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comparison picard_MarkDuplicates.xml @ 27:fdca9493e09b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 70d2a66c405be58d4413753792bcadf212a4da84
author iuc
date Sat, 25 Feb 2023 20:32:54 +0000
parents e65f2d5fd3d8
children c943f4a04af0
comparison
equal deleted inserted replaced
26:fc3866ddc7b6 27:fdca9493e09b
1 <tool name="MarkDuplicates" id="picard_MarkDuplicates" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> 1 <tool name="MarkDuplicates" id="picard_MarkDuplicates" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
2 <description>examine aligned records in BAM datasets to locate duplicate molecules</description> 2 <description>examine aligned records in BAM datasets to locate duplicate molecules</description>
3 <macros> 3 <macros>
4 <import>picard_macros.xml</import> 4 <import>picard_macros.xml</import>
5 <token name="@WRAPPER_VERSION@">3</token> 5 <token name="@WRAPPER_VERSION@">4</token>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 @java_options@ 9 @java_options@
10 @symlink_element_identifier@ 10 @symlink_element_identifier@
54 </param> 54 </param>
55 55
56 <param name="read_name_regex" type="text" value="" label="Regular expression that can be used in unusual situations to parse non-standard read names in the incoming SAM/BAM dataset" help="READ_NAME_REGEX; Read names are parsed to extract three variables: tile/region, x coordinate and y coordinate. These values are used to estimate the rate of optical duplication in order to give a more accurate estimated library size. See help below for more info; default='' (uses : separation)"> 56 <param name="read_name_regex" type="text" value="" label="Regular expression that can be used in unusual situations to parse non-standard read names in the incoming SAM/BAM dataset" help="READ_NAME_REGEX; Read names are parsed to extract three variables: tile/region, x coordinate and y coordinate. These values are used to estimate the rate of optical duplication in order to give a more accurate estimated library size. See help below for more info; default='' (uses : separation)">
57 <expand macro="sanitize_query" /> 57 <expand macro="sanitize_query" />
58 </param> 58 </param>
59 <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"/> 59 <param name="optical_duplicate_pixel_distance" type="integer" value="100" min="0" max="5000" label="The maximum offset between two duplicte clusters in order to consider them optical duplicates" help="OPTICAL_DUPLICATE_PIXEL_DISTANCE; default=100"/>
60 60
61 <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' "/> 61 <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' "/>
62 62
63 <expand macro="VS" /> 63 <expand macro="VS" />
64 64
65 </inputs> 65 </inputs>
66 66
67 <outputs> 67 <outputs>
68 <data format="txt" name="metrics_file" label="${tool.name} on ${on_string}: MarkDuplicate metrics"/> 68 <data format="txt" name="metrics_file" label="${tool.name} on ${on_string}: tabular"/>
69 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: MarkDuplicates BAM output"/> 69 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: BAM"/>
70 </outputs> 70 </outputs>
71 71
72 <tests> 72 <tests>
73 <test> 73 <test>
74 <param name="inputFile" value="picard_MarkDuplicates.bam" ftype="bam"/> 74 <param name="inputFile" value="picard_MarkDuplicates.bam" ftype="bam"/>