Mercurial > repos > devteam > picard
diff picard_MarkDuplicates.xml @ 25:7d34178f2812 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit a0fcbda330469051d130fd0802c55960ae948e3b
| author | iuc |
|---|---|
| date | Tue, 11 Jun 2019 02:36:54 -0400 |
| parents | 6f9c0884a3e7 |
| children | 881d7645d1bf |
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--- a/picard_MarkDuplicates.xml Fri May 31 03:21:52 2019 -0400 +++ b/picard_MarkDuplicates.xml Tue Jun 11 02:36:54 2019 -0400 @@ -2,7 +2,7 @@ <description>examine aligned records in BAM datasets to locate duplicate molecules</description> <macros> <import>picard_macros.xml</import> - <token name="@WRAPPER_VERSION@">1</token> + <token name="@WRAPPER_VERSION@">2</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -29,7 +29,6 @@ #end if OPTICAL_DUPLICATE_PIXEL_DISTANCE='${optical_duplicate_pixel_distance}' - # Optional arguments #if $barcode_tag: BARCODE_TAG='${barcode_tag}' #end if @@ -58,7 +57,7 @@ </param> <param name="optical_duplicate_pixel_distance" type="integer" value="100" min="0" max="500" label="The maximum offset between two duplicte clusters in order to consider them optical duplicates" help="OPTICAL_DUPLICATE_PIXEL_DISTANCE; default=100"/> - <param name="barcode_tag" type="text" optional="True" label="Barcode Tag" help="Barcode SAM tag. This tag can be utilized when you have data from an assay that includes Unique Molecular Indices."/> + <param name="barcode_tag" type="text" optional="True" label="Barcode Tag" help="Barcode SAM tag. This tag can be utilized when you have data from an assay that includes Unique Molecular Indices. Typically 'RX' "/> <expand macro="VS" /> @@ -92,6 +91,18 @@ <param name="validation_stringency" value="LENIENT"/> <output name="outFile" file="picard_MarkDuplicates_test2.bam" ftype="bam" lines_diff="4"/> </test> + <test> + <param name="inputFile" value="picard_MarkDuplicates.bam" ftype="bam"/> + <param name="comment" value="test-run"/> + <param name="assume_sorted" value="True"/> + <param name="remove_duplicates" value="False"/> + <param name="read_name_regex" value=""/> + <param name="optical_duplicate_pixel_distance" value="100"/> + <param name="duplicate_scoring_strategy" value="SUM_OF_BASE_QUALITIES"/> + <param name="validation_stringency" value="LENIENT"/> + <param name='barcode_tag' value="RX"/> + <output name="outFile" file="picard_MarkDuplicates_test2.bam" ftype="bam" lines_diff="4"/> + </test> </tests>