diff bcftools_mpileup.xml @ 4:256e65e460b7 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5

--- a/bcftools_mpileup.xml	Mon May 27 14:23:55 2019 -0400
+++ b/bcftools_mpileup.xml	Wed Jun 05 13:18:11 2019 -0400
@@ -1,5 +1,5 @@
 <?xml version='1.0' encoding='utf-8'?>
-<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy1">
+<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy2">
     <description>Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files</description>
     <macros>
         <token name="@EXECUTABLE@">mpileup</token>
@@ -291,8 +291,10 @@
         </section>
 
         <section name="sec_restrict" expanded="false" title="Restrict to">
-            <expand macro="macro_regions" />
-            <expand macro="macro_targets" />
+            <expand macro="macro_restrict" />
+            <expand macro="macro_restrict" type="target" label_type="Target">
+                <expand macro="macro_invert_targets" />
+            </expand>
         </section>
         <section name="sec_subset" expanded="false" title="Subset Options">
             <expand macro="macro_samples" />
@@ -346,8 +348,8 @@
         <test>
             <param name="input_number" value="single" />
             <param name="input_bam" ftype="bam" value="mpileup.1.bam" />
-            <param name="reference_source_selector" value="history" />
-            <param name="ref_file" ftype="fasta" value="mpileup.ref.fa" />
+            <param name="reference_source_selector" value="cached" />
+            <param name="ref_file" value="mpileup" />
             <param name="quality_settings" value="adjust" />
             <param name="output_type" value="v" />
             <output name="output_file">
@@ -378,8 +380,16 @@
             <param name="input_bams" ftype="bam" value="mpileup.1.bam,mpileup.2.bam,mpileup.3.bam" />
             <param name="reference_source_selector" value="history" />
             <param name="ref_file" ftype="fasta" value="mpileup.ref.fa" />
-            <param name="regions_src" value="regions" />
-            <param name="regions" value="17:100-110" />
+            <section name="sec_restrict">
+                <conditional name="regions">
+                    <param name="regions_src" value="regions" />
+                    <repeat name="regions">
+                        <param name="chrom" value="17" />
+                        <param name="start" value="100" />
+                        <param name="stop" value="110" />
+                    </repeat>
+                </conditional>
+            </section>
             <param name="output_tags" value="DP,INFO/AD,DV" />
             <param name="output_type" value="v" />
             <output name="output_file">
@@ -399,10 +409,16 @@
             <param name="input_bams" ftype="bam" value="mpileup.1.bam,mpileup.2.bam,mpileup.3.bam" />
             <param name="reference_source_selector" value="history" />
             <param name="ref_file" ftype="fasta" value="mpileup.ref.fa" />
-            <param name="regions_src" value="regions_file" />
-            <param name="regions_file" ftype="bed" value="mpileup.regions.bed" />
-            <param name="targets_src" value="targets" />
-            <param name="targets" value="17:100-104" />
+            <section name="sec_restrict">
+                <conditional name="targets">
+                    <param name="targets_src" value="targets" />
+                    <repeat name="targets">
+                        <param name="chrom" value="17" />
+                        <param name="start" value="100" />
+                        <param name="stop" value="104" />
+                    </repeat>
+                </conditional>
+            </section>
             <param name="output_tags" value="DP,INFO/AD,DV" />
             <param name="output_type" value="v" />
             <output name="output_file">
@@ -422,8 +438,16 @@
             <param name="input_bams" ftype="bam" value="mpileup.1.bam,mpileup.2.bam,mpileup.3.bam" />
             <param name="reference_source_selector" value="history" />
             <param name="ref_file" ftype="fasta" value="mpileup.ref.fa" />
-            <param name="regions_src" value="regions" />
-            <param name="regions" value="17:1050-1060" />
+            <section name="sec_restrict">
+                <conditional name="regions">
+                    <param name="regions_src" value="regions" />
+                    <repeat name="regions">
+                        <param name="chrom" value="17" />
+                        <param name="start" value="1050" />
+                        <param name="stop" value="1060" />
+                    </repeat>
+                </conditional>
+            </section>
             <param name="filter_flags" value="filter" />
             <param name="exclude_flags" value="4,16" />
             <param name="output_type" value="v" />