| Previous changeset 19:382326c1b1e1 (2025-01-29) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit 11a7415c7f8a44a3f990080533c1de43a41d1e2e |
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modified:
macros.xml test-data/dedup_out1.bam test-data/dedup_out2.bam test-data/dedup_out3.bam test-data/dedup_out4.bam test-data/dedup_out5.bam test-data/dedup_out6.bam umi-tools_whitelist.xml |
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| diff -r 382326c1b1e1 -r f19dee633d4a macros.xml --- a/macros.xml Wed Jan 29 10:08:15 2025 +0000 +++ b/macros.xml Fri Feb 28 20:42:33 2025 +0000 |
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| @@ -9,7 +9,8 @@ <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">umi_tools</requirement> - <yield /> + <requirement type="package" version="1.21">samtools</requirement> + <requirement type="package" version="4.7">sed</requirement> </requirements> </xml> <xml name="citations"> @@ -551,7 +552,9 @@ <token name="@GROUPDEDUP_OPTIONS@"><![CDATA[ $gd.buffer_whole_contig $gd.whole_contig - $gd.multimapping_detection_method + #if $gd.multimapping_detection_method + --multimapping-detection-method $gd.multimapping_detection_method + #end if ]]></token> <xml name="log_input_macro"> |
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| diff -r 382326c1b1e1 -r f19dee633d4a test-data/dedup_out1.bam |
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| Binary file test-data/dedup_out1.bam has changed |
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| diff -r 382326c1b1e1 -r f19dee633d4a test-data/dedup_out2.bam |
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| Binary file test-data/dedup_out2.bam has changed |
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| diff -r 382326c1b1e1 -r f19dee633d4a test-data/dedup_out3.bam |
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| Binary file test-data/dedup_out3.bam has changed |
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| diff -r 382326c1b1e1 -r f19dee633d4a test-data/dedup_out4.bam |
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| Binary file test-data/dedup_out4.bam has changed |
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| diff -r 382326c1b1e1 -r f19dee633d4a test-data/dedup_out5.bam |
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| Binary file test-data/dedup_out5.bam has changed |
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| diff -r 382326c1b1e1 -r f19dee633d4a test-data/dedup_out6.bam |
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| Binary file test-data/dedup_out6.bam has changed |
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| diff -r 382326c1b1e1 -r f19dee633d4a umi-tools_whitelist.xml --- a/umi-tools_whitelist.xml Wed Jan 29 10:08:15 2025 +0000 +++ b/umi-tools_whitelist.xml Fri Feb 28 20:42:33 2025 +0000 |
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| @@ -141,10 +141,10 @@ <conditional name="extract_method_cond"> <param name="prime3" value="false" /> </conditional> - <param name="use_cell_opts" value="advanced" /> + <param name="celloptions|use_cell_opts" value="advanced" /> + <param name="celloptions|expect_cells" value="5" /> + <param name="celloptions|error_correct_threshold" value="3" /> <param name="knee_method" value="density"/> - <param name="expect_cells" value="5" /> - <param name="error_correct_threshold" value="3" /> <param name="log" value="true" /> <output name="out_whitelist" file="out_wl_paired.txt" /> <output name="out_log" file="out_wl_paired.log" lines_diff="50" /> @@ -167,12 +167,11 @@ <conditional name="extract_method_cond"> <param name="prime3" value="false" /> </conditional> - <param name="use_cell_opts" value="advanced" /> <param name="knee_method" value="density"/> - <param name="expect_cells" value="5" /> - <param name="error_correct_threshold" value="3" /> + <param name="celloptions|use_cell_opts" value="advanced" /> + <param name="celloptions|expect_cells" value="5" /> + <param name="celloptions|error_correct_threshold" value="3" /> <param name="log" value="true" /> - <param name="filtered_out_bool" value="true"/> <output name="out_whitelist" file="out_wl_paired.txt" /> <output name="out_log" file="out_wl_paired.log" lines_diff="50" /> <output name="out_html_report" file="out_wl_paired.html" /> @@ -183,13 +182,13 @@ <conditional name="input_type_cond" > <param name="input_type" value="single" /> <param name="input_read1" value="testYYY.40k.fastq.gz" ftype="fastqsanger.gz" /> + <param name="bc_pattern" value="(?P<cell_1>.{8,10})(?P<discard_1>ACTGGCCTGCGA){s<=3}(?P<cell_2>.{9})(?P<discard_2>GGTAGCGGTGACA){s<=3}(?P<cell_3>.{9})(?P<umi_1>.{8})T{3}.*" /> </conditional> - <param name="bc_pattern" value="(?P<cell_1>.{8,10})(?P<discard_1>ACTGGCCTGCGA){s<=3}(?P<cell_2>.{9})(?P<discard_2>GGTAGCGGTGACA){s<=3}(?P<cell_3>.{9})(?P<umi_1>.{8})T{3}.*" /> - <param name="extract_method" value="regex" /> + <param name="extract_method_cond|extract_method" value="regex" /> + <param name="extract_method_cond|filtered_out_bool" value="true"/> <param name="method" value="umis" /> <param name="knee_method" value="density"/> - <param name="prime3" value="true" /> - <param name="filtered_out_bool" value="true"/> + <output name="out_whitelist" file="out_wl_user.single.txt" /> <output name="out_thresh" file="out_wl_user.single.tresh.tab" /> <output name="out_html_report" file="out_wl_user.single.html" /> |