fix a few tests

galaxyproject · Aug 24, 2024 · 43702a7 · 43702a7
1 parent 8e3dbc1
commit 43702a7
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Showing 4 changed files with 9 additions and 7 deletions.
diff --git a/tools/bcftools/bcftools_call.xml b/tools/bcftools/bcftools_call.xml
@@ -237,7 +237,7 @@ For example: --prior-freqs REF_AN,REF_AC
             <param name="output_type" value="v" />
             <output name="output_file">
                 <assert_contents>
-                    <has_text text="MinDP" />
+                    <has_text text="MIN_DP" />
                     <has_text text="DP4=2,4,8,11;MQ=49" />
                 </assert_contents>
             </output>

diff --git a/tools/bcftools/bcftools_consensus.xml b/tools/bcftools/bcftools_consensus.xml
@@ -194,7 +194,8 @@ ${section.iupac_codes}
             </section>
             <output name="output_file">
                 <assert_contents>
-                    <has_text text="TACAAAATATGACATATCAAAAAGAACATAACCTACGTATCAACTAAAGTGGTTGTTTGA" />
+                    <has_text text="TACMATATRTGACATATMAAAAAGAACATAACCTACGTATCAACTAAAGTGGTTGTTTGM" />
+                    <has_text text=">1"/>
                 </assert_contents>
             </output>
         </test>
@@ -208,7 +209,8 @@ ${section.iupac_codes}
             <param name="absent" value="W"/>
             <output name="output_file">
                 <assert_contents>
-                    <has_text text="WWWAWAWWAWWWWWWWWCWWWWWWWW" />
+                    <has_text text="WWWMWWWWRWWWWWWWWMWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWM" />
+                    <has_text text=">1"/>
                 </assert_contents>
             </output>
             <assert_command>
@@ -229,7 +231,8 @@ ${section.iupac_codes}
             </section>
             <output name="output_file">
                 <assert_contents>
-                    <has_text text="TACAAAATATGACATATCAAAAAGAACATAACCTACGTATCAACTAAAGTGGTTGTTTGA" />
+                    <has_text text="TACMATATRTGACATATMAAAAAGAACATAACCTACGTATCAACTAAAGTGGTTGTTTGM" />
+                    <has_text text=">1"/>
                 </assert_contents>
             </output>
             <assert_command>

diff --git a/tools/bcftools/bcftools_plugin_frameshifts.xml b/tools/bcftools/bcftools_plugin_frameshifts.xml
@@ -59,8 +59,7 @@ bcftools plugin @EXECUTABLE@
             <output name="output_file" ftype="vcf">
                 <assert_contents>
                     <has_line_matching expression="##INFO=&lt;ID=OOF,.+" />
-                    <has_line_matching expression="1&#09;3106154&#09;.&#09;CAAA&#09;C&#09;.+&#09;.+&#09;OOF=0.+" />
-                    <has_line_matching expression="1&#09;3106154&#09;.&#09;C&#09;CT&#09;.+&#09;.+&#09;OOF=1.+" />
+                    <has_line_matching expression="1&#09;3106154&#09;.&#09;CAAA&#09;C&#09;342&#09;PASS&#09;OOF=-1"/>
                 </assert_contents>
             </output>
         </test>

diff --git a/tools/bcftools/bcftools_stats.xml b/tools/bcftools/bcftools_stats.xml
@@ -235,7 +235,7 @@ ${section.verbose}
             <output name="output_file">
                 <assert_contents>
                     <has_text_matching expression="bcftools stats  --samples - "/>
-                    <has_text_matching expression="PSC\t0\tHG00101\t0\t0\t0\t0\t0\t0\t4.8"/>
+                    <has_text_matching expression="PSC\t0\tHG00101\t0\t0\t0\t0\t0\t0\t4.9"/>
                     <has_text_matching expression="PSI\t0\tHG00102\t0"/>
                 </assert_contents>
             </output>