Mercurial > repos > iuc > mosdepth
changeset 6:b1a8d09e5a82 draft default tip
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 | |
files | mosdepth.xml |
diffstat | 1 files changed, 4 insertions(+), 2 deletions(-) [+] |
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--- a/mosdepth.xml Mon May 06 18:41:03 2024 +0000 +++ b/mosdepth.xml Fri Jul 25 13:53:55 2025 +0000 @@ -25,11 +25,11 @@ </sanitizer> <validator type="regex">([0-9A-Za-z!#$%&+./:;?@^_|~-][0-9A-Za-z!#$%&*+./:;=?@^_|~-]*)?</validator> </xml> - <token name="@TOOL_VERSION@">0.3.8</token> + <token name="@TOOL_VERSION@">0.3.11</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">mosdepth</requirement> - <requirement type="package" version="1.13">gzip</requirement> + <requirement type="package" version="1.14">gzip</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ #if $advanced.options == "yes" and len($advanced.quantize) @@ -66,6 +66,7 @@ #end if --mapq $advanced.mapq $advanced.no_fast + $advanced.fragment_mode #if str($advanced.thresholds) --thresholds '$advanced.thresholds' #end if @@ -131,6 +132,7 @@ <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" /> <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" /> <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" /> + <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"/> <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" /> <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"> <sanitizer invalid_char="">