diff bcftools_stats.xml @ 16:4d3ce9dc1525 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49

--- a/bcftools_stats.xml	Sat Jul 23 13:50:21 2022 +0000
+++ b/bcftools_stats.xml	Tue Sep 20 12:54:05 2022 +0000
@@ -1,5 +1,5 @@
 <?xml version='1.0' encoding='utf-8'?>
-<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy1" profile="18.01">
+<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Parses VCF or BCF and produces stats which can be plotted using plot-vcfstats</description>
     <macros>
         <token name="@EXECUTABLE@">stats</token>
@@ -198,6 +198,49 @@
             </output>
             <output name="output_pdf" file="summary.pdf" compare="sim_size" delta="25000" />
         </test>
+        <!-- Test region overlap option-->
+        <test>
+            <param name="input_file" ftype="vcf" value="stats.b.vcf" />
+            <param name="inputB_file" ftype="vcf" value="stats.a.vcf" />
+            <section name="sec_restrict">
+                <param name="regions_overlap" value="1"/>
+            </section>
+            <output name="output_file">
+                <assert_contents>
+                    <has_text_matching expression="SN\t0\tnumber of samples:\t3"/>
+                    <has_text_matching expression="SN\t1\tnumber of samples:\t3"/>
+                </assert_contents>
+            </output>
+            <assert_command>
+                <has_text text="--regions-overlap" />
+            </assert_command>
+        </test>
+        <!-- Test VCF.gz input file -> REQUIRES https://github.com/galaxyproject/galaxy/pull/14605
+        <test>
+            <param name="input_file"  value="mpileup.vcf.gz" />
+            <output name="output_file">
+                <assert_contents>
+                    <has_text_matching expression="bcftools stats  input0.vcf.gz"/>
+                    <has_text_matching expression="SN\t0\tnumber of samples:\t3"/>
+                    <has_text_matching expression="SN\t0\tnumber of records:\t4103"/>
+                </assert_contents>
+            </output>
+        </test>
+        -->
+        <!-- Test modification in samples option -->
+        <test>
+            <param name="input_file" ftype="vcf" value="mpileup.vcf" />
+            <section name="sec_restrict">
+                <param name="samples" value="-" />
+            </section>
+            <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="PSI\t0\tHG00102\t0"/>
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help><![CDATA[
 =====================================