diff bcftools_annotate.xml @ 3:12c14f97429b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e

--- a/bcftools_annotate.xml	Mon Oct 03 12:16:18 2016 -0400
+++ b/bcftools_annotate.xml	Tue Jan 31 12:41:19 2017 -0500
@@ -13,12 +13,12 @@
 #set $annotation_file = None
 #set $annotation_hdr = None
 #set $section = $sec_annofile
-#if $section.annofile.anno_fmt == 'vcf': 
+#if $section.annofile.anno_fmt == 'vcf':
   #set $annotation_file = 'annotations.vcf.gz'
   bgzip -c "$section.annofile.annotations" > $annotation_file &&
   bcftools index $annotation_file &&
 #elif $section.annofile.anno_fmt == 'tab':
-  #if $section.annofile.annotations.ext == 'bed'
+  #if $section.annofile.annotations.is_of_type('bed')
     #set $annotation_file = 'annotations.bed.gz'
     bgzip -c "$section.annofile.annotations" > $annotation_file &&
     tabix -s 1 -b 2 -e 3 $annotation_file &&
@@ -87,7 +87,7 @@
         <section name="sec_annofile" expanded="false" title="Add Annotations">
             <expand macro="macro_columns" />
             <conditional name="annofile">
-                <param name="anno_fmt" type="select" label="Annotations File"> 
+                <param name="anno_fmt" type="select" label="Annotations File">
                     <option value="none">None</option>
                     <option value="vcf">From a VCF/BCF file</option>
                     <option value="tab">From a BED or tab-delimited file</option>
@@ -99,9 +99,9 @@
                 <when value="tab">
                     <param name="annotations" type="data" format="tabular,bed" label="Annotations">
                         <help><![CDATA[
-                        BED, or a tab-delimited file with mandatory columns CHROM, POS (or, alternatively, FROM and TO), 
-                        optional columns REF and ALT, and arbitrary number of annotation columns. 
-                        Note that in case of tab-delimited file, the coordinates POS, FROM and TO are one-based and inclusive. 
+                        BED, or a tab-delimited file with mandatory columns CHROM, POS (or, alternatively, FROM and TO),
+                        optional columns REF and ALT, and arbitrary number of annotation columns.
+                        Note that in case of tab-delimited file, the coordinates POS, FROM and TO are one-based and inclusive.
                         ]]></help>
                     </param>
                     <param name="header_file" type="data" format="txt" label="Header Lines File" optional="True" help="lines which should be appended to the VCF header" />
@@ -114,12 +114,12 @@
                     </param>
                 </when>
             </conditional>
-            <param name="mark_sites" type="text" value="" label="Mark Sites TAG" 
+            <param name="mark_sites" type="text" value="" label="Mark Sites TAG"
                 help="add INFO/TAG flag to sites which are (&quot;+&quot;) or are not (&quot;-&quot;) listed in the annotations file" />
             <param name="set_id" type="text" value="" optional="true" label="Set Id">
                 <help>Assign ID on the fly using the given format.
-                By default all existing IDs are replaced. 
-                If the format string is preceded by "+", only missing IDs will be set. 
+                By default all existing IDs are replaced.
+                If the format string is preceded by "+", only missing IDs will be set.
                 For example: '%CHROM\_%POS\_%REF\_%FIRST_ALT'
                 </help>
                 <sanitizer sanitize="False"/>
@@ -127,17 +127,17 @@
             </param>
         </section>
         <section name="sec_annotate" expanded="false" title="Change Annotations">
-            <param name="remove" type="text" value="" label="Remove annotations" optional="true"> 
+            <param name="remove" type="text" value="" label="Remove annotations" optional="true">
                 <help><![CDATA[
-                 List of annotations to remove. 
-                 Use "FILTER" to remove all filters or "FILTER/SomeFilter" to remove a specific filter. 
-                 Similarly, "INFO" can be used to remove all INFO tags and "FORMAT" to remove all FORMAT tags except GT. 
-                 To remove all INFO tags except "FOO" and "BAR", use "^INFO/FOO,INFO/BAR" (and similarly for FORMAT and FILTER). 
-                 "INFO" can be abbreviated to "INF" and "FORMAT" to "FMT". 
+                 List of annotations to remove.
+                 Use "FILTER" to remove all filters or "FILTER/SomeFilter" to remove a specific filter.
+                 Similarly, "INFO" can be used to remove all INFO tags and "FORMAT" to remove all FORMAT tags except GT.
+                 To remove all INFO tags except "FOO" and "BAR", use "^INFO/FOO,INFO/BAR" (and similarly for FORMAT and FILTER).
+                 "INFO" can be abbreviated to "INF" and "FORMAT" to "FMT".
                 ]]></help>
                 <validator type="regex" message="">^(\^?[A-Z]+(/\w+)?(,\^?[A-Z]+(/\w+)?)*)?$</validator>
             </param>
-            <param name="rename_chrs" type="data" format="tabular" label="Rename CHROM" optional="True" 
+            <param name="rename_chrs" type="data" format="tabular" label="Rename CHROM" optional="True"
                    help="rename chromosomes according to the map in file, with old_name new_name pairs separated by whitespaces, each on a separate line." />
         </section>
         <section name="sec_restrict" expanded="false" title="Restrict to">