Previous changeset 7:359e043a285c (2021-11-08) Next changeset 9:7ecb45126cd2 (2024-06-10) |
Commit message:
planemo upload for repository https://github.com/davebx/bioext-gx/ commit 473fd4bfc9bc6dc149978013545525529978b988 |
modified:
bam2msa.xml macros.xml test-data/bealign-out1.bam test-data/bealign-out2.bam test-data/bealign-out3-background.bam test-data/bealign-out3.bam test-data/bealign-out4.bam |
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diff -r 359e043a285c -r 27673f5b5343 bam2msa.xml --- a/bam2msa.xml Mon Nov 08 11:40:50 2021 +0000 +++ b/bam2msa.xml Sun Feb 25 19:30:19 2024 +0000 |
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@@ -3,18 +3,18 @@ <description>to FASTA multiple sequence alignment</description> <macros> <import>macros.xml</import> - <token name="@VERSION_SUFFIX@">0</token> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ ## avoid bam2msa to create .bai in inputdir - ln -s '$input' input_bam && - ln -s '$input.metadata.bam_index' input_bam.bai && + ln -sf '$input' input_bam && + ln -sf '$input.metadata.bam_index' input_bam.bai && bam2msa #if $region_start and $region_end: -r $region_start:$region_end #end if - 'input_bam' '$output' + 'input_bam' + '$output' ]]></command> <inputs> <param name="input" type="data" format="bam,sam" label="Input BAM file"/> |
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diff -r 359e043a285c -r 27673f5b5343 macros.xml --- a/macros.xml Mon Nov 08 11:40:50 2021 +0000 +++ b/macros.xml Sun Feb 25 19:30:19 2024 +0000 |
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@@ -1,7 +1,8 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">0.20.4</token> - <token name="@PROFILE@">20.05</token> + <token name="@TOOL_VERSION@">0.21.2</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">22.05</token> <token name="@SANITIZE@"><![CDATA[| gawk '{ if (\$0 ~ "^[^>]") {a = gensub(/[^ACGTURYKMSWBDHVNacgturykmswbdhvn?-]/, "", "g"); } else {a=gensub(/[^>A-Za-z0-9_]/, "_", "g"); }; print a } ' | sed 's,_\\+,_,g' >]]></token> <xml name="requirements"> <requirements> |
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diff -r 359e043a285c -r 27673f5b5343 test-data/bealign-out1.bam |
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diff -r 359e043a285c -r 27673f5b5343 test-data/bealign-out2.bam |
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diff -r 359e043a285c -r 27673f5b5343 test-data/bealign-out3-background.bam |
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diff -r 359e043a285c -r 27673f5b5343 test-data/bealign-out3.bam |
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diff -r 359e043a285c -r 27673f5b5343 test-data/bealign-out4.bam |
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