| Previous changeset 16:6741a8ace658 (2017-02-08) Next changeset 18:7615ac66c6e5 (2018-01-20) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit a55cff7dfc145ed17ec2ee9f6a70d51c6f9d74b6 |
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modified:
picard_CollectRnaSeqMetrics.xml picard_MarkDuplicates.xml |
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| diff -r 6741a8ace658 -r fc288950c3b7 picard_CollectRnaSeqMetrics.xml --- a/picard_CollectRnaSeqMetrics.xml Wed Feb 08 12:45:35 2017 -0500 +++ b/picard_CollectRnaSeqMetrics.xml Thu Apr 13 19:09:24 2017 -0400 |
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| @@ -219,12 +219,12 @@ 9. A new dataset will appear in the current Galaxy history 10. Use this dataset as the input for **Gene annotations in refFlat form** dropdown of this tool -.. _refFlat: http://genome.ucsc.edu/goldenPath/gbdDescriptionsOld.html#RefFlat +.. _refFlat: https://genome.ucsc.edu/FAQ/FAQformat.html#format9 @description@ REF_FLAT=File Gene annotations in refFlat form. Format described here: - http://genome.ucsc.edu/goldenPath/gbdDescriptionsOld.html#RefFlat Required. + https://genome.ucsc.edu/FAQ/FAQformat.html#format9 Required. RIBOSOMAL_INTERVALS=File Location of rRNA sequences in genome, in interval_list format. If not specified no bases will be identified as being ribosomal. Format described here: |
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| diff -r 6741a8ace658 -r fc288950c3b7 picard_MarkDuplicates.xml --- a/picard_MarkDuplicates.xml Wed Feb 08 12:45:35 2017 -0500 +++ b/picard_MarkDuplicates.xml Thu Apr 13 19:09:24 2017 -0400 |
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| @@ -1,4 +1,4 @@ -<tool name="MarkDuplicates" id="picard_MarkDuplicates" version="@TOOL_VERSION@.0"> +<tool name="MarkDuplicates" id="picard_MarkDuplicates" version="@TOOL_VERSION@.1"> <description>examine aligned records in BAM datasets to locate duplicate molecules</description> <macros> <import>picard_macros.xml</import> @@ -11,22 +11,28 @@ MarkDuplicates INPUT='$escaped_element_identifier' - OUTPUT="${outFile}" + OUTPUT='${outFile}' - METRICS_FILE="${metrics_file}" + METRICS_FILE='${metrics_file}' #for $element in $comments: - COMMENT="${element.comment}" + COMMENT='${element.comment}' #end for - REMOVE_DUPLICATES="${remove_duplicates}" - ASSUME_SORTED="${assume_sorted}" - DUPLICATE_SCORING_STRATEGY="${duplicate_scoring_strategy}" + REMOVE_DUPLICATES='${remove_duplicates}' + ASSUME_SORTED='${assume_sorted}' + + DUPLICATE_SCORING_STRATEGY='${duplicate_scoring_strategy}' #import pipes READ_NAME_REGEX=${ pipes.quote( str( $read_name_regex ) ) or "''" } - OPTICAL_DUPLICATE_PIXEL_DISTANCE="${optical_duplicate_pixel_distance}" + OPTICAL_DUPLICATE_PIXEL_DISTANCE='${optical_duplicate_pixel_distance}' - VALIDATION_STRINGENCY="${validation_stringency}" + # Optional arguments + #if $barcode_tag: + BARCODE_TAG='${barcode_tag}' + #end if + + VALIDATION_STRINGENCY='${validation_stringency}' QUIET=true VERBOSITY=ERROR @@ -53,6 +59,8 @@ </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."/> + <expand macro="VS" /> </inputs> @@ -116,6 +124,8 @@ unless using later versions of the Illumina pipeline that multiply pixel values by 10, in which case 50-100 is more normal. Default value: 100. + BARCODE_TAG=String Barcode SAM tag (ex. BC for 10X Genomics) Default value: null. + @more_info@ </help> |