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comparison samtools_markdup.xml @ 9:40fa6c240105 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
author iuc
date Sun, 08 Sep 2024 03:26:14 +0000
parents a389f74c3630
children
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8:a389f74c3630 9:40fa6c240105
125 <!-- 5) check that stderr is not swallowed w test data from fixmate --> 125 <!-- 5) check that stderr is not swallowed w test data from fixmate -->
126 <test expect_exit_code="1" expect_failure="true"> 126 <test expect_exit_code="1" expect_failure="true">
127 <param name="bamfile" value="3_two_read_mapped.sam" ftype="sam" /> 127 <param name="bamfile" value="3_two_read_mapped.sam" ftype="sam" />
128 <param name="stats" value="yes"/> 128 <param name="stats" value="yes"/>
129 <assert_stderr> 129 <assert_stderr>
130 <has_line line="[markdup] error: no MC tag. Please run samtools fixmate on file first."/> 130 <has_line line="samtools markdup: error, no MC tag. Please run samtools fixmate on file first."/>
131 <has_line line="samtools markdup: error, unable to assign pair hash key."/>
131 </assert_stderr> 132 </assert_stderr>
132 </test> 133 </test>
133 <!-- 6) check optical distance and check -c option --> 134 <!-- 6) check optical distance and check -c option -->
134 <test expect_num_outputs="1"> 135 <test expect_num_outputs="1">
135 <param name="bamfile" value="1_markdup.sam" ftype="sam"/> 136 <param name="bamfile" value="1_markdup.sam" ftype="sam"/>