| Previous changeset 17:9cd1c2f5d90e (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_dedup.xml |
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| diff -r 9cd1c2f5d90e -r 6ec3233f30a6 macros.xml --- a/macros.xml Wed Jan 29 10:09:34 2025 +0000 +++ b/macros.xml Fri Feb 28 20:41:43 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 9cd1c2f5d90e -r 6ec3233f30a6 test-data/dedup_out1.bam |
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| Binary file test-data/dedup_out1.bam has changed |
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| diff -r 9cd1c2f5d90e -r 6ec3233f30a6 test-data/dedup_out2.bam |
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| Binary file test-data/dedup_out2.bam has changed |
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| diff -r 9cd1c2f5d90e -r 6ec3233f30a6 test-data/dedup_out3.bam |
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| Binary file test-data/dedup_out3.bam has changed |
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| diff -r 9cd1c2f5d90e -r 6ec3233f30a6 test-data/dedup_out4.bam |
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| Binary file test-data/dedup_out4.bam has changed |
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| diff -r 9cd1c2f5d90e -r 6ec3233f30a6 test-data/dedup_out5.bam |
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| Binary file test-data/dedup_out5.bam has changed |
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| diff -r 9cd1c2f5d90e -r 6ec3233f30a6 test-data/dedup_out6.bam |
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| Binary file test-data/dedup_out6.bam has changed |
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| diff -r 9cd1c2f5d90e -r 6ec3233f30a6 umi-tools_dedup.xml --- a/umi-tools_dedup.xml Wed Jan 29 10:09:34 2025 +0000 +++ b/umi-tools_dedup.xml Fri Feb 28 20:41:43 2025 +0000 |
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| @@ -4,9 +4,7 @@ <import>macros.xml</import> </macros> <expand macro="bio_tools"/> - <expand macro="requirements"> - <requirement type="package" version="1.21">samtools</requirement> - </expand> + <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ @LINK_SAM_BAM_INPUT@ @@ -111,12 +109,12 @@ <output name="output" file="dedup_out4.bam" ftype="bam" lines_diff="2"/> </test> <test expect_num_outputs="1"> - <param name="input" value="group_in5.bam" ftype="bam" /> + <param name="input" value="group_in4.bam" ftype="bam" /> <section name="advanced"> <param name="random_seed" value="0" /> </section> <conditional name="bc"> - <param name="extract_umi_method" value="read_id" /> + <param name="extract_umi_method" value="tag" /> <param name="umi_tag" value="BX" /> </conditional> <section name="umi"> @@ -125,12 +123,12 @@ <output name="output" file="dedup_out5.bam" ftype="bam" lines_diff="2"/> </test> <test expect_num_outputs="1"> - <param name="input" value="group_in6.bam" ftype="bam" /> + <param name="input" value="group_in4.bam" ftype="bam" /> <section name="advanced"> <param name="random_seed" value="0" /> </section> <conditional name="bc"> - <param name="extract_umi_method" value="read_id" /> + <param name="extract_umi_method" value="tag" /> <param name="umi_tag" value="BX" /> </conditional> <section name="umi"> @@ -139,12 +137,12 @@ <output name="output" file="dedup_out6.bam" ftype="bam" lines_diff="2"/> </test> <test expect_num_outputs="5"> - <param name="input" value="group_in6.bam" ftype="bam" /> + <param name="input" value="group_in4.bam" ftype="bam" /> <section name="advanced"> <param name="random_seed" value="0" /> </section> <conditional name="bc"> - <param name="extract_umi_method" value="read_id" /> + <param name="extract_umi_method" value="tag" /> <param name="umi_tag" value="BX" /> </conditional> <section name="umi"> |