| Previous changeset 12:48d39ee9eb30 (2026-01-22) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 |
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modified:
lastz.xml lastz_d.xml lastz_macros.xml |
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added:
test-data/test7.out test-data/test7.png test-data/test8.bam |
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| diff -r 48d39ee9eb30 -r bf107d23242b lastz.xml --- a/lastz.xml Thu Jan 22 18:28:16 2026 +0000 +++ b/lastz.xml Thu Feb 05 12:52:06 2026 +0000 |
| [ |
| b'@@ -1,15 +1,10 @@\n-<tool id="lastz_wrapper_2" name="LASTZ" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">\n- <description>: align long sequences</description>\n+<tool id="lastz_wrapper_2" name="LASTZ" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n+ <description>align long sequences</description>\n <macros>\n <import>lastz_macros.xml</import>\n </macros>\n <expand macro="bio_tools"/>\n- <requirements>\n- <requirement type="package" version="@TOOL_VERSION@">lastz</requirement>\n- <requirement type="package" version="1.14">samtools</requirement>\n- <requirement type="package" version="3.6.3">r-base</requirement>\n- <requirement type="package" version="1.0.8">bzip2</requirement>\n- </requirements>\n+ <expand macro="requirements"/>\n <command detect_errors="exit_code"><![CDATA[\n #if $lastz_32:\n lastz_32\n@@ -260,7 +255,7 @@\n #elif str( $output_format.out.format ) == "blastn":\n --format=BLASTN-\n #elif str( $output_format.out.format ) == "paf":\n- --format=PAF-\n+ --format=PAF\n #elif str( $output_format.out.format ) == "general_full":\n \'--format=general-:${output_format.out.fields}\'\n #elif str( $output_format.out.format ) == "differences":\n@@ -269,7 +264,7 @@\n --action:target=multiple\n $output_format.rplot\n #if str( $output_format.out.format ) == "bam":\n- | samtools sort -@\\${GALAXY_SLOTS:-2} -T "\\${TMPDIR:-.}" -O bam -o \'${output}\'\n+ | samtools sort --no-PG -l 0 -T "\\${TMPDIR:-.}" -O bam | samtools view --no-PG -O bam -@ \\${GALAXY_SLOTS:-1} -o \'${output}\'\n #else:\n > \'${output}\'\n #end if\n@@ -298,40 +293,40 @@\n </configfiles>\n <inputs>\n <expand macro="target_input"/>\n- <param name="query" format="fasta,fastq,fasta.gz,fastq.gz,fastq.bz2" type="data" label="Select QUERY sequence(s)" help="These are the sequences that you are aligning against TARGET"/>\n+ <param name="query" format="fasta,fastqsanger,fastqillumina,fasta.gz,fastq.gz,fastqsanger.gz,fastqillumina.gz,fastq.bz2,fastqsanger.bz2,fastqillumina.bz2" type="data" label="Select QUERY sequence(s)" help="These are the sequences that you are aligning against TARGET"/>\n <param name="lastz_32" type="boolean" checked="false" label="Use lastz_32" help="It is highly recommended to use lastz_32 instead of lastz if the reference genome size is greater than 2G"/>\n <section name="where_to_look" expanded="False" title="Where to look">\n- <param type="select" display="radio" label="which strand to search" argument="--strand" help="Search both strands or choose plus or minus">\n+ <param type="select" label="which strand to search" argument="--strand" help="Search both strands or choose plus or minus">\n <option value="--strand=both" selected="True">Both</option>\n <option value="--strand=plus">Plus</option>\n <option value="--strand=minus">Minus</option>\n </param>\n- <param type="boolean" display="radio" truevalue="--self" falsevalue="" checked="False" argument="--self" label="Perform a self-alignment: the target sequence is also the query." help="Computation is more efficient than it would be without this option, since only one of each mirror-image pair of alignment blocks is processed (the other, redundant one is skipped during processing, but re-created in the output). Also, the trivial self-alignment block along the main diagonal is omitted from the output. THIS OPTION CANNOT BE USED IF THE TARGET IS COMPRIZED OF MULTIPLE SEQUENCES"/>\n- <param type="boolean" display="radio" truevalue="--nomirror" falsevalue="" checked="False" label="Inhibit the re-creation of mirror-image alignments." argument="--nomirror" help="Output consists of only one copy of each meaningful alignment block in a self-alignment. This optio'..b'<param name="lastz_32" value="true" />\n+ <section name="where_to_look">\n+ <param name="strand" value="--strand=both" />\n+ </section>\n+ <section name="output_format">\n+ <conditional name="out">\n+ <param name="format" value="blastn" />\n+ </conditional>\n+ </section>\n <output name="output" value="test5.out" />\n </test>\n <test expect_num_outputs="1">\n- <param name="ref_source" value="history" />\n- <param name="target" ftype="fasta.gz" value="chrM_human.fa.gz" />\n- <param name="query" ftype="fastq" value="chrM_mouse.fq" />\n- <param name="lastz_32" value="true" />\n- <param name="strand" value="--strand=both" />\n- <param name="format" value="blastn" />\n- <output name="output" value="test5.out" />\n+ <conditional name="source">\n+ <param name="ref_source" value="cached" />\n+ <param name="target_2bit" value="phiX174" />\n+ </conditional>\n+ <param name="query" value="phiX_split.fasta" />\n+ <section name="where_to_look">\n+ <param name="strand" value="--strand=both" />\n+ </section>\n+ <section name="output_format">\n+ <conditional name="out">\n+ <param name="format" value="differences" />\n+ </conditional>\n+ </section>\n+ <output name="output" value="test6.out" />\n+ </test>\n+ <test expect_num_outputs="2">\n+ <conditional name="source">\n+ <param name="ref_source" value="history" />\n+ <param name="target" ftype="fasta.gz" value="chrM_human.fa.gz" />\n+ </conditional>\n+ <param name="query" ftype="fastq.gz" value="chrM_mouse.fq.gz" />\n+ <section name="where_to_look">\n+ <param name="strand" value="--strand=both" />\n+ </section>\n+ <section name="output_format">\n+ <conditional name="out">\n+ <param name="format" value="paf" />\n+ </conditional>\n+ <param name="rplot" value="true"/>\n+ </section>\n+ <output name="output" value="test7.out" ftype="paf"/>\n+ <output name="out_plot" value="test7.png"/>\n </test>\n <test expect_num_outputs="1">\n- <param name="ref_source" value="cached" />\n- <param name="target_2bit" value="phiX174" />\n- <param name="query" value="phiX_split.fasta" />\n- <param name="strand" value="--strand=both" />\n- <param name="format" value="differences" />\n- <output name="output" value="test6.out" />\n+ <conditional name="source">\n+ <param name="ref_source" value="history" />\n+ <param name="target" ftype="fasta.gz" value="chrM_human.fa.gz" />\n+ </conditional>\n+ <param name="query" ftype="fastq.gz" value="chrM_mouse.fq.gz" />\n+ <section name="where_to_look">\n+ <param name="strand" value="--strand=both" />\n+ </section>\n+ <section name="output_format">\n+ <conditional name="out">\n+ <param name="format" value="bam" />\n+ </conditional>\n+ </section>\n+ <output name="output" value="test8.bam" ftype="bam"/>\n </test>\n </tests>\n \n@@ -737,7 +832,7 @@\n \n **Substitution matrix**\n \n-By default the HOXD70 substitution scores are used (from `Chiaromonte et al. 2002 <https://www.ncbi.nlm.nih.gov/pubmed/11928468>`_)::\n+By default the HOXD70 substitution scores are used (from `Chiaromonte et al. 2002 <https://doi.org/10.1142/9789812799623_0012>`_)::\n \n bad_score = X:-1000 # used for sub[\'X\'][*] and sub[*][\'X\']\n fill_score = -100 # used when sub[*][*] is not defined\n' |
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| diff -r 48d39ee9eb30 -r bf107d23242b lastz_d.xml --- a/lastz_d.xml Thu Jan 22 18:28:16 2026 +0000 +++ b/lastz_d.xml Thu Feb 05 12:52:06 2026 +0000 |
| [ |
| @@ -1,13 +1,10 @@ -<tool id="lastz_d_wrapper" name="LASTZ_D" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> - <description>: estimate substitution scores matrix</description> +<tool id="lastz_d_wrapper" name="LASTZ_D" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>estimate substitution scores matrix</description> <macros> <import>lastz_macros.xml</import> </macros> <expand macro="bio_tools"/> - <requirements> - <requirement type="package" version="@TOOL_VERSION@">lastz</requirement> - <requirement type="package" version="1.0.8">bzip2</requirement> - </requirements> + <expand macro="requirements"/> <command detect_errors="exit_code"><