| Previous changeset 7:a07a2d9ddd42 (2021-11-27) Next changeset 9:396cc0c65700 (2024-06-10) |
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Commit message:
planemo upload for repository https://github.com/davebx/bioext-gx/ commit 473fd4bfc9bc6dc149978013545525529978b988 |
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modified:
bealign.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 a07a2d9ddd42 -r 8a7462c0ac14 bealign.xml --- a/bealign.xml Sat Nov 27 10:07:57 2021 +0000 +++ b/bealign.xml Sun Feb 25 19:30:06 2024 +0000 |
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| @@ -1,13 +1,11 @@ -<?xml version="1.0"?> <tool id="bioext_bealign" name="Align sequences" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>to a reference using a codon alignment algorithm</description> <macros> <import>macros.xml</import> - <token name="@VERSION_SUFFIX@">0</token> </macros> <expand macro="requirements"> - <requirement type="package" version="5.1.0">gawk</requirement> - <requirement type="package" version="1.14">samtools</requirement> + <requirement type="package" version="5.3.0">gawk</requirement> + <requirement type="package" version="1.19.2">samtools</requirement> </expand> <version_command>bealign --version</version_command> <command detect_errors="exit_code"> @@ -143,7 +141,7 @@ <option value="dna">DNA</option> <option value="amino">Amino acids</option> </param> - <param name="score_matrix" argument="--score-matrix" type="select" label="Parametrize using score matrix"> + <param argument="--score-matrix" type="select" label="Parametrize using score matrix"> <option value="BLOSUM62" selected="True">Blocks substitution</option> <option value="DNA65">DNA, 65% expected identity</option> <option value="DNA70">DNA, 70% expected identity</option> @@ -155,8 +153,8 @@ <option value="HIV_BETWEEN_F">HIV between+F</option> </param> <param argument="--discard" type="boolean" checked="False" truevalue="--discard" falsevalue="" label="Output discarded sequences to a separate dataset" /> - <param name="reverse_complement" argument="--reverse-complement" type="boolean" checked="False" truevalue="--reverse-complement" falsevalue="" label="Also try to align against reverse complement of reference" /> - <param name="keep_reference" argument="--keep-reference" type="boolean" checked="False" truevalue="--keep-reference" falsevalue="" label="Include reference as first sequence in aligned BAM" /> + <param argument="--reverse-complement" type="boolean" checked="False" truevalue="--reverse-complement" falsevalue="" label="Also try to align against reverse complement of reference" /> + <param argument="--keep-reference" type="boolean" checked="False" truevalue="--keep-reference" falsevalue="" label="Include reference as first sequence in aligned BAM" /> </section> </inputs> <outputs> @@ -165,21 +163,21 @@ <filter>background_source['sequences']</filter> </data> <data name="saved_reference" format="fasta" label="${tool.name} on ${on_string} - Reference" > - <filter>select_reference['save_reference']</filter> + <filter>select_reference['reference_type'] == 'preset' and select_reference['save_reference']</filter> </data> <data name="discarded_reads" format="fasta"> <filter>advanced['discard']</filter> </data> </outputs> <tests> - <test> + <test expect_num_outputs="1"> <param name="input" ftype="fasta" value="query.fa" /> <param name="reference_type" value="dataset" /> <param name="score_matrix" value="HIV_BETWEEN_F" /> <param name="reference" ftype="fasta" value="reference.fa" /> <output name="output" file="bealign-out1.bam" ftype="bam" lines_diff="2" /> </test> - <test> + <test expect_num_outputs="1"> <param name="input" ftype="fasta" value="query.fa" /> <param name="reference_type" value="preset" /> <param name="reference" value="CoV2-nsp8" /> |
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| diff -r a07a2d9ddd42 -r 8a7462c0ac14 macros.xml --- a/macros.xml Sat Nov 27 10:07:57 2021 +0000 +++ b/macros.xml Sun Feb 25 19:30:06 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 a07a2d9ddd42 -r 8a7462c0ac14 test-data/bealign-out1.bam |
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| diff -r a07a2d9ddd42 -r 8a7462c0ac14 test-data/bealign-out2.bam |
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| diff -r a07a2d9ddd42 -r 8a7462c0ac14 test-data/bealign-out3-background.bam |
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| diff -r a07a2d9ddd42 -r 8a7462c0ac14 test-data/bealign-out4.bam |
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