Mercurial > repos > iuc > samtools_coverage
changeset 2:8a477224dfee draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 3a5a4ad75547c6c27430d85e6ddf3c2ff1ece0ba
| author | iuc |
|---|---|
| date | Wed, 31 May 2023 17:15:17 +0000 |
| parents | ae36fab06bc2 |
| children | c4ff13d2aab3 |
| files | samtools_coverage.xml test-data/results_1.tabular test-data/results_2.txt test-data/results_3.txt |
| diffstat | 4 files changed, 93 insertions(+), 8 deletions(-) [+] |
line wrap: on
line diff
--- a/samtools_coverage.xml Mon Aug 15 09:15:40 2022 +0000 +++ b/samtools_coverage.xml Wed May 31 17:15:17 2023 +0000 @@ -1,4 +1,4 @@ -<tool id="samtools_coverage" name="Samtools coverage" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> +<tool id="samtools_coverage" name="Samtools coverage" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> <description>computes the depth at each position or region</description> <macros> <import>macros.xml</import> @@ -7,11 +7,15 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @PREPARE_IDX@ + #if $condition_input.input_pooling == "No": + @PREPARE_IDX@ + #else: + @PREPARE_IDX_MULTIPLE@ + #end if samtools coverage #if $condition_input.input_pooling == "Yes": - ${ ' '.join( [ "'%s'" % $x for $x in $condition_input.input] ) } + ${ ' '.join( [ "'%s'" % $x for $x in $condition_input.input_bams] ) } #else '$condition_input.input' #end if @@ -22,11 +26,11 @@ #set $filter = $additional_options.required_flags @FLAGS@ - -rf $flags + --rf $flags #set $filter = $additional_options.skipped_flags @FLAGS@ - -ff $flags + --ff $flags #if $condition_histogram.histogram_select == "yes" -m @@ -45,10 +49,10 @@ <option value="Yes">Yes</option> </param> <when value="No" > - <param name="input" type="data" format="bam" multiple="true" label="BAM file"/> + <param name="input" type="data" format="bam" label="BAM file"/> </when> <when value="Yes"> - <param name="input" type="data" format="bam" multiple="true" label="BAM files to be pooled"/> + <param name="input_bams" type="data" format="bam" multiple="true" label="BAM files to be pooled"/> </when> </conditional> @@ -96,7 +100,7 @@ </test> <test> <param name="input_pooling" value="Yes" /> - <param name="input" value="test_1.bam,test_2.bam" ftype="bam" /> + <param name="input_bams" value="test_1.bam,test_2.bam" ftype="bam" /> <param name="histogram_select" value="yes" /> <param name="n_bins" value="100" /> <output name="output" file="results_3.txt" ftype="tabular" />
--- a/test-data/results_1.tabular Mon Aug 15 09:15:40 2022 +0000 +++ b/test-data/results_1.tabular Wed May 31 17:15:17 2023 +0000 @@ -0,0 +1,5 @@ +#rname startpos endpos numreads covbases coverage meandepth meanbaseq meanmapq +insert 1 599 2 20 3.3389 0.033389 32 30 +ref1 1 45 6 31 68.8889 1.24444 255 30 +ref2 1 40 6 36 90 3.375 63.3 30 +ref3 1 4 0 0 0 0 0 0
--- a/test-data/results_2.txt Mon Aug 15 09:15:40 2022 +0000 +++ b/test-data/results_2.txt Wed May 31 17:15:17 2023 +0000 @@ -0,0 +1,38 @@ +insert (599bp) +> 73.64% │ █ │ Number of reads: 2 +> 65.45% │ █ │ +> 57.27% │ █ │ Covered bases: 20bp +> 49.09% │ ▅ █ │ Percent covered: 3.339% +> 40.91% │ █ █ │ Mean coverage: 0.0334x +> 32.73% │ █▄ █ │ Mean baseQ: 32 +> 24.55% │ ██ █ │ Mean mapQ: 30 +> 16.36% │ ██ █ │ +> 8.18% │ ██ █▁ │ Histo bin width: 11bp +> 0.00% │ ██ ██ │ Histo max bin: 81.818% + 1 110 220 330 440 599 + +ref1 (45bp) +> 90.00% │ ████████████████ █████ ██████████│ Number of reads: 6 +> 80.00% │ ████████████████ █████ ██████████│ +> 70.00% │ ████████████████ █████ ██████████│ Covered bases: 31bp +> 60.00% │ ████████████████ █████ ██████████│ Percent covered: 68.89% +> 50.00% │ ████████████████ █████ ██████████│ Mean coverage: 1.24x +> 40.00% │ ████████████████ █████ ██████████│ Mean baseQ: 255 +> 30.00% │ ████████████████ █████ ██████████│ Mean mapQ: 30 +> 20.00% │ ████████████████ █████ ██████████│ +> 10.00% │ ████████████████ █████ ██████████│ Histo bin width: 1bp +> 0.00% │ ████████████████ █████ ██████████│ Histo max bin: 100% + 1 10 20 30 45 + +ref2 (40bp) +> 90.00% │████████████████████████████████████ │ Number of reads: 6 +> 80.00% │████████████████████████████████████ │ +> 70.00% │████████████████████████████████████ │ Covered bases: 36bp +> 60.00% │████████████████████████████████████ │ Percent covered: 90% +> 50.00% │████████████████████████████████████ │ Mean coverage: 3.38x +> 40.00% │████████████████████████████████████ │ Mean baseQ: 63.3 +> 30.00% │████████████████████████████████████ │ Mean mapQ: 30 +> 20.00% │████████████████████████████████████ │ +> 10.00% │████████████████████████████████████ │ Histo bin width: 1bp +> 0.00% │████████████████████████████████████ │ Histo max bin: 100% + 1 10 20 30 40
--- a/test-data/results_3.txt Mon Aug 15 09:15:40 2022 +0000 +++ b/test-data/results_3.txt Wed May 31 17:15:17 2023 +0000 @@ -0,0 +1,38 @@ +insert (599bp) +> 90.00% │ █ █ │ Number of reads: 4 +> 80.00% │ █ █ │ +> 70.00% │ ██ ██ │ Covered bases: 20bp +> 60.00% │ ██ ██ │ Percent covered: 3.339% +> 50.00% │ ██ ██ │ Mean coverage: 0.0668x +> 40.00% │ ██ ██ │ Mean baseQ: 32 +> 30.00% │ ██ ██ │ Mean mapQ: 30 +> 20.00% │ ██ ██ │ +> 10.00% │ ███ ███ │ Histo bin width: 5bp +> 0.00% │ ███ ███ │ Histo max bin: 100% + 1 50 100 150 200 250 300 350 400 450 599 + +ref1 (45bp) +> 90.00% │ ████████████████ █████ ██████████│ Number of reads: 12 +> 80.00% │ ████████████████ █████ ██████████│ +> 70.00% │ ████████████████ █████ ██████████│ Covered bases: 31bp +> 60.00% │ ████████████████ █████ ██████████│ Percent covered: 68.89% +> 50.00% │ ████████████████ █████ ██████████│ Mean coverage: 2.49x +> 40.00% │ ████████████████ █████ ██████████│ Mean baseQ: 255 +> 30.00% │ ████████████████ █████ ██████████│ Mean mapQ: 30 +> 20.00% │ ████████████████ █████ ██████████│ +> 10.00% │ ████████████████ █████ ██████████│ Histo bin width: 1bp +> 0.00% │ ████████████████ █████ ██████████│ Histo max bin: 100% + 1 10 20 30 45 + +ref2 (40bp) +> 90.00% │████████████████████████████████████ │ Number of reads: 12 +> 80.00% │████████████████████████████████████ │ +> 70.00% │████████████████████████████████████ │ Covered bases: 36bp +> 60.00% │████████████████████████████████████ │ Percent covered: 90% +> 50.00% │████████████████████████████████████ │ Mean coverage: 6.75x +> 40.00% │████████████████████████████████████ │ Mean baseQ: 63.3 +> 30.00% │████████████████████████████████████ │ Mean mapQ: 30 +> 20.00% │████████████████████████████████████ │ +> 10.00% │████████████████████████████████████ │ Histo bin width: 1bp +> 0.00% │████████████████████████████████████ │ Histo max bin: 100% + 1 10 20 30 40