Mercurial > repos > iuc > bioext_bam2msa
changeset 8:27673f5b5343 draft default tip
planemo upload for repository https://github.com/davebx/bioext-gx/ commit 473fd4bfc9bc6dc149978013545525529978b988
| author | iuc |
|---|---|
| date | Sun, 25 Feb 2024 19:30:19 +0000 |
| parents | 359e043a285c |
| children | |
| files | 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 |
| diffstat | 7 files changed, 7 insertions(+), 6 deletions(-) [+] |
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--- a/bam2msa.xml Mon Nov 08 11:40:50 2021 +0000 +++ b/bam2msa.xml Sun Feb 25 19:30:19 2024 +0000 @@ -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"/>
--- a/macros.xml Mon Nov 08 11:40:50 2021 +0000 +++ b/macros.xml Sun Feb 25 19:30:19 2024 +0000 @@ -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>