# HG changeset patch
# User iuc
# Date 1550782336 18000
# Node ID 4422d017fe79fda6a67ed86c5833096d895f3153
# Parent  410cdd7cf2bc5609f904ee27ee0dab8243de2b21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69

diff -r 410cdd7cf2bc -r 4422d017fe79 bcftools_mpileup.xml
--- a/bcftools_mpileup.xml	Tue Dec 12 13:53:56 2017 -0500
+++ b/bcftools_mpileup.xml	Thu Feb 21 15:52:16 2019 -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="@TOOL_VERSION@">
     <description>Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files</description>
     <macros>
         <token name="@EXECUTABLE@">mpileup</token>
@@ -16,7 +16,7 @@
             <option value="256">The alignment or this read is not primary</option>
             <option value="512">The read fails platform/vendor quality checks</option>
             <option value="1024">The read is a PCR or optical duplicate</option>
-         </xml>
+        </xml>
     </macros>
     <expand macro="requirements">
         <expand macro="samtools_requirement"/>
@@ -37,9 +37,9 @@
     #silent $bam_list.append($input_name)
     ln -s '${input.input_bam}' ${input_name} &&
     #if $input.input_bam.ext == 'bam':
-      ln -s '${input.input_bam.metadata.bam_index}' ${input_name}.${idx_ext} &&
+        ln -s '${input.input_bam.metadata.bam_index}' ${input_name}.${idx_ext} &&
     #else:
-      ln -s '${input.input_bam.metadata.cram_index}' ${input_name}.${idx_ext} &&
+        ln -s '${input.input_bam.metadata.cram_index}' ${input_name}.${idx_ext} &&
     #end if
 #else:
     #for $bam_count, $input_bam in enumerate( $input.input_bams ):
@@ -59,11 +59,11 @@
 
 #set $input_fa_ref = None
 #if $reference_source.reference_source_selector == "history":
-  #set $input_fa_ref = 'ref.fa'
-  ln -s '${reference_source.ref_file}' $input_fa_ref &&
-  samtools faidx $input_fa_ref &&
+    #set $input_fa_ref = 'ref.fa'
+    ln -s '${reference_source.ref_file}' $input_fa_ref &&
+    samtools faidx $input_fa_ref &&
 #elif $reference_source.reference_source_selector == "cached":
-  #set $input_fa_ref = $reference_source.ref_file.fields.path
+    #set $input_fa_ref = $reference_source.ref_file.fields.path
 #end if
 
 #set $section = $sec_restrict
@@ -81,53 +81,53 @@
 ## Indel Calling section
 #set $section = $sec_indel
 #if $section.perform_indel_calling.perform_indel_calling_selector == 'do_not_perform_indel_calling':
-  --skip-indels
+    --skip-indels
 #elif $section.perform_indel_calling.perform_indel_calling_selector == 'perform_indel_calling':
-  -o "${section.perform_indel_calling.gap_open_sequencing_error_probability}"
-  -e "${section.perform_indel_calling.gap_extension_sequencing_error_probability}"
-  -h "${section.perform_indel_calling.coefficient_for_modeling_homopolymer_errors}"
-  -L "${section.perform_indel_calling.skip_indel_calling_above_sample_depth}"
-  -m "${section.perform_indel_calling.minimum_gapped_reads_for_indel_candidates}"
-  --open-prob "${section.perform_indel_calling.open_seq_error_probability}"
-  -F "${section.perform_indel_calling.minimum_gapped_read_fraction}"
-  ${section.perform_indel_calling.gapped_read_per_sample}
-  #if len( $section.perform_indel_calling.platform_list_repeat ):
-    -P "${ ",".join( [ str( platform.platform_entry ) for platform in $section.perform_indel_calling.platform_list_repeat ] ) }"
-  #end if
+    -o "${section.perform_indel_calling.gap_open_sequencing_error_probability}"
+    -e "${section.perform_indel_calling.gap_extension_sequencing_error_probability}"
+    -h "${section.perform_indel_calling.coefficient_for_modeling_homopolymer_errors}"
+    -L "${section.perform_indel_calling.skip_indel_calling_above_sample_depth}"
+    -m "${section.perform_indel_calling.minimum_gapped_reads_for_indel_candidates}"
+    --open-prob "${section.perform_indel_calling.open_seq_error_probability}"
+    -F "${section.perform_indel_calling.minimum_gapped_read_fraction}"
+    ${section.perform_indel_calling.gapped_read_per_sample}
+    #if len( $section.perform_indel_calling.platform_list_repeat ):
+        -P "${ ",".join( [ str( platform.platform_entry ) for platform in $section.perform_indel_calling.platform_list_repeat ] ) }"
+    #end if
 #end if
 
 ## Filter section
 #set $section = $sec_filtering
 #if str( $section.filter_by_flags.filter_flags ) == "filter":
-  #if $section.filter_by_flags.require_flags:
-    --rf ${sum([int(flag) for flag in str($section.filter_by_flags.require_flags).split(',')])}
-  #end if
-  #if $section.filter_by_flags.exclude_flags:
-    --ff ${sum([int(flag) for flag in str($section.filter_by_flags.exclude_flags).split(',')])}
-  #end if
+    #if $section.filter_by_flags.require_flags:
+        --rf ${sum([int(flag) for flag in str($section.filter_by_flags.require_flags).split(',')])}
+    #end if
+    #if $section.filter_by_flags.exclude_flags:
+        --ff ${sum([int(flag) for flag in str($section.filter_by_flags.exclude_flags).split(',')])}
+    #end if
 #end if
 -d "${section.max_reads_per_bam}"
 ${section.skip_anomalous_read_pairs}
 #if str( $section.quality.quality_settings ) == "adjust":
-  $section.quality.baq
-  -q "${section.quality.minimum_mapping_quality}"
-  -Q "${section.quality.minimum_base_quality}"
-  -C "${section.quality.coefficient_for_downgrading}"
+    $section.quality.baq
+    -q "${section.quality.minimum_mapping_quality}"
+    -Q "${section.quality.minimum_base_quality}"
+    -C "${section.quality.coefficient_for_downgrading}"
 #end if
 #if str( $section.read_groups.read_groups_selector ) == "ignore_rg":
-  --ignore-RG
+    --ignore-RG
 #elif str( $section.read_groups.read_groups_selector ) == "paste":
-  -G "${section.read_groups.rg_action}${read_groups_file}"
+    -G "${section.read_groups.rg_action}${read_groups_file}"
 #elif str( $section.read_groups.read_groups_selector ) == "history"
-  -G "${section.read_groups.rg_action}${section.read_groups.read_groups}"
+    -G "${section.read_groups.rg_action}${section.read_groups.read_groups}"
 #end if
 
 #set $section = $sec_output_options
 #if $section.output_tags:
- --annotate "$section.output_tags"
+    --annotate "$section.output_tags"
 #end if
 #if $section.gvcf:
- --gvcf "$section.gvcf"
+    --gvcf "$section.gvcf"
 #end if
 
 ## Subset section
@@ -147,18 +147,17 @@
 #echo ' '.join($bam_list)#
 > '$output_file'
 #if str( $sec_filtering.read_groups.read_groups_selector ) == "paste":
-&& echo 'read-groups:'
-&& cat ${read_groups_file}
+    && echo 'read-groups:'
+    && cat ${read_groups_file}
 #end if
-]]>
-    </command>
+    ]]></command>
     <configfiles>
         <configfile name="read_groups_file">
 <![CDATA[#slurp
 #set pasted_data = ''
 #set $section = $sec_filtering
 #if str( $section.read_groups.read_groups_selector ) == "paste":
-  #set pasted_data = '\t'.join( str( $section.read_groups.group_paste).split() )
+    #set pasted_data = '\t'.join( str( $section.read_groups.group_paste).split() )
 #end if
 #slurp
 ${pasted_data}
@@ -444,7 +443,6 @@
 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
 
 @BCFTOOLS_WIKI@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>
diff -r 410cdd7cf2bc -r 4422d017fe79 macros.xml
--- a/macros.xml	Tue Dec 12 13:53:56 2017 -0500
+++ b/macros.xml	Thu Feb 21 15:52:16 2019 -0500
@@ -1,5 +1,5 @@
 <macros>
-  <token name="@VERSION@">1.4.0</token>
+  <token name="@TOOL_VERSION@">1.9</token>
   <xml name="stdio">
     <stdio>
       <exit_code range="1:" />
@@ -10,13 +10,13 @@
   </xml>
   <xml name="requirements">
     <requirements>
-      <requirement type="package" version="1.4">bcftools</requirement>
-      <requirement type="package" version="1.4">htslib</requirement>
+      <requirement type="package" version="@TOOL_VERSION@">bcftools</requirement>
+      <requirement type="package" version="1.9">htslib</requirement>
       <yield />
     </requirements>
   </xml>
   <xml name="samtools_requirement">
-      <requirement type="package" version="1.3.1">samtools</requirement>
+      <requirement type="package" version="1.9">samtools</requirement>
   </xml>
   <xml name="version_command">
     <version_command>bcftools 2&gt;&amp;1 | grep 'Version:'</version_command>
@@ -39,7 +39,7 @@
 ]]>
   </token>
   <xml name="macro_input">
-    <param name="input_file" type="data" format="vcf,vcf_bgzip,bcf,bcf_bgzip" label="VCF/BCF Data" />
+    <param name="input_file" type="data" format="vcf,vcf_bgzip,bcf" label="VCF/BCF Data" />
   </xml>
   <token name="@PREPARE_INPUT_FILE@">
 <![CDATA[
@@ -50,6 +50,11 @@
   bcftools index $input_vcf &&
 #elif $input_file.is_of_type('vcf_bgzip')
   ln -s '$input_file' $input_vcf &&
+  #if $input_file.metadata.tabix_index:
+    ln -s '${input_file.metadata.tabix_index}' ${input_vcf}.tbi &&
+  #else
+    bcftools index $input_vcf &&
+  #end if
 #elif $input_file.is_of_type('bcf')
   #set $input_vcf = 'input.bcf'
   ln -s '$input_file' $input_vcf &&
@@ -58,8 +63,6 @@
   #else
     bcftools index $input_vcf &&
   #end if
-#elif $input_file.is_of_type('bcf_bgzip')
-  ln -s '$input_file' $input_vcf &&
 #end if
 ]]>
   </token>
@@ -68,7 +71,7 @@
   </token>
 
   <xml name="macro_inputs">
-    <param name="input_files" type="data" format="vcf,bcf" label="Other VCF/BCF Datasets" multiple="True" />
+    <param name="input_files" type="data" format="vcf,vcf_bgzip,bcf" label="Other VCF/BCF Datasets" multiple="True" />
   </xml>
   <token name="@PREPARE_INPUT_FILES@">
 <![CDATA[
@@ -80,8 +83,13 @@
   #if $input_file.is_of_type('vcf')
     bgzip -c '$input_file' > $input_vcf &&
     bcftools index $input_vcf &&
-  #elif $input_file.is_of_type('vcf_bgz')
-    ln -s '$input_file' $input_vcf
+  #elif $input_file.is_of_type('vcf_bgzip')
+    ln -s '$input_file' $input_vcf &&
+    #if $input_file.metadata.tabix_index:
+      ln -s '${input_file.metadata.tabix_index}' ${input_vcf}.tbi &&
+    #else
+      bcftools index $input_vcf &&
+    #end if
   #elif $input_file.is_of_type('bcf')
     #set $input_vcf = 'input' + str($i) + '.bcf.gz'
     ln -s '$input_file' $input_vcf &&
@@ -90,8 +98,6 @@
     #else
       bcftools index $input_vcf &&
     #end if
-  #elif $input_file.is_of_type('bcfvcf_bgz')
-    ln -s '$input_file' $input_vcf &&
   #end if
   echo '$input_vcf' >> $vcfs_list_file &&
   $input_vcfs.append($input_vcf)
@@ -106,7 +112,7 @@
   </token>
 
   <xml name="macro_fasta_ref">
-    <param name="fasta_ref" argument="--fasta-ref" type="data" format="data" label="Reference sequence in FASTA format" optional="True" />
+    <param name="fasta_ref" argument="--fasta-ref" type="data" format="data" optional="true" label="Reference sequence in FASTA format" />
   </xml>
   <token name="@PREPARE_FASTA_REF@">
 <![CDATA[
@@ -148,7 +154,7 @@
 
 
   <xml name="macro_AF_file">
-    <param name="AF_file" argument="--AF-file" type="data" format="tabular" label="Allele frequencies file" optional="True" help="Tab-delimited file containing the columns CHR,POS,REF,ALT,AF" />
+    <param name="AF_file" argument="--AF-file" type="data" format="tabular" optional="true" label="Allele frequencies file" help="Tab-delimited file containing the columns CHR,POS,REF,ALT,AF" />
   </xml>
   <!-- This may need to bgzip and tabix the file -->
   <token name="@PREPARE_AF_FILE@">
@@ -165,7 +171,7 @@
   </token>
 
   <xml name="macro_estimate_AF">
-      <param name="estimate_AF" argument="--estimate-AF" type="data" format="data" label="Estimate allele frequency" optional="True" help="calculate AC,AN counts on the fly, using either all samples (&quot;-&quot;) or samples listed in &lt;file&gt;" />
+      <param name="estimate_AF" argument="--estimate-AF" type="data" format="data" optional="true" label="Estimate allele frequency" help="Calculate AC,AN counts on the fly, using either all samples (&quot;-&quot;) or samples listed in &lt;file&gt;" />
   </xml>
   <token name="@ESTIMATE_AF@">
 #if 'estimate_AF' in $section and $section.estimate_AF:
@@ -174,7 +180,7 @@
   </token>
 
   <xml name="macro_exons_file">
-    <param name="exons_file" type="data" format="tabular" label="exons file" optional="True" help="tab-delimited file with exons for indel frameshifts (chr,from,to; 1-based, inclusive, bgzip compressed)" />
+    <param name="exons_file" type="data" format="tabular" optional="true" label="Exons file" help="Tab-delimited file with exons for indel frameshifts (chr,from,to; 1-based, inclusive, bgzip compressed)" />
   </xml>
   <token name="@PREPARE_EXONS_FILE@">
 <![CDATA[
@@ -193,7 +199,7 @@
   </token>
 
   <xml name="macro_ploidy_file">
-    <param name="ploidy_file" type="data" format="tabular" label="Ploidy file" optional="True" help="tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY" />
+    <param name="ploidy_file" type="data" format="tabular" optional="true" label="Ploidy file" help="Tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY" />
   </xml>
   <token name="@PLOIDY_FILE@">
 #if 'ploidy_file' in $section and $section.ploidy_file:
@@ -208,7 +214,7 @@
       <option value="id">id - only records with identical ID column are compatible. </option>
   </xml>
   <xml name="macro_collapse">
-    <param name="collapse" type="select" label="Collapse" optional="True" help="Controls how to treat records with duplicate positions and defines compatible records across multiple input files">
+    <param name="collapse" type="select" optional="true" label="Collapse" help="Controls how to treat records with duplicate positions and defines compatible records across multiple input files">
       <option value="snps">snps - allow different alleles, as long as they all are SNPs</option>
       <option value="indels">indels - allow different alleles, as long as they all are indels</option>
       <option value="both">both - indels and snps </option>
@@ -224,8 +230,8 @@
   </token>
 
   <xml name="macro_apply_filters">
-    <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;)">
+    <param argument="--apply_filters" type="text" value="" optional="true" label="Apply filters"
+           help="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,]+)*)?$</validator>
     </param>
   </xml>
@@ -271,13 +277,13 @@
         </param>
         <when value="__none__"/>
         <when value="regions">
-            <param name="regions" type="text" value="" label="restrict to comma-separated list of regions" optional="true"
+            <param name="regions" type="text" value="" optional="true" label="Restrict to comma-separated list of regions"
                    help="Each region is specifed as: chr or chr:pos or chr:from-to">
                  <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator>
             </param>
         </when>
         <when value="regions_file">
-            <param name="regions_file" type="data" format="vcf,bed,tabular" label="Regions File" optional="True" help="restrict to regions listed in a file" />
+            <param name="regions_file" type="data" format="vcf,bed,tabular" optional="true" label="Regions file" help="Restrict to regions listed in a file" />
         </when>
     </conditional>
   </xml>
@@ -346,7 +352,7 @@
         </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="" optional="true" label="Restrict to comma-separated list of targets"
                    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>
@@ -373,16 +379,16 @@
   </token>
 
   <xml name="macro_samples">
-      <param name="samples" type="text" value="" label="Samples" optional="true"
-             help="(-s) comma separated list of samples to annotate (or exclude)">
+      <param argument="--samples" type="text" value="" optional="true" label="Samples"
+             help="Comma separated list of samples to annotate (or exclude)">
           <validator type="regex" message="">^(\w+(,\w+)*)?$</validator>
       </param>
       <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples"
-             help="inverts the query/filtering applied by Samples (adds &quot;^&quot; prefix to exclude)" />
-      <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"
-             help="inverts the query/filtering applied by Samples File" />
+             help="Inverts the query/filtering applied by Samples (adds &quot;^&quot; prefix to exclude)" />
+      <param argument="--samples_file" type="data" format="tabular" optional="true" label="Samples file"
+             help="File of samples to include" />
+      <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@">
 #set $samples_defined = False
@@ -397,7 +403,7 @@
   </token>
 
   <xml name="macro_sample">
-      <param name="sample" type="text" label="Sample" optional="True" help="apply variants of the given sample" />
+      <param name="sample" type="text" optional="true" label="Sample" help="Apply variants of the given sample" />
   </xml>
   <token name="@SAMPLE@">
 #if $section.sample:
@@ -407,7 +413,7 @@
 
 
   <xml name="macro_include">
-    <param name="include" type="text" label="Include" optional="True" help="(-i) select sites for which the expression is true">
+    <param argument="--include" type="text" optional="true" label="Include" help="Select sites for which the expression is true">
         <validator type="regex" message="Single quote not allowed">^[^']*$</validator>
         <sanitizer sanitize="False"/>
     </param>
@@ -419,7 +425,7 @@
   </token>
 
   <xml name="macro_exclude">
-    <param name="exclude" type="text" label="Exclude" optional="True" help="(-e) exclude sites for which the expression is true">
+    <param argument="--exclude" type="text" optional="true" label="Exclude" help="Exclude sites for which the expression is true">
         <validator type="regex" message="Single quote not allowed">^[^']*$</validator>
         <sanitizer sanitize="False"/>
     </param>
@@ -431,8 +437,8 @@
   </token>
 
   <xml name="macro_columns">
-    <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">
+    <param name="columns" type="text" value="" optional="true" label="Columns"
+            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>
   </xml>
diff -r 410cdd7cf2bc -r 4422d017fe79 test-data/summary.pdf
Binary file test-data/summary.pdf has changed
diff -r 410cdd7cf2bc -r 4422d017fe79 test-data/view.bcf
Binary file test-data/view.bcf has changed
diff -r 410cdd7cf2bc -r 4422d017fe79 test-data/view.bcf.csi
Binary file test-data/view.bcf.csi has changed
diff -r 410cdd7cf2bc -r 4422d017fe79 test-data/view.vcf_bgzip
Binary file test-data/view.vcf_bgzip has changed