| Previous changeset 10:3e1ea2facca6 (2021-11-27) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c |
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modified:
lastz.xml lastz_d.xml lastz_macros.xml |
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| diff -r 3e1ea2facca6 -r 37b497aa133f lastz.xml --- a/lastz.xml Sat Nov 27 10:41:24 2021 +0000 +++ b/lastz.xml Sun Jul 02 12:10:46 2023 +0000 |
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| b'@@ -297,15 +297,15 @@\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="lastz_32" type="boolean" checked="false" label="Use lastz_32" help="It is highly recommended to use lastz_32 instead of lastz if the refernece genome size is greater than 2G"/>\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 name="strand" type="select" display="radio" label="which strand to search" argument="--strand" help="Search both strands or choose plus or minus">\n+ <param type="select" display="radio" 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 name="self" 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 name="nomirror" 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 option is only applicable when the \xe2\x80\x91\xe2\x80\x91self option is used."/>\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 option is only applicable when the \xe2\x80\x91\xe2\x80\x91self option is used."/>\n <conditional name="qhsplimit">\n <param name="qhsplimit_selector" type="select" display="radio" label="Set HSP limit" argument="--queryhsplimit">\n <option value="yes">Yes</option>\n@@ -415,8 +415,8 @@\n </conditional>\n </section>\n <section name="hsp" expanded="false" title="HSPs (Gap-free extension)">\n- <param name="gfextend" type="boolean" truevalue="--gfextend" checked="false" argument="--gfextend" label="Perform gap-free extension of seeds to HSPs" help="This will take into account other papermeters in this section"/>\n- <param name="nogfextend" type="boolean" truevalue="--nogfextend" argument="--nogfextend" label="Skip the gap-free extension stage" help="Instead, pass the seeds al'..b'<test>\n+ <test expect_num_outputs="1">\n <param name="ref_source" value="history" />\n <param name="target" value="phiX_split.fasta" />\n <param name="query" value="phiX.fasta" />\n@@ -612,7 +612,7 @@\n <param name="format" value="general_def" />\n <output name="output" value="test2.out" />\n </test>\n- <test>\n+ <test expect_num_outputs="1">\n <param name="ref_source" value="history" />\n <param name="target" value="phiX_split.fasta" />\n <param name="query" value="phiX.fasta" />\n@@ -621,7 +621,7 @@\n <param name="format" value="general_def" />\n <output name="output" value="test3.out" />\n </test>\n- <test>\n+ <test expect_num_outputs="1">\n <param name="ref_source" value="history" />\n <param name="target" value="chrM_mouse.fa.gz" />\n <param name="query" value="chrM_human.fa.gz" />\n@@ -629,17 +629,15 @@\n <param name="format" value="blastn" />\n <output name="output" value="test4.out" />\n </test>\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.bz2" value="chrM_mouse.fq.bz2" />\n- <param name="traceback" value="83886080" />\n- <param name="word" value="28" />\n <param name="strand" value="--strand=both" />\n <param name="format" value="blastn" />\n <output name="output" value="test5.out" />\n </test>\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.gz" value="chrM_mouse.fq.gz" />\n@@ -647,7 +645,7 @@\n <param name="format" value="blastn" />\n <output name="output" value="test5.out" />\n </test>\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@@ -656,7 +654,7 @@\n <param name="format" value="blastn" />\n <output name="output" value="test5.out" />\n </test>\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@@ -674,11 +672,11 @@\n \n .. class:: infomark\n \n-**Read documentation** before proceeding. LASTZ is a complex tool with many parameter options. Fortunately, there is a `great manual <https://lastz.github.io/lastz/>`_ maintained by its author. Default parameters may be sufficient to obtain the initial idea about how similar your sequences are, but to produce reliable alignments you may need to tweak the parameters. So RTFM!\n+**Read documentation** before proceeding. LASTZ is a complex tool with many parameter options. Fortunately, there is a `great manual <https://lastz.github.io/lastz/>`_ maintained by its author. Default parameters may be sufficient to obtain the initial idea about how similar your sequences are, but to produce reliable alignments you may need to tweak the parameters. Read the manual.\n \n .. class:: warningmark\n \n-Galaxy version of LASTZ sets **--ambiguous=iupac** as default (see **Scoring** section). This prevents LASTZ from erroring out if one of the DNA inputrs contains "non-strandard" nucleotides. \n+Galaxy version of LASTZ sets **--ambiguous=iupac** as default (see **Scoring** section). This prevents LASTZ from erroring out if one of the DNA inputrs contains "non-standard" nucleotides.\n \n **About LASTZ parameters**\n \n' |
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| diff -r 3e1ea2facca6 -r 37b497aa133f lastz_d.xml --- a/lastz_d.xml Sat Nov 27 10:41:24 2021 +0000 +++ b/lastz_d.xml Sun Jul 02 12:10:46 2023 +0000 |
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| @@ -26,7 +26,7 @@ <param name="score_file" type="data" format="txt" optional="true" label="Control file for inference" argument="--inferonly[=control_file]" help="Optional controf file. If nothing is selected, LASTZ_D uses default described in the manual"/> </inputs> <outputs> - <data format="txt" name="output" label="${tool.name} on ${on_string}: substituion matrix"/> + <data format="txt" name="output" label="${tool.name} on ${on_string}: substitution matrix"/> </outputs> <tests> <test> |
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| diff -r 3e1ea2facca6 -r 37b497aa133f lastz_macros.xml --- a/lastz_macros.xml Sat Nov 27 10:41:24 2021 +0000 +++ b/lastz_macros.xml Sun Jul 02 12:10:46 2023 +0000 |
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| @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">1.04.15</token> + <token name="@TOOL_VERSION@">1.04.22</token> <token name="@VERSION_SUFFIX@">0</token> <token name="@TARGET_INPUT_COMMAND_LINE@"><![CDATA[ #if $source.ref_source=="history": @@ -30,7 +30,7 @@ </xml> <xml name="target_input"> <conditional name="source"> - <param name="ref_source" type="select" label="Select TARGET sequnce(s) to align against" help="If your TARGET is in history, choose 'from your history' option"> + <param name="ref_source" type="select" label="Select TARGET sequence(s) to align against" help="If your TARGET is in history, choose 'from your history' option"> <option value="cached">locally cached</option> <option value="history">from your history</option> </param> |