diff bcftools_consensus.xml @ 8:70b8e9908ea8 draft

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

--- a/bcftools_consensus.xml	Thu Feb 21 15:54:32 2019 -0500
+++ b/bcftools_consensus.xml	Wed Jun 05 12:58:42 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>Create consensus sequence by applying VCF variants to a reference fasta file</description>
     <macros>
         <token name="@EXECUTABLE@">consensus</token>
@@ -12,14 +12,15 @@
     <command detect_errors="aggressive"><![CDATA[
 @PREPARE_ENV@
 @PREPARE_INPUT_FILE@
-#set $section = $sec_default
+#set $section = $reference_source
 @PREPARE_FASTA_REF@
 
 bcftools @EXECUTABLE@
 
+@FASTA_REF@
+
 ## Default section
 #set $section = $sec_default
-@FASTA_REF@
 
 ${section.iupac_codes}
 
@@ -43,10 +44,9 @@
     </command>
     <inputs>
         <expand macro="macro_input" />
+        <expand macro="macro_fasta_ref" />
         <section name="sec_default" expanded="true" title="Default Options">
-            <expand macro="macro_fasta_ref" />
             <param name="mask" type="data" format="tabular" label="Mask" optional="True" help="Replace regions with N" />
-
             <param name="iupac_codes" type="boolean" truevalue="--iupac-codes" falsevalue="" label="Iupac Codes" 
                    help="Output variants in the form of IUPAC ambiguity codes" />
             <expand macro="macro_sample" />
@@ -65,7 +65,7 @@
     </outputs>
     <tests>
         <test>
-            <param name="fasta_ref" ftype="fasta" value="consensus.fa" />
+            <expand macro="test_using_reference" ref="consensus.fa" />
             <param name="input_file" ftype="vcf" value="consensus.vcf" />
             <param name="mask" ftype="tabular" value="consensus.tab" />
             <param name="chain" value="True" />
@@ -80,6 +80,22 @@
                 </assert_contents>
             </output>
         </test>
+        <test>
+            <expand macro="test_using_reference" select_from="cached" ref="consensus" />
+            <param name="input_file" ftype="vcf" dbkey="?" value="consensus.vcf" />
+            <param name="mask" ftype="tabular" value="consensus.tab" />
+            <param name="chain" value="True" />
+            <output name="output_file">
+                <assert_contents>
+                    <has_text text="NNNNNNNNNNNNNNNNNNNNNNNNNN" />
+                </assert_contents>
+            </output>
+            <output name="chain_file">
+                <assert_contents>
+                    <has_text text="chain 497 1 501 + 1 501 1 502 + 1 502 1" />
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help><![CDATA[
 =====================================