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comparison mosdepth.xml @ 6:b1a8d09e5a82 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit 078ade4ee3f8566373ff88bdab4c0c766e62a347
author iuc
date Fri, 25 Jul 2025 13:53:55 +0000
parents 5854d0da92b4
children 2fe966f8532e
comparison
equal deleted inserted replaced
5:5854d0da92b4 6:b1a8d09e5a82
23 <yield /> 23 <yield />
24 </valid> 24 </valid>
25 </sanitizer> 25 </sanitizer>
26 <validator type="regex">([0-9A-Za-z!#$%&amp;+./:;?@^_|~-][0-9A-Za-z!#$%&amp;*+./:;=?@^_|~-]*)?</validator> 26 <validator type="regex">([0-9A-Za-z!#$%&amp;+./:;?@^_|~-][0-9A-Za-z!#$%&amp;*+./:;=?@^_|~-]*)?</validator>
27 </xml> 27 </xml>
28 <token name="@TOOL_VERSION@">0.3.8</token> 28 <token name="@TOOL_VERSION@">0.3.11</token>
29 </macros> 29 </macros>
30 <requirements> 30 <requirements>
31 <requirement type="package" version="@TOOL_VERSION@">mosdepth</requirement> 31 <requirement type="package" version="@TOOL_VERSION@">mosdepth</requirement>
32 <requirement type="package" version="1.13">gzip</requirement> 32 <requirement type="package" version="1.14">gzip</requirement>
33 </requirements> 33 </requirements>
34 <command detect_errors="exit_code"><![CDATA[ 34 <command detect_errors="exit_code"><![CDATA[
35 #if $advanced.options == "yes" and len($advanced.quantize) 35 #if $advanced.options == "yes" and len($advanced.quantize)
36 #set $quantize_depths = [] 36 #set $quantize_depths = []
37 #for $i, $quant_group in enumerate($advanced.quantize) 37 #for $i, $quant_group in enumerate($advanced.quantize)
64 #if $advanced.include_flag 64 #if $advanced.include_flag
65 --include-flag $advanced.include_flag 65 --include-flag $advanced.include_flag
66 #end if 66 #end if
67 --mapq $advanced.mapq 67 --mapq $advanced.mapq
68 $advanced.no_fast 68 $advanced.no_fast
69 $advanced.fragment_mode
69 #if str($advanced.thresholds) 70 #if str($advanced.thresholds)
70 --thresholds '$advanced.thresholds' 71 --thresholds '$advanced.thresholds'
71 #end if 72 #end if
72 $advanced.use_median 73 $advanced.use_median
73 #if str($advanced.read_groups) 74 #if str($advanced.read_groups)
129 <expand macro="bam_identifier" /> 130 <expand macro="bam_identifier" />
130 </param> 131 </param>
131 <param argument="--flag" name="exclude_flag" type="integer" min="0" value="0" label="Exclude reads with these bits set in FLAG" help="Exclude reads where any of these bits are set in the value of the read flags column" /> 132 <param argument="--flag" name="exclude_flag" type="integer" min="0" value="0" label="Exclude reads with these bits set in FLAG" help="Exclude reads where any of these bits are set in the value of the read flags column" />
132 <param argument="--include-flag" type="integer" min="1" optional="true" label="Only include reads with these bits set in FLAG" help="Only include reads where any of these bits are set in the value of the read flags column" /> 133 <param argument="--include-flag" type="integer" min="1" optional="true" label="Only include reads with these bits set in FLAG" help="Only include reads where any of these bits are set in the value of the read flags column" />
133 <param argument="--fast-mode" name="no_fast" type="boolean" truevalue="" falsevalue="-x" label="Disable fast mode" help="Fast mode doesn't look up internal cigar operations or correct mate overlaps. Disabling it is not recommended" /> 134 <param argument="--fast-mode" name="no_fast" type="boolean" truevalue="" falsevalue="-x" label="Disable fast mode" help="Fast mode doesn't look up internal cigar operations or correct mate overlaps. Disabling it is not recommended" />
135 <param argument="--fragment-mode" type="boolean" truevalue="--fragment-mode" falsevalue="" checked="false" label="Use fragment mode" help="Count the coverage of the full fragment including the full insert (proper pairs only). Note that you can use either of fast mode or fragment mode, but not both"/>
134 <param argument="--mapq" type="integer" min="0" value="0" label="Minimum mapping quality" help="Reads with a mapping quality lower than this value are ignored" /> 136 <param argument="--mapq" type="integer" min="0" value="0" label="Minimum mapping quality" help="Reads with a mapping quality lower than this value are ignored" />
135 <param argument="--thresholds" type="text" value="" label="Specify thresholds for output when using region output" help="The number of bases covered by these thresholds will be reported. Multiple thresholds can be separated by commas"> 137 <param argument="--thresholds" type="text" value="" label="Specify thresholds for output when using region output" help="The number of bases covered by these thresholds will be reported. Multiple thresholds can be separated by commas">
136 <sanitizer invalid_char=""> 138 <sanitizer invalid_char="">
137 <valid initial="string.digits"> 139 <valid initial="string.digits">
138 <add value="," /> 140 <add value="," />