Repository 'bcftools_plugin_dosage'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_dosage

Changeset 16:2514e684f8a3 (2022-09-20)
Previous changeset 15:52f9e4a660e3 (2022-07-23) Next changeset 17:79f7a1acc2cd (2022-09-26)
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
modified:
bcftools_plugin_dosage.xml
macros.xml
test-data/summary.pdf
added:
test-data/mpileup.AD.vcf
b
diff -r 52f9e4a660e3 -r 2514e684f8a3 bcftools_plugin_dosage.xml
--- a/bcftools_plugin_dosage.xml Sat Jul 23 13:43:43 2022 +0000
+++ b/bcftools_plugin_dosage.xml Tue Sep 20 13:02:07 2022 +0000
b
@@ -1,5 +1,5 @@
 <?xml version='1.0' encoding='utf-8'?>
-<tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@TOOL_VERSION@">
+<tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>plugin genotype dosage</description>
     <macros>
         <token name="@EXECUTABLE@">dosage</token>
b
diff -r 52f9e4a660e3 -r 2514e684f8a3 macros.xml
--- a/macros.xml Sat Jul 23 13:43:43 2022 +0000
+++ b/macros.xml Tue Sep 20 13:02:07 2022 +0000
[
@@ -1,5 +1,7 @@
 <macros>
-  <token name="@TOOL_VERSION@">1.10</token>
+  <token name="@TOOL_VERSION@">1.15.1</token>
+  <token name="@VERSION_SUFFIX@">0</token>
+  <token name="@PROFILE@">20.01</token>
   <xml name="bio_tools">
       <xrefs>
           <xref type="bio.tools">bcftools</xref>
@@ -8,15 +10,15 @@
   <xml name="requirements">
     <requirements>
       <requirement type="package" version="@TOOL_VERSION@">bcftools</requirement>
-      <requirement type="package" version="1.10">htslib</requirement>
+      <requirement type="package" version="1.15.1">htslib</requirement>
       <yield />
     </requirements>
   </xml>
   <xml name="samtools_requirement">
-      <requirement type="package" version="1.10">samtools</requirement>
+      <requirement type="package" version="1.15.1">samtools</requirement>
   </xml>
   <xml name="matplotlib_requirement">
-      <requirement type="package" version="3.4.3">matplotlib</requirement>
+      <requirement type="package" version="3.5.3">matplotlib</requirement>
   </xml>
   <xml name="version_command">
     <version_command>bcftools 2&gt;&amp;1 | grep 'Version:'</version_command>
@@ -39,6 +41,10 @@
 ]]>
   </token>
   <xml name="macro_input">
+    <!-- 
+    REQUIRES https://github.com/galaxyproject/galaxy/pull/14605/files
+    <param name="input_files" type="data" format="vcf,vcf.gz,vcf_bgzip,bcf" label="Other VCF/BCF Datasets" multiple="True" />
+    -->
     <param name="input_file" type="data" format="vcf,vcf_bgzip,bcf" label="VCF/BCF Data" />
   </xml>
   <token name="@PREPARE_INPUT_FILE@">
@@ -48,6 +54,7 @@
 #if $input_file.is_of_type('vcf')
   bgzip -c '$input_file' > $input_vcf &&
   bcftools index $input_vcf &&
+##elif $input_file.is_of_type('vcf_bgzip') or $input_file.is_of_type('vcf.gz')
 #elif $input_file.is_of_type('vcf_bgzip')
   ln -s '$input_file' $input_vcf &&
   #if $input_file.metadata.tabix_index:
@@ -71,6 +78,10 @@
   </token>
 
   <xml name="macro_inputs">
+    <!-- 
+    REQUIRES https://github.com/galaxyproject/galaxy/pull/14605/files
+    <param name="input_files" type="data" format="vcf,vcf.gz,vcf_bgzip,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@">
@@ -83,7 +94,8 @@
   #if $input_file.is_of_type('vcf')
     bgzip -c '$input_file' > $input_vcf &&
     bcftools index $input_vcf &&
-  #elif $input_file.is_of_type('vcf_bgzip')
+  ##elif $input_file.is_of_type('vcf_bgzip') or $input_file.is_of_type('vcf.gz') -> REQUIRES  https://github.com/galaxyproject/galaxy/pull/14605
+  #elif $input_file.is_of_type('vcf_bgzip') or $input_file.is_of_type('vcf.gz')
     ln -s '$input_file' $input_vcf &&
     #if $input_file.metadata.tabix_index:
       ln -s '${input_file.metadata.tabix_index}' ${input_vcf}.tbi &&
@@ -318,6 +330,11 @@
             <yield />
         </when>        
     </conditional>
+    <param argument="--@TYPE@s-overlap" type="select" optional="true" label="@LABEL_TYPE@ overlap" help="Include if POS in the region (0), record overlaps (1), variant overlaps (2)">
+        <option value="0">0: POS in the region</option>
+        <option value="1">1: Record overlaps</option>
+        <option value="2">2: Variant overlaps</option>
+    </param>
   </xml>
 
   <token name="@PARSE_INTERVALS@">
@@ -337,6 +354,28 @@
 ]]>
   </token>
   
+  <token name="@MASK@">
+<![CDATA[
+#if $section.conditional_soft_filter.selector == 'enabled' and $section.conditional_soft_filter.soft_filter
+  #if $section.conditional_soft_filter.masks.masks_src == 'regions':
+    #set $intervals = $section.conditional_soft_filter.masks.masks
+    @PARSE_INTERVALS@
+    --mask '$intervals_spec'
+  #elif $section.conditional_soft_filter.masks.masks_src == 'masks_file' and $section.conditional_soft_filter.masks.masks_file:
+    #if $masks_path is not None:
+      --mask-file '$masks_path'
+    #else:
+      --mask-file '$section.conditional_soft_filter.masks.masks_file'
+    #end if
+  #end if
+  #if $section.conditional_soft_filter.masks_overlap
+    --mask-overlap $section.conditional_soft_filter.masks_overlap
+  #end if
+#end if
+
+]]>
+  </token>
+
   <token name="@REGIONS@">
 <![CDATA[
 #if $section.regions.regions_src == 'regions':
@@ -350,6 +389,10 @@
     --regions-file '$section.regions.regions_file'
   #end if
 #end if
+#if $section.regions_overlap
+  --regions-overlap $section.regions_overlap
+#end if
+
 ]]>
   </token>
   
@@ -364,6 +407,9 @@
 #elif $section.targets.targets_src == 'targets_file' and $section.targets.targets_file:
   --targets-file "${section.targets.invert_targets_file}${section.targets.targets_file}"
 #end if
+#if $section.targets_overlap
+  --targets-overlap $section.targets_overlap
+#end if
 ]]>
   </token>
 
@@ -410,8 +456,8 @@
 
   <xml name="macro_samples">
       <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+)*)?$</validator>
+             help="Comma-separated list of samples to annotate (or exclude) or - to include all samples">
+          <validator type="regex" message="Comma-separated list of samples or - to include all samples">^(-|\w+(,\w+)*)?$</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)" />
@@ -476,7 +522,7 @@
   <xml name="macro_columns">
     <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">^([^,]+(,[^,]+)*)?$</validator>
+        <validator type="regex" message="COLUMN names separated by commas">^([^,]+(,[^,]+)*)?$</validator>
     </param>
   </xml>
   <token name="@COLUMNS@">
@@ -496,7 +542,18 @@
 ${section.vcf_ids}
   </token>
 
+<xml name="macro_output_tags">
+  <param name="output_tags" argument="--annotate" type="select" optional="true" multiple="True" display="checkboxes" label="Optional tags to output" help="--annotate">
+      <yield />
+  </param>
+</xml>
+
+<xml name="macro_overlap" token_argument="" token_label="">
+</xml>
+
+
   <token name="@OUTPUT_HELP@">
+
       <![CDATA[
 Output Type
 -----------
b
diff -r 52f9e4a660e3 -r 2514e684f8a3 test-data/mpileup.AD.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mpileup.AD.vcf Tue Sep 20 13:02:07 2022 +0000
b
b'@@ -0,0 +1,4131 @@\n+##fileformat=VCFv4.2\n+##FILTER=<ID=PASS,Description="All filters passed">\n+##bcftoolsVersion=1.11-21-g0987715+htslib-1.11-3-g450c912\n+##bcftoolsCommand=mpileup -O v -a AD,DP,INFO/ADR,INFO/ADF,DP4,INFO/DPR -f xxx//mpileup.ref.fa -b xxx//bamlist.txt\n+##reference=file://mpileup.ref.fa\n+##contig=<ID=17,length=4200>\n+##ALT=<ID=*,Description="Represents allele(s) other than observed.">\n+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">\n+##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of raw reads supporting an indel">\n+##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of raw reads supporting an indel">\n+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">\n+##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">\n+##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">\n+##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">\n+##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">\n+##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">\n+##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">\n+##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">\n+##INFO=<ID=I16,Number=16,Type=Float,Description="Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h">\n+##INFO=<ID=QS,Number=R,Type=Float,Description="Auxiliary tag used for calling">\n+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">\n+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Number of high-quality bases">\n+##INFO=<ID=DPR,Number=R,Type=Integer,Description="Number of high-quality bases observed for each allele">\n+##FORMAT=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-fwd, ref-reverse, alt-fwd and alt-reverse bases">\n+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths (high-quality bases)">\n+##INFO=<ID=ADF,Number=R,Type=Integer,Description="Total allelic depths on the forward strand (high-quality bases)">\n+##INFO=<ID=ADR,Number=R,Type=Integer,Description="Total allelic depths on the reverse strand (high-quality bases)">\n+#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tHG00100\tHG00101\tHG00102\tHG99999\n+17\t1\t.\tA\t<*>\t0\t.\tDP=14;ADF=0,0;ADR=0,0;DPR=0,0;I16=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;QS=0,0;MQ0F=0\tPL:DP:DP4:AD\t0,0,0:0:0,0,0,0:0,0\t0,0,0:0:0,0,0,0:0,0\t0,0,0:0:0,0,0,0:0,0\t0,0,0:0:0,0,0,0:0,0\n+17\t2\t.\tA\t<*>\t0\t.\tDP=14;ADF=0,0;ADR=0,0;DPR=0,0;I16=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;QS=0,0;MQ0F=0\tPL:DP:DP4:AD\t0,0,0:0:0,0,0,0:0,0\t0,0,0:0:0,0,0,0:0,0\t0,0,0:0:0,0,0,0:0,0\t0,0,0:0:0,0,0,0:0,0\n+17\t3\t.\tG\t<*>\t0\t.\tDP=14;ADF=0,0;ADR=0,0;DPR=0,0;I16=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;QS=0,0;MQ0F=0\tPL:DP:DP4:AD\t0,0,0:0:0,0,0,0:0,0\t0,0,0:0:0,0,0,0:0,0\t0,0,0:0:0,0,0,0:0,0\t0,0,0:0:0,0,0,0:0,0\n+17\t4\t.\tC\t<*>\t0\t.\tDP=14;ADF=0,0;ADR=0,0;DPR=0,0;I16=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;QS=0,0;MQ0F=0\tPL:DP:DP4:AD\t0,0,0:0:0,0,0,0:0,0\t0,0,0:0:0,0,0,0:0,0\t0,0,0:0:0,0,0,0:0,0\t0,0,0:0:0,0,0,0:0,0\n+17\t5\t.\tT\t<*>\t0\t.\tDP=14;ADF=0,0;ADR=0,0;DPR=0,0;I16=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;QS=0,0;MQ0F=0\tPL:DP:DP4:AD\t0,0,0:0:0,0,0,0:0,0\t0,0,0:0:0,0,0,0:0,0\t0,0,0:0:0,0,0,0:0,0\t0,0,0:0:0,0,0,0:0,0\n+17\t6\t.\tT\t<*>\t0\t.\tDP=14;ADF=0,0;ADR=0,0;DPR=0,0;I16=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;QS=0,0;MQ0F=0\tPL:DP:DP4:AD\t0,0,0:0:0,0,0,0:0,0\t0,0,0:0:0,0,0,0:0,0\t0,0,0:0:0,0,0,0:0,0\t0,0,0:0:0,0,0,0:0,0\n+17\t7\t.\tC\t<*>\t0\t.\tDP=14;ADF=0,0;ADR=0,0;DPR=0,0;I16=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;QS=0,0;MQ0F=0\tPL:DP:DP4:AD\t0,0,0:0:0,0,0,0:0,0\t0,0,0:0:0,0,0,0:0,0\t0,0,0:0:0,0,0,0:0,0\t0,0,0:0:0,0,0,0:0,0\n+17\t8\t.\tT\t<*>\t0\t.\tDP=14;ADF=0,0;ADR=0,0;DPR=0,0;I16=0,0,0,0,0,0,0,0,0,0,0,0,0,'..b'L:DP:DP4:AD\t0,9,103:3:2,1,0,0:3,0\t0,0,0:0:0,0,0,0:0,0\t0,0,0:0:0,0,0,0:0,0\t0,0,0:0:0,0,0,0:0,0\n+17\t4083\t.\tC\t<*>\t0\t.\tDP=3;ADF=2,0;ADR=1,0;DPR=3,0;I16=2,1,0,0,104,3648,0,0,134,6338,0,0,22,340,0,0;QS=1,0;MQSB=1;MQ0F=0\tPL:DP:DP4:AD\t0,9,98:3:2,1,0,0:3,0\t0,0,0:0:0,0,0,0:0,0\t0,0,0:0:0,0,0,0:0,0\t0,0,0:0:0,0,0,0:0,0\n+17\t4084\t.\tA\t<*>\t0\t.\tDP=2;ADF=1,0;ADR=1,0;DPR=2,0;I16=1,1,0,0,78,3050,0,0,97,4969,0,0,20,298,0,0;QS=1,0;MQSB=1;MQ0F=0\tPL:DP:DP4:AD\t0,6,74:2:1,1,0,0:2,0\t0,0,0:0:0,0,0,0:0,0\t0,0,0:0:0,0,0,0:0,0\t0,0,0:0:0,0,0,0:0,0\n+17\t4085\t.\tC\t<*>\t0\t.\tDP=2;ADF=1,0;ADR=1,0;DPR=2,0;I16=1,1,0,0,62,1940,0,0,97,4969,0,0,18,260,0,0;QS=1,0;MQSB=1;MQ0F=0\tPL:DP:DP4:AD\t0,6,62:2:1,1,0,0:2,0\t0,0,0:0:0,0,0,0:0,0\t0,0,0:0:0,0,0,0:0,0\t0,0,0:0:0,0,0,0:0,0\n+17\t4086\t.\tG\t<*>\t0\t.\tDP=2;ADF=1,0;ADR=1,0;DPR=2,0;I16=1,1,0,0,56,1640,0,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diff -r 52f9e4a660e3 -r 2514e684f8a3 test-data/summary.pdf
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