Mercurial > repos > iuc > mosdepth
changeset 1:a387f00796c0 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/mosdepth commit 42dc2863caa2105d8467575366147d1164945157
| author | iuc |
|---|---|
| date | Mon, 10 Nov 2025 12:15:26 +0000 |
| parents | b08cd2e5e61a |
| children | |
| files | mosdepth.xml test-data/output_region_distribution.tabular test-data/output_region_distribution_median.tabular |
| diffstat | 3 files changed, 21 insertions(+), 11 deletions(-) [+] |
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--- a/mosdepth.xml Mon Jul 31 06:09:19 2023 +0000 +++ b/mosdepth.xml Mon Nov 10 12:15:26 2025 +0000 @@ -25,11 +25,11 @@ </sanitizer> <validator type="regex">([0-9A-Za-z!#$%&+./:;?@^_|~-][0-9A-Za-z!#$%&*+./:;=?@^_|~-]*)?</validator> </xml> - <token name="@TOOL_VERSION@">0.3.4</token> + <token name="@TOOL_VERSION@">0.3.12</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">mosdepth</requirement> - <requirement type="package" version="1.12">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) @@ -56,7 +56,7 @@ $per_base_coverage #if $advanced.options == "yes" #if str($advanced.chrom) - --chrom '$advanced.chrom' + --chrom '$advanced.chrom' #end if #if $advanced.exclude_flag --flag $advanced.exclude_flag @@ -66,6 +66,7 @@ #end if --mapq $advanced.mapq $advanced.no_fast + $advanced.fragment_mode #if str($advanced.thresholds) --thresholds '$advanced.thresholds' #end if @@ -74,7 +75,13 @@ --read-groups '$read_groups' #end if #if len($advanced.quantize) - --quantize '$quant_groups_depths_str' + --quantize '$quant_groups_depths_str' + #end if + #if str($advanced.min_frag_len): + --min-frag-len $advanced.min_frag_len + #end if + #if str($advanced.max_frag_len): + --max-frag-len $advanced.max_frag_len #end if #end if output input_alignment @@ -125,6 +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=""> @@ -141,6 +149,8 @@ <add value=" " /> </expand> </param> + <param argument="--min-frag-len" type="integer" min="0" optional="true" label="Reads with a smaller insert size than this are ignored" /> + <param argument="--max-frag-len" type="integer" min="0" optional="true" label="Reads with a larger insert size than this are ignored" /> <repeat name="quantize" title="Read depth thresholds for depth-defined regions"> <param name="quant_group_mindepth" type="integer" min="0" value="0" label="Minimum depth for depth-defined region" help="Regions with this depth or lower will be included in this depth-defined region" /> <param name="quant_group_name" type="text" label="Depth-defined region name" help="Name include in BED output for regions in this depth-defined region"> @@ -273,7 +283,7 @@ It can compute: -* mean (or median) depth in fixed sized windows +* mean (or median) depth in fixed-sized windows * mean (or median) depth in regions specified by a BED file * per base depths * a histogram of read depths @@ -281,7 +291,7 @@ * a distribution of proportion of based covered over a particular threshold * a BED format report on regions that are defined by coverage thresholds -By default only a summary and depth histogram is computed, but the other options mentioned above can +By default, only a summary and depth histogram is computed, but the other options mentioned above can be enabled using different options in the "Compute depth by region" selector and some of the Advanced options. @@ -290,4 +300,4 @@ <citations> <citation type="doi">10.1093/bioinformatics/btx699</citation> </citations> -</tool> \ No newline at end of file +</tool>
--- a/test-data/output_region_distribution.tabular Mon Jul 31 06:09:19 2023 +0000 +++ b/test-data/output_region_distribution.tabular Mon Nov 10 12:15:26 2025 +0000 @@ -1,4 +1,4 @@ -sample 999 0.40 +sample 511 0.40 sample 300 0.40 sample 299 0.40 sample 298 0.40 @@ -300,7 +300,7 @@ sample 2 1.00 sample 1 1.00 sample 0 1.00 -total 999 0.40 +total 511 0.40 total 300 0.40 total 299 0.40 total 298 0.40
--- a/test-data/output_region_distribution_median.tabular Mon Jul 31 06:09:19 2023 +0000 +++ b/test-data/output_region_distribution_median.tabular Mon Nov 10 12:15:26 2025 +0000 @@ -1,4 +1,4 @@ -sample 999 0.40 +sample 511 0.40 sample 300 0.40 sample 299 0.40 sample 298 0.40 @@ -300,7 +300,7 @@ sample 2 0.80 sample 1 1.00 sample 0 1.00 -total 999 0.40 +total 511 0.40 total 300 0.40 total 299 0.40 total 298 0.40