Mercurial > repos > iuc > samtools_markdup
diff samtools_markdup.xml @ 2:a312a0fdaf31 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit e33502c1fc025859ccbcd2a273f837fac9d322e0"
| author | iuc |
|---|---|
| date | Thu, 22 Apr 2021 12:58:55 +0000 |
| parents | 83b8e36e9cbe |
| children | d0a568e1904b |
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--- a/samtools_markdup.xml Fri Sep 06 06:35:26 2019 -0400 +++ b/samtools_markdup.xml Thu Apr 22 12:58:55 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="samtools_markdup" name="Samtools markdup" version="@TOOL_VERSION@+galaxy2"> +<tool id="samtools_markdup" name="Samtools markdup" version="@TOOL_VERSION@+galaxy3"> <description>marks duplicate alignments</description> <macros> <import>macros.xml</import> @@ -31,7 +31,7 @@ coordsort.sam '$output' #if $stats - 2> '$stats_output' + 2> >(tee -a '$stats_output' >&2) #end if ]]></command> <inputs> @@ -44,7 +44,7 @@ <outputs> <!-- output bam, if input was name sorted then restore this sorting order --> <data name="output" format="bam"/> - <data name="stats_output" format="txt"> + <data name="stats_output" format="txt" label="${tool.name} on ${on_string}: statistics"> <filter>stats</filter> </data> </outputs> @@ -81,6 +81,20 @@ <output name="output" file="5_markdup.expected.bam" /> <output name="stats_output" file="stats.txt" /> </test> + <!-- check that stderr is not swallowed w test data from fixmate --> + <test expect_num_outputs="2" expect_exit_code="1" expect_failure="true"> + <param name="bamfile" value="7_two_read_mapped.sam" /> + <param name="stats" value="true"/> + <!-- for some reason this is not possible at the moment + <output name="stats_output"> + <assert_contents> + <has_line line="[markdup] error: no MC tag. Please run samtools fixmate on file first."/> + </assert_contents> + </output> --> + <assert_stderr> + <has_line line="[markdup] error: no MC tag. Please run samtools fixmate on file first."/> + </assert_stderr> + </test> </tests> <help> Mark duplicate alignments from a coordinate sorted file that has been run through fixmate with the -m option. This program relies on the MC and ms tags that fixmate provides.