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comparison picard_MarkDuplicates.xml @ 25:7d34178f2812 draft

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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
comparison
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24:b9fbec5ac6b2 25:7d34178f2812
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@">1</token> 5 <token name="@WRAPPER_VERSION@">2</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@
27 #if $read_name_regex: 27 #if $read_name_regex:
28 READ_NAME_REGEX='${ str( $read_name_regex ) }' 28 READ_NAME_REGEX='${ str( $read_name_regex ) }'
29 #end if 29 #end if
30 OPTICAL_DUPLICATE_PIXEL_DISTANCE='${optical_duplicate_pixel_distance}' 30 OPTICAL_DUPLICATE_PIXEL_DISTANCE='${optical_duplicate_pixel_distance}'
31 31
32 # Optional arguments
33 #if $barcode_tag: 32 #if $barcode_tag:
34 BARCODE_TAG='${barcode_tag}' 33 BARCODE_TAG='${barcode_tag}'
35 #end if 34 #end if
36 35
37 VALIDATION_STRINGENCY='${validation_stringency}' 36 VALIDATION_STRINGENCY='${validation_stringency}'
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)"> 55 <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" /> 56 <expand macro="sanitize_query" />
58 </param> 57 </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"/> 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"/>
60 59
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."/> 60 <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 61
63 <expand macro="VS" /> 62 <expand macro="VS" />
64 63
65 </inputs> 64 </inputs>
66 65
88 <param name="remove_duplicates" value="False"/> 87 <param name="remove_duplicates" value="False"/>
89 <param name="read_name_regex" value=""/> 88 <param name="read_name_regex" value=""/>
90 <param name="optical_duplicate_pixel_distance" value="100"/> 89 <param name="optical_duplicate_pixel_distance" value="100"/>
91 <param name="duplicate_scoring_strategy" value="SUM_OF_BASE_QUALITIES"/> 90 <param name="duplicate_scoring_strategy" value="SUM_OF_BASE_QUALITIES"/>
92 <param name="validation_stringency" value="LENIENT"/> 91 <param name="validation_stringency" value="LENIENT"/>
92 <output name="outFile" file="picard_MarkDuplicates_test2.bam" ftype="bam" lines_diff="4"/>
93 </test>
94 <test>
95 <param name="inputFile" value="picard_MarkDuplicates.bam" ftype="bam"/>
96 <param name="comment" value="test-run"/>
97 <param name="assume_sorted" value="True"/>
98 <param name="remove_duplicates" value="False"/>
99 <param name="read_name_regex" value=""/>
100 <param name="optical_duplicate_pixel_distance" value="100"/>
101 <param name="duplicate_scoring_strategy" value="SUM_OF_BASE_QUALITIES"/>
102 <param name="validation_stringency" value="LENIENT"/>
103 <param name='barcode_tag' value="RX"/>
93 <output name="outFile" file="picard_MarkDuplicates_test2.bam" ftype="bam" lines_diff="4"/> 104 <output name="outFile" file="picard_MarkDuplicates_test2.bam" ftype="bam" lines_diff="4"/>
94 </test> 105 </test>
95 </tests> 106 </tests>
96 107
97 108