# HG changeset patch
# User iuc
# Date 1484999568 18000
# Node ID 1665205084735402fe5cf6773fda52abcef4054e
# Parent  d548c5551f014ac14d3d3f8ae8b75e932282110d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 5725fea947162618d77de7b8011d18b2f16c7094

diff -r d548c5551f01 -r 166520508473 bcftools_gtcheck.xml
--- a/bcftools_gtcheck.xml	Wed Jul 13 10:50:59 2016 -0400
+++ b/bcftools_gtcheck.xml	Sat Jan 21 06:52:48 2017 -0500
@@ -1,5 +1,5 @@
 <?xml version='1.0' encoding='utf-8'?>
-<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0">
+<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.1">
     <description>Check sample identity</description>
     <macros>
         <token name="@EXECUTABLE@">gtcheck</token>
@@ -15,16 +15,16 @@
 #set $section = $sec_default
 #set $genotypes_vcf = None
 #if $section.genotypes:
-  #if $section.genotypes.datatype.file_ext == 'vcf'
+  #if $section.genotypes.is_of_type('vcf')
     #set $genotypes_vcf = 'genotypes.vcf.gz'
     bgzip -c "$section.genotypes" > $genotypes_vcf &&
     bcftools index $genotypes_vcf &&
-  #elif $section.genotypes.datatype.file_ext == 'bcf'
+  #elif $section.genotypes.is_of_type('bcf')
     #set $genotypes_vcf = 'genotypes.bcf'
-    ln -s "$ection.genotypes" $genotypes_vcf && 
+    ln -s "$ection.genotypes" $genotypes_vcf &&
     #if $section.genotypes.metadata.bcf_index:
       ln -s $section.genotypes.metadata.bcf_index ${genotypes_vcf}.csi &&
-    #else 
+    #else
       bcftools index $genotypes_vcf &&
     #end if
   #end if
@@ -80,10 +80,10 @@
             <expand macro="macro_targets" />
         </section>
         <section name="sec_default" expanded="true" title="Default Options">
-            <param name="genotypes" type="data" format="vcf,bcf" label="Genotypes to compare against" optional="True" 
+            <param name="genotypes" type="data" format="vcf,bcf" label="Genotypes to compare against" optional="True"
                    help="(-g) Checks sample identity or wehn omitted a multi-sample cross-check is performed"/>
             <param name="target_sample" type="text" label="Target Sample" optional="True" help="Target sample in the -g file (used only for plotting)" />
-            <param name="GTs_only" type="integer" label="Gts Only" default="99" optional="True" help="Use GTs, ignore PLs, using &lt;int&gt; for unseen genotypes" />
+            <param name="GTs_only" type="integer" label="Gts Only" value="99" optional="True" help="Use GTs, ignore PLs, using &lt;int&gt; for unseen genotypes" />
             <param name="all_sites" type="boolean" truevalue="--all-sites" falsevalue="" label="All Sites" help="Output comparison for all sites" />
             <param name="homs_only" type="boolean" truevalue="--homs-only" falsevalue="" label="Homs Only" help="Homozygous genotypes only (useful for low coverage data)" />
             <param name="query_sample" type="text" label="Query Sample" optional="True" help="Query sample (by default the first sample is checked)" />
@@ -96,6 +96,7 @@
     <tests>
         <test>
             <param name="input_file" ftype="vcf" value="view.vcf" />
+            <param name="GTs_only" value="" />
             <output name="output_file">
                 <assert_contents>
                     <has_text_matching expression="SM\t10328.0+\t80.68\t12\tNA00002\t0"/>
diff -r d548c5551f01 -r 166520508473 macros.xml
--- a/macros.xml	Wed Jul 13 10:50:59 2016 -0400
+++ b/macros.xml	Sat Jan 21 06:52:48 2017 -0500
@@ -21,7 +21,7 @@
   <xml name="version_command">
     <version_command>bcftools 2&gt;&amp;1 | grep 'Version:'</version_command>
   </xml>
-  
+
   <xml name="citations">
     <citations>
       <citation type="doi">10.1093/bioinformatics/btp352</citation>
@@ -45,20 +45,20 @@
 <![CDATA[
 ## May need to symlink input if there is an associated
 #set $input_vcf = 'input.vcf.gz'
-#if $input_file.datatype.file_ext == 'vcf'
+#if $input_file.is_of_type('vcf')
   bgzip -c "$input_file" > $input_vcf &&
   bcftools index $input_vcf &&
-#elif $input_file.datatype.file_ext == 'vcf_bgzip'
+#elif $input_file.is_of_type('vcf_bgzip')
   ln -s "$input_file" $input_vcf
-#elif $input_file.datatype.file_ext == 'bcf'
+#elif $input_file.is_of_type('bcf')
   #set $input_vcf = 'input.bcf'
-  ln -s "$input_file" $input_vcf && 
+  ln -s "$input_file" $input_vcf &&
   #if $input_file.metadata.bcf_index:
     ln -s $input_file.metadata.bcf_index ${input_vcf}.csi &&
-  #else 
+  #else
     bcftools index $input_vcf &&
   #end if
-#elif $input_file.datatype.file_ext == 'bcf_bgzip'
+#elif $input_file.is_of_type('bcf_bgzip')
   ln -s "$input_file" $input_vcf
 #end if
 ]]>
@@ -77,21 +77,21 @@
 #set $vcfs_list_file = 'vcfs_list'
 #for (i,input_file) in enumerate($input_files):
   #set $input_vcf = 'input' + str($i) + '.vcf.gz'
-  #if $input_file.datatype.file_ext == 'vcf'
+  #if $input_file.is_of_type('vcf')
     bgzip -c "$input_file" > $input_vcf &&
     bcftools index $input_vcf &&
-  #elif $input_file.datatype.file_ext == 'vcf_bgz'
+  #elif $input_file.is_of_type('vcf_bgz')
     ln -s "$input_file" $input_vcf
-  #elif $input_file.datatype.file_ext == 'bcf'
+  #elif $input_file.is_of_type('bcf')
     #set $input_vcf = 'input' + str($i) + '.bcf.gz'
     ## bgzip -c "$input_file" > $input_vcf &&
     ln -s "$input_file" $input_vcf &&
     #if $input_file.metadata.bcf_index:
       ln -s $input_file.metadata.bcf_index ${input_vcf}.csi &&
-    #else 
+    #else
       bcftools index $input_vcf &&
     #end if
-  #elif $input_file.datatype.file_ext == 'bcfvcf_bgz'
+  #elif $input_file.is_of_type('bcfvcf_bgz')
     ln -s "$input_file" $input_vcf &&
   #end if
   echo '$input_vcf' >> $vcfs_list_file &&
@@ -225,7 +225,7 @@
   </token>
 
   <xml name="macro_apply_filters">
-    <param name="apply_filters" type="text" value="" label="Apply Filters" optional="true" 
+    <param name="apply_filters" type="text" value="" label="Apply Filters" optional="true"
            help="(-f --apply-filters) Skip sites where FILTER column does not contain any of the strings listed (e.g. &quot;PASS,.&quot;)">
       <validator type="regex" message="FILTER terms separated by commas">^([^ \t\n\r\f\v,]+(,[^ \t\n\r\f\v,]+)*)?$</validator>
     </param>
@@ -272,7 +272,7 @@
         </param>
         <when value="__none__"/>
         <when value="regions">
-            <param name="regions" type="text" value="" label="restrict to comma-separated list of regions" optional="true" 
+            <param name="regions" type="text" value="" label="restrict to comma-separated list of regions" optional="true"
                    help="Each region is specifed as: chr or chr:pos or chr:from-to">
                  <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator>
             </param>
@@ -299,7 +299,7 @@
   <token name="@PREPARE_TARGETS_FILE@">
 <![CDATA[
 #set $targets_path = None
-#if 'targets' in $section 
+#if 'targets' in $section
   #if $section.targets.targets_src == 'targets_file':
     #set $targets_path = 'targets_file.tab.gz'
     bgzip -c "$section.targets.targets_file" > $targets_path &&
@@ -331,7 +331,7 @@
         </param>
         <when value="__none__"/>
         <when value="targets">
-            <param name="targets" type="text" value="" label="Restrict to comma-separated list of targets" optional="true" 
+            <param name="targets" type="text" value="" label="Restrict to comma-separated list of targets" optional="true"
                    help="Each target is specifed as: chr or chr:pos or chr:from-to">
                  <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator>
             </param>
@@ -339,7 +339,6 @@
         </when>
         <when value="targets_file">
             <expand macro="macro_targets_file">
-               <optional>true</optional>
             </expand>
         </when>
     </conditional>
@@ -359,15 +358,15 @@
   </token>
 
   <xml name="macro_samples">
-      <param name="samples" type="text" value="" label="Samples" optional="true" 
+      <param name="samples" type="text" value="" label="Samples" optional="true"
              help="(-s) comma separated list of samples to annotate (or exclude with &quot;^&quot; prefix)">
           <validator type="regex" message="">^(\w+(,\w+)*)?$</validator>
       </param>
-      <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples" 
+      <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples"
              help="inverts the query/filtering applied by Samples" />
-      <param name="samples_file" type="data" format="tabular" label="Samples File" optional="True" 
+      <param name="samples_file" type="data" format="tabular" label="Samples File" optional="True"
              help="(-S) file of samples to include" />
-      <param name="invert_samples_file" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples File" 
+      <param name="invert_samples_file" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples File"
              help="inverts the query/filtering applied by Samples File" />
   </xml>
   <token name="@SAMPLES@">
@@ -417,7 +416,7 @@
   </token>
 
   <xml name="macro_columns">
-    <param name="columns" type="text" value="" label="Columns" optional="true" 
+    <param name="columns" type="text" value="" label="Columns" optional="true"
             help="list of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. See man page for details">
         <validator type="regex" message="COLUMN names  separated by commas">^([^,]+(,[^,]+)*)?$</validator>
     </param>
@@ -444,7 +443,7 @@
 Output Type
 -----------
 
-Output compressed BCF (b), or uncompressed VCF (v). 
+Output compressed BCF (b), or uncompressed VCF (v).
 Use the BCF option when piping between bcftools subcommands to speed up
 performance by removing unecessary compression/decompression
 and VCF<->BCF conversion.