Mercurial > repos > iuc > mosdepth
comparison mosdepth.xml @ 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 |
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| 0:b08cd2e5e61a | 1:a387f00796c0 |
|---|---|
| 23 <yield /> | 23 <yield /> |
| 24 </valid> | 24 </valid> |
| 25 </sanitizer> | 25 </sanitizer> |
| 26 <validator type="regex">([0-9A-Za-z!#$%&+./:;?@^_|~-][0-9A-Za-z!#$%&*+./:;=?@^_|~-]*)?</validator> | 26 <validator type="regex">([0-9A-Za-z!#$%&+./:;?@^_|~-][0-9A-Za-z!#$%&*+./:;=?@^_|~-]*)?</validator> |
| 27 </xml> | 27 </xml> |
| 28 <token name="@TOOL_VERSION@">0.3.4</token> | 28 <token name="@TOOL_VERSION@">0.3.12</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="1.12">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) |
| 54 --by '$window.region_file' | 54 --by '$window.region_file' |
| 55 #end if | 55 #end if |
| 56 $per_base_coverage | 56 $per_base_coverage |
| 57 #if $advanced.options == "yes" | 57 #if $advanced.options == "yes" |
| 58 #if str($advanced.chrom) | 58 #if str($advanced.chrom) |
| 59 --chrom '$advanced.chrom' | 59 --chrom '$advanced.chrom' |
| 60 #end if | 60 #end if |
| 61 #if $advanced.exclude_flag | 61 #if $advanced.exclude_flag |
| 62 --flag $advanced.exclude_flag | 62 --flag $advanced.exclude_flag |
| 63 #end if | 63 #end if |
| 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($advanced.read_groups) |
| 74 --read-groups '$read_groups' | 75 --read-groups '$read_groups' |
| 75 #end if | 76 #end if |
| 76 #if len($advanced.quantize) | 77 #if len($advanced.quantize) |
| 77 --quantize '$quant_groups_depths_str' | 78 --quantize '$quant_groups_depths_str' |
| 79 #end if | |
| 80 #if str($advanced.min_frag_len): | |
| 81 --min-frag-len $advanced.min_frag_len | |
| 82 #end if | |
| 83 #if str($advanced.max_frag_len): | |
| 84 --max-frag-len $advanced.max_frag_len | |
| 78 #end if | 85 #end if |
| 79 #end if | 86 #end if |
| 80 output input_alignment | 87 output input_alignment |
| 81 #if $per_base_coverage | 88 #if $per_base_coverage |
| 82 && gunzip output.per-base.bed.gz | 89 && gunzip output.per-base.bed.gz |
| 123 <expand macro="bam_identifier" /> | 130 <expand macro="bam_identifier" /> |
| 124 </param> | 131 </param> |
| 125 <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" /> |
| 126 <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" /> |
| 127 <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"/> | |
| 128 <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" /> |
| 129 <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"> |
| 130 <sanitizer invalid_char=""> | 138 <sanitizer invalid_char=""> |
| 131 <valid initial="string.digits"> | 139 <valid initial="string.digits"> |
| 132 <add value="," /> | 140 <add value="," /> |
| 139 <!-- while read group IDs are not well specified in the BAM specification, they appear to be like IDs but with spaces allowed --> | 147 <!-- while read group IDs are not well specified in the BAM specification, they appear to be like IDs but with spaces allowed --> |
| 140 <expand macro="bam_identifier"> | 148 <expand macro="bam_identifier"> |
| 141 <add value=" " /> | 149 <add value=" " /> |
| 142 </expand> | 150 </expand> |
| 143 </param> | 151 </param> |
| 152 <param argument="--min-frag-len" type="integer" min="0" optional="true" label="Reads with a smaller insert size than this are ignored" /> | |
| 153 <param argument="--max-frag-len" type="integer" min="0" optional="true" label="Reads with a larger insert size than this are ignored" /> | |
| 144 <repeat name="quantize" title="Read depth thresholds for depth-defined regions"> | 154 <repeat name="quantize" title="Read depth thresholds for depth-defined regions"> |
| 145 <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" /> | 155 <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" /> |
| 146 <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"> | 156 <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"> |
| 147 <sanitizer invalid_char=""> | 157 <sanitizer invalid_char=""> |
| 148 <valid initial="string.letters,string.digits"> | 158 <valid initial="string.letters,string.digits"> |
| 271 <help><![CDATA[ | 281 <help><![CDATA[ |
| 272 mosdepth_ is a tool for fast and flexible calculation of read depths from BAM or CRAM files. | 282 mosdepth_ is a tool for fast and flexible calculation of read depths from BAM or CRAM files. |
| 273 | 283 |
| 274 It can compute: | 284 It can compute: |
| 275 | 285 |
| 276 * mean (or median) depth in fixed sized windows | 286 * mean (or median) depth in fixed-sized windows |
| 277 * mean (or median) depth in regions specified by a BED file | 287 * mean (or median) depth in regions specified by a BED file |
| 278 * per base depths | 288 * per base depths |
| 279 * a histogram of read depths | 289 * a histogram of read depths |
| 280 * the mean or median coverage histogram for windows / regions | 290 * the mean or median coverage histogram for windows / regions |
| 281 * a distribution of proportion of based covered over a particular threshold | 291 * a distribution of proportion of based covered over a particular threshold |
| 282 * a BED format report on regions that are defined by coverage thresholds | 292 * a BED format report on regions that are defined by coverage thresholds |
| 283 | 293 |
| 284 By default only a summary and depth histogram is computed, but the other options mentioned above can | 294 By default, only a summary and depth histogram is computed, but the other options mentioned above can |
| 285 be enabled using different options in the "Compute depth by region" selector and some of the Advanced | 295 be enabled using different options in the "Compute depth by region" selector and some of the Advanced |
| 286 options. | 296 options. |
| 287 | 297 |
| 288 .. _mosdepth: https://github.com/brentp/mosdepth | 298 .. _mosdepth: https://github.com/brentp/mosdepth |
| 289 ]]></help> | 299 ]]></help> |