diff bcftools_call.xml @ 9:cb30a39055d0 draft

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

--- a/bcftools_call.xml	Thu Feb 21 16:09:28 2019 -0500
+++ b/bcftools_call.xml	Wed Jun 05 13:17:26 2019 -0400
@@ -1,5 +1,5 @@
 <?xml version='1.0' encoding='utf-8'?>
-<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@">
+<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy1">
     <description>SNP/indel variant calling from VCF/BCF</description>
     <macros>
         <token name="@EXECUTABLE@">call</token>
@@ -112,7 +112,7 @@
     <inputs>
         <expand macro="macro_input" />
         <section name="sec_restrict" expanded="false" title="Restrict to">
-            <expand macro="macro_regions" />
+            <expand macro="macro_restrict" />
             <expand macro="macro_samples" />
         </section>
         <section name="sec_consensus_variant_calling" expanded="true" title="Consensus/variant calling Options">
@@ -129,14 +129,14 @@
                             <option value="trio">trio - call genotypes given the father-mother-child constraint</option>
                         </param>
                         <when value="none">
-                            <expand macro="macro_targets" />
+                            <expand macro="macro_restrict" type="target" label_type="Target" />
                         </when>
                         <when value="alleles">
-                            <expand macro="macro_targets_file"/>
+                            <expand macro="macro_restrictions_file" type="target" label_type="Target" />
                             <param name="insert_missed" argument="--insert-missed" type="boolean" truevalue="--insert-missed" falsevalue="" label="Insert missed" help="Output also sites missed by mpileup but present in -T" />
                         </when>
                         <when value="trio">
-                            <expand macro="macro_targets" />
+                            <expand macro="macro_restrict" type="target" label_type="Target" />
                             <expand macro="macro_novel_rate" />
                         </when>
                     </conditional>
@@ -165,7 +165,7 @@
                             <expand macro="macro_novel_rate" />
                         </when>
                     </conditional>
-                    <expand macro="macro_targets" />
+                    <expand macro="macro_restrict" type="target" label_type="Target" />
                     <param name="pval_threshold" argument="--pval-threshold" type="float" value="0.5" optional="true" label="Pval Threshold" help="Accept variant if P(ref|D)&lt;FLOAT" />
                 </when>
             </conditional>
@@ -179,7 +179,7 @@
                 <option value="1">1 - Treat all samples as haploid</option>
             </param>
             <param name="ploidy_file" argument="--ploidy-file" type="data" format="tabular" optional="true" label="Ploidy file" help="Space/tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY" />
-            <expand macro="macro_regions" />
+            <expand macro="macro_restrict" />
             <expand macro="macro_samples" />
         </section>
         <section name="sec_input_output" expanded="false" title="Input/output Options">