by a user-defined number of bases. While something like this could be done with an awk '{OFS="\t" print $1,$2-&lt;slop>,$3+&lt;slop>}', bedtools slop will restrict the resizing to the size of the chromosome (i.e. no start &lt; 0 and no end > chromosome size).
@@ -67,8 +64,8 @@
 .. class:: warningmark
 
 In order to prevent the extension of intervals beyond chromosome boundaries, bedtools slop requires a genome file defining the length of each chromosome or contig.
+
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>