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comparison picard_MarkDuplicatesWithMateCigar.xml @ 31:585027e65f3b 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 20:33:49 +0000
parents 881d7645d1bf
children f9242e01365a
comparison
equal deleted inserted replaced
30:b502c227b5e6 31:585027e65f3b
1 <tool name="MarkDuplicatesWithMateCigar" id="picard_MarkDuplicatesWithMateCigar" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> 1 <tool name="MarkDuplicatesWithMateCigar" id="picard_MarkDuplicatesWithMateCigar" 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@">2</token> 5 <token name="@WRAPPER_VERSION@">3</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@
53 53
54 54
55 <param name="read_name_regex" type="text" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*." label="Regular expression that can be used to parse 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=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*."> 55 <param name="read_name_regex" type="text" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*." label="Regular expression that can be used to parse 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=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*.">
56 <expand macro="sanitize_query" /> 56 <expand macro="sanitize_query" />
57 </param> 57 </param>
58 <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"/> 58 <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"/>
59 59
60 <expand macro="VS" /> 60 <expand macro="VS" />
61 61
62 </inputs> 62 </inputs>
63 63
64 <outputs> 64 <outputs>
65 <data format="txt" name="metrics_file" label="${tool.name} on ${on_string}: MarkDuplicate metrics"/> 65 <data format="txt" name="metrics_file" label="${tool.name} on ${on_string}: metrics"/>
66 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: MarkDuplicates BAM output"/> 66 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: BAM"/>
67 </outputs> 67 </outputs>
68 68
69 <tests> 69 <tests>
70 <test> 70 <test>
71 <param name="inputFile" value="picard_MarkDuplicatesWithMateCigar.bam" ftype="bam"/> 71 <param name="inputFile" value="picard_MarkDuplicatesWithMateCigar.bam" ftype="bam"/>