Mercurial > repos > iuc > samtools_view
diff samtools_view.xml @ 4:fdc58a0cc1d4 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 640b53919bfc0ae4b895451218e919a52ac14b9d
| author | iuc |
|---|---|
| date | Tue, 20 Nov 2018 06:21:33 -0500 |
| parents | 02afb5ea2fce |
| children | ff313de5f7f4 |
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--- a/samtools_view.xml Sun Oct 14 13:56:29 2018 -0400 +++ b/samtools_view.xml Tue Nov 20 06:21:33 2018 -0500 @@ -41,7 +41,7 @@ ## filter options (regions filter is the last parameter) #if $cond_filter.select_filter == 'yes': #if $cond_filter.cond_region.select_region == 'bed' and str( $cond_filter.cond_region.bedfile ) != 'None' - -L '$cond_filter.bedfile' + -L '$cond_filter.cond_region.bedfile' #end if #if $cond_filter.cond_rg.select_rg == 'text': -r '$cond_filter.cond_rg.readgr' @@ -263,7 +263,7 @@ <when input="outtype" value="cram" format="cram" /> </change_format> </data> - <data name="outputcnt" format="txt" from_work_dir="sam" label="${tool.name} on ${on_string}: Counts"> + <data name="outputcnt" format="txt" from_work_dir="outfile" label="${tool.name} on ${on_string}: Counts"> <filter>outtype == 'count'</filter> </data> </outputs> @@ -312,6 +312,12 @@ </conditional> <output name="outputsam" file="test.cram" ftype="cram" compare="sim_size" delta="250" /> </test> + <!-- count alignments --> + <test> + <param name="input" value="test.bam" ftype="bam" /> + <param name="outtype" value="count" /> + <output name="outputcnt" file="test_counts.tab" ftype="txt" /> + </test> <test> <param name="input" value="test.sam" ftype="sam" /> <param name="outtype" value="cram" /> @@ -425,7 +431,7 @@ <param name="seed" value="7" /> <param name="target" value="2" /> </conditional> - <output name="outputsam" file="test_ds.sam" ftype="sam" compare="diff" lines_diff="4" /> + <output name="outputsam" file="test_ds.sam" ftype="sam" compare="diff" lines_diff="6" /> </test> <test> <param name="input" value="test.bam" ftype="bam" />