diff nanopolish_variants.xml @ 5:63af3144371a draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit dff183f4eb2d3df42917ec4fed0fbdb2ea11e19a"

--- a/nanopolish_variants.xml	Sun Jun 23 06:04:27 2019 -0400
+++ b/nanopolish_variants.xml	Fri May 29 13:29:14 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="nanopolish_variants" name="Nanopolish variants" version="0.11.1">
+<tool id="nanopolish_variants" name="Nanopolish variants" version="@VERSION@+galaxy0">
     <description>- Find SNPs of basecalled merged Nanopore reads and polishes the consensus sequences</description>
     <macros>
         <import>macros.xml</import>
@@ -167,7 +167,18 @@
             <param name="ref_file" value="draft_single_seq.fa" />
             <param name="w" value="tig00000001:200000-202000" />
             <output name="output_polished" file="polished.fa" />
-            <output name="output_variants" file="variants.vcf"/>
+            <output name="output_variants">
+              <assert_contents>
+                <has_text text="TotalReads" />
+                <has_text text="AlleleCount" />
+                <has_text text="SupportFraction" />
+                <has_text text="200061" />
+                <has_text text="200776" />
+                <has_text text="201588" />
+                <has_text text="tig00000001" />
+                <has_n_lines n="27" />
+              </assert_contents>
+            </output>
         </test>
         <test>
             <param name="input_merged" ftype="fasta" value="reads.fasta" />
@@ -177,7 +188,18 @@
             <param name="ref_file" value="draft_single_seq.fa" />
             <param name="w" value="tig00000001:200000-202000" />
             <output name="output_polished" file="t3_polished.fa" />
-            <output name="output_variants" file="t3_variants.vcf"/>
+            <output name="output_variants">
+              <assert_contents>
+                <has_text text="TotalReads" />
+                <has_text text="AlleleCount" />
+                <has_text text="SupportFraction" />
+                <has_text text="200061" />
+                <has_text text="200776" />
+                <has_text text="201588" />
+                <has_text text="tig00000001" />
+                <has_n_lines n="27" />
+              </assert_contents>
+            </output>
         </test>
         <test>
             <param name="input_merged" ftype="fasta" value="reads.fasta" />
@@ -187,7 +209,18 @@
             <param name="ref_file" value="draft_single_seq.fa" />
             <param name="w" value="tig00000001:200000-202000" />
             <output name="output_polished" file="t4_polished.fa" />
-            <output name="output_variants" file="t4_variants.vcf"/>
+            <output name="output_variants">
+              <assert_contents>
+                <has_text text="TotalReads" />
+                <has_text text="AlleleCount" />
+                <has_text text="SupportFraction" />
+                <has_text text="200061" />
+                <has_text text="200776" />
+                <has_text text="201588" />
+                <has_text text="tig00000001" />
+                <has_n_lines n="27" />
+              </assert_contents>
+            </output>
         </test>
         <test>
             <param name="input_merged" ftype="fasta" value="reads.fasta" />
@@ -203,7 +236,16 @@
             <param name="consensus" value="false" /> 
             <param name="min_flanking_sequence" value="10" />
             <output name="output_polished" file="t2-polished.fa" />
-            <output name="output_variants" file="t2-variants.vcf"/>
+            <output name="output_variants">
+              <assert_contents>
+                <has_text text="TotalReads" />
+                <has_text text="AlleleCount" />
+                <has_text text="SupportFraction" />
+                <has_text text="tig00000001" />
+                <has_text text="198000-202000" />
+                <has_n_lines n="15" />
+              </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[