| Next changeset 1:69f93450c57d (2023-07-31) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth commit 7b66f2b9af9221cac930dfd0e078401472bb0e30 |
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added:
mosdepth.xml test-data/input.bam test-data/input.cram test-data/input_regions.bed test-data/output_distribution.tabular test-data/output_per_base_depth.bed test-data/output_quantized.bed test-data/output_region_depths.bed test-data/output_region_distribution.tabular test-data/output_region_distribution_bed.tabular test-data/output_region_distribution_median.tabular test-data/output_region_summary.tabular test-data/output_region_summary_windowed.tabular test-data/output_region_summary_windowed_median.tabular test-data/output_summary.tabular test-data/output_thresholds.bed test-data/output_window_depths.bed test-data/output_window_depths_median.bed |
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| diff -r 000000000000 -r 32ea013ae290 mosdepth.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mosdepth.xml Sun Dec 04 18:30:36 2022 +0000 |
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| b'@@ -0,0 +1,293 @@\n+<tool id="mosdepth" name="mosdepth" version="@TOOL_VERSION@+galaxy0" profile="21.05">\n+ <description>- fast and flexible depth coverage calculation</description>\n+ <macros>\n+ <xml name="bam_identifier">\n+ <!-- this is based on section 1.2.1 of the SAM/BAM specification https://samtools.github.io/hts-specs/SAMv1.pdf -->\n+ <sanitizer invalid_char="\'">\n+ <valid initial="string.ascii_letters,string.digits,string.punctuation">\n+ <remove value="{" />\n+ <remove value="}" />\n+ <remove value="=" />\n+ <remove value="*" />\n+ <remove value="`" />\n+ <remove value=")" />\n+ <remove value="<" />\n+ <remove value="\'" />\n+ <remove value=\'"\' />\n+ <remove value="(" />\n+ <remove value="\\" />\n+ <remove value="[" />\n+ <remove value=">" />\n+ <remove value="]" />\n+ <remove value="," />\n+ <yield />\n+ </valid>\n+ </sanitizer>\n+ <validator type="regex">([0-9A-Za-z!#$%&+./:;?@^_|~-][0-9A-Za-z!#$%&*+./:;=?@^_|~-]*)?</validator>\n+ </xml>\n+ <token name="@TOOL_VERSION@">0.3.3</token>\n+ </macros>\n+ <requirements>\n+ <requirement type="package" version="@TOOL_VERSION@">mosdepth</requirement>\n+ <requirement type="package" version="1.12">gzip</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[\n+ #if $advanced.options == "yes" and len($advanced.quantize)\n+ #set $quantize_depths = []\n+ #for $i, $quant_group in enumerate($advanced.quantize)\n+ #set $quantize_depths = $quantize_depths + [str ($quant_group.quant_group_mindepth)]\n+ #set $quant_group_name = str($quant_group.quant_group_name)\n+ export MOSDEPTH_Q${i}=$quant_group.quant_group_name &&\n+ #end for\n+ #set $quant_groups_depths_str = ":".join($quantize_depths) + \':\'\n+ #end if\n+ ln -s \'$input_alignment\' input_alignment &&\n+ #if $input_alignment.is_of_type(\'bam\'):\n+ ln -s \'${input_alignment.metadata.bam_index}\' input_alignment.bai &&\n+ #elif $input_alignment.is_of_type(\'cram\'):\n+ ln -s \'${input_alignment.metadata.cram_index}\' input_alignment.crai &&\n+ #end if\n+ mosdepth -t \\${GALAXY_SLOTS:-1} \n+ #if $window.window_mode == \'window\'\n+ --by $window.window_size\n+ #elif $window.window_mode == \'bed\'\n+ --by \'$window.region_file\'\n+ #end if\n+ $per_base_coverage \n+ #if $advanced.options == "yes"\n+ #if str($advanced.chrom)\n+ --chrom \'$advanced.chrom\'\n+ #end if\n+ #if $advanced.exclude_flag\n+ --flag $advanced.exclude_flag\n+ #end if\n+ #if $advanced.include_flag\n+ --include-flag $advanced.include_flag\n+ #end if\n+ --mapq $advanced.mapq\n+ $advanced.no_fast\n+ #if str($advanced.thresholds)\n+ --thresholds \'$advanced.thresholds\'\n+ #end if\n+ $advanced.use_median\n+ #if str($advanced.read_groups)\n+ --read-groups \'$read_groups\'\n+ #end if\n+ #if len($advanced.quantize)\n+ --quantize \'$quant_groups_depths_str\'\n+ #end if\n+ #end if \n+ output input_alignment\n+ #if $per_base_coverage\n+ && gunzip output.per-base.bed.gz\n+ #end if\n+ #if $window.window_mode == "bed" or $window.window_mode == "window"\n+ && gunzip output.reg'..b'utput_region_summary_windowed.tabular" ftype="tabular" />\n+ <output name="output_regions_bed" file="output_window_depths.bed" ftype="bed" />\n+ </test>\n+ <!-- test 5 -->\n+ <test expect_num_outputs="4">\n+ <param name="input_alignment" value="input.bam" ftype="bam" />\n+ <conditional name="window">\n+ <param name="window_mode" value="window" />\n+ <param name="window_size" value="200" />\n+ </conditional>\n+ <conditional name="advanced">\n+ <param name="options" value="yes" />\n+ <param name="use_median" value="yes" />\n+ </conditional>\n+ <output name="output_region_dist" file="output_region_distribution_median.tabular" ftype="tabular" />\n+ <output name="output_summary" file="output_region_summary_windowed_median.tabular" ftype="tabular" />\n+ <output name="output_regions_bed" file="output_window_depths_median.bed" ftype="bed" />\n+ </test>\n+ <!-- test 6 -->\n+ <test expect_num_outputs="3">\n+ <param name="input_alignment" value="input.bam" ftype="bam" />\n+ <conditional name="advanced">\n+ <param name="options" value="yes" />\n+ <repeat name="quantize">\n+ <param name="quant_group_mindepth" value="0" />\n+ <param name="quant_group_name" value="NO_COVERAGE" />\n+ </repeat>\n+ <repeat name="quantize">\n+ <param name="quant_group_mindepth" value="1" />\n+ <param name="quant_group_name" value="LOW_COVERAGE" />\n+ </repeat>\n+ <repeat name="quantize">\n+ <param name="quant_group_mindepth" value="20" />\n+ <param name="quant_group_name" value="SUFFICIENT_COVERAGE" />\n+ </repeat>\n+ </conditional>\n+ <output name="output_quantized_bed" file="output_quantized.bed" ftype="bed" />\n+ </test>\n+ <!-- test 7 -->\n+ <test expect_num_outputs="5">\n+ <param name="input_alignment" value="input.bam" ftype="bam" />\n+ <conditional name="window">\n+ <param name="window_mode" value="bed" />\n+ <param name="region_file" value="input_regions.bed" ftype="bed" />\n+ </conditional>\n+ <conditional name="advanced">\n+ <param name="options" value="yes" />\n+ <param name="thresholds" value="20,40" />\n+ </conditional>\n+ <output name="output_thresholds_bed" file="output_thresholds.bed" ftype="bed" />\n+ </test>\n+ <!-- test 7 -->\n+ <test expect_num_outputs="2">\n+ <param name="input_alignment" value="input.cram" ftype="cram" />\n+ <output name="output_summary" file="output_summary.tabular" ftype="tabular" />\n+ <output name="output_global_dist" file="output_distribution.tabular" ftype="tabular" />\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+mosdepth_ is a tool for fast and flexible calculation of read depths from BAM or CRAM files.\n+\n+It can compute:\n+\n+* mean (or median) depth in fixed sized windows\n+* mean (or median) depth in regions specified by a BED file\n+* per base depths\n+* a histogram of read depths\n+* the mean or median coverage histogram for windows / regions\n+* a distribution of proportion of based covered over a particular threshold\n+* a BED format report on regions that are defined by coverage thresholds\n+\n+By default only a summary and depth histogram is computed, but the other options mentioned above can\n+be enabled using different options in the "Compute depth by region" selector and some of the Advanced\n+options.\n+\n+.. _mosdepth: https://github.com/brentp/mosdepth\n+ ]]></help>\n+ <citations>\n+ <citation type="doi">10.1093/bioinformatics/btx699</citation>\n+ </citations>\n+</tool>\n\\ No newline at end of file\n' |
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| diff -r 000000000000 -r 32ea013ae290 test-data/input.bam |
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| diff -r 000000000000 -r 32ea013ae290 test-data/input.cram |
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| diff -r 000000000000 -r 32ea013ae290 test-data/input_regions.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_regions.bed Sun Dec 04 18:30:36 2022 +0000 |
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| diff -r 000000000000 -r 32ea013ae290 test-data/output_distribution.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_distribution.tabular Sun Dec 04 18:30:36 2022 +0000 |
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| diff -r 000000000000 -r 32ea013ae290 test-data/output_per_base_depth.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_per_base_depth.bed Sun Dec 04 18:30:36 2022 +0000 |
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|
| b |
| diff -r 000000000000 -r 32ea013ae290 test-data/output_quantized.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_quantized.bed Sun Dec 04 18:30:36 2022 +0000 |
| b |
| @@ -0,0 +1,5 @@ +sample 0 46 NO_COVERAGE +sample 46 440 SUFFICIENT_COVERAGE +sample 440 644 LOW_COVERAGE +sample 644 976 SUFFICIENT_COVERAGE +sample 976 1000 NO_COVERAGE |
| b |
| diff -r 000000000000 -r 32ea013ae290 test-data/output_region_depths.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_region_depths.bed Sun Dec 04 18:30:36 2022 +0000 |
| b |
| @@ -0,0 +1,2 @@ +sample 22 581 varskip-0317-1_01 1026.10 +sample 418 998 varskip-0317-1_02 51.50 |
| b |
| diff -r 000000000000 -r 32ea013ae290 test-data/output_region_distribution.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_region_distribution.tabular Sun Dec 04 18:30:36 2022 +0000 |
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| diff -r 000000000000 -r 32ea013ae290 test-data/output_region_distribution_bed.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_region_distribution_bed.tabular Sun Dec 04 18:30:36 2022 +0000 |
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| diff -r 000000000000 -r 32ea013ae290 test-data/output_region_distribution_median.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_region_distribution_median.tabular Sun Dec 04 18:30:36 2022 +0000 |
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|
| b |
| diff -r 000000000000 -r 32ea013ae290 test-data/output_region_summary.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_region_summary.tabular Sun Dec 04 18:30:36 2022 +0000 |
| b |
| @@ -0,0 +1,5 @@ +chrom length bases mean min max +sample 1000 585663 585.66 0 1697 +sample_region 1139 603460 529.82 0 1697 +total 1000 585663 585.66 0 1697 +total_region 1139 603460 529.82 0 1697 |
| b |
| diff -r 000000000000 -r 32ea013ae290 test-data/output_region_summary_windowed.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_region_summary_windowed.tabular Sun Dec 04 18:30:36 2022 +0000 |
| b |
| @@ -0,0 +1,5 @@ +chrom length bases mean min max +sample 1000 585663 585.66 0 1697 +sample_region 1000 585663 585.66 0 1697 +total 1000 585663 585.66 0 1697 +total_region 1000 585663 585.66 0 1697 |
| b |
| diff -r 000000000000 -r 32ea013ae290 test-data/output_region_summary_windowed_median.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_region_summary_windowed_median.tabular Sun Dec 04 18:30:36 2022 +0000 |
| b |
| @@ -0,0 +1,5 @@ +chrom length bases mean min max +sample 1000 599548 599.55 0 1700 +sample_region 1000 599548 599.55 0 1700 +total 1000 599548 599.55 0 1700 +total_region 1000 599548 599.55 0 1700 |
| b |
| diff -r 000000000000 -r 32ea013ae290 test-data/output_summary.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_summary.tabular Sun Dec 04 18:30:36 2022 +0000 |
| b |
| @@ -0,0 +1,3 @@ +chrom length bases mean min max +sample 1000 585663 585.66 0 1697 +total 1000 585663 585.66 0 1697 |
| b |
| diff -r 000000000000 -r 32ea013ae290 test-data/output_thresholds.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_thresholds.bed Sun Dec 04 18:30:36 2022 +0000 |
| b |
| @@ -0,0 +1,3 @@ +#chrom start end region 20X 40X +sample 22 581 varskip-0317-1_01 394 394 +sample 418 998 varskip-0317-1_02 354 22 |
| b |
| diff -r 000000000000 -r 32ea013ae290 test-data/output_window_depths.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_window_depths.bed Sun Dec 04 18:30:36 2022 +0000 |
| b |
| @@ -0,0 +1,5 @@ +sample 0 200 1175.42 +sample 200 400 1477.54 +sample 400 600 215.08 +sample 600 800 27.68 +sample 800 1000 32.59 |
| b |
| diff -r 000000000000 -r 32ea013ae290 test-data/output_window_depths_median.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_window_depths_median.bed Sun Dec 04 18:30:36 2022 +0000 |
| b |
| @@ -0,0 +1,5 @@ +sample 0 200 1526.00 +sample 200 400 1523.00 +sample 400 600 1.00 +sample 600 800 38.00 +sample 800 1000 38.00 |