diff samtools_idxstats.xml @ 2:04d5581db1f5 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_idxstats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4

--- a/samtools_idxstats.xml	Tue May 09 11:19:02 2017 -0400
+++ b/samtools_idxstats.xml	Thu Sep 27 09:03:08 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="samtools_idxstats" name="IdxStats" version="2.0.1">
+<tool id="samtools_idxstats" name="Samtools idxstats" version="2.0.2">
     <description>reports stats of the BAM index file</description>
     <macros>
         <import>macros.xml</import>
@@ -7,18 +7,23 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        ln -f -s '${input.metadata.bam_index}' '${input}.bai' &&
-
-        samtools idxstats '${input}' > '${output}'
+        @PREPARE_IDX@
+        samtools idxstats infile > '${output}'
     ]]></command>
     <inputs>
-        <param name="input" type="data" format="bam" label="BAM file" />
+        <param name="input" type="data" format="bam,cram" label="BAM file" />
     </inputs>
     <outputs>
         <data format="tabular" name="output" label="${tool.name} on ${on_string}" />
     </outputs>
     <tests>
+        <!-- test from https://github.com/samtools/samtools/blob/9ce8c64493f7ea3fa69bc5c1ac980b1a8e3dcf1f/test/test.pl#L2556 -->
         <test>
+            <param name="input" value="test_input_1_a.bam" ftype="bam" />
+            <output name="output" file="test_input_1_a.bam.expected" compare="diff" ftype="tabular" />
+        </test>
+        <!-- test from original tool -->
+	<test>
             <param name="input" value="phiX.bam" ftype="bam" />
             <output name="output" file="samtools_idxstats_out.tabular" compare="diff" ftype="tabular" />
         </test>