| Previous changeset 9:2ff111fac1d7 (2021-04-02) Next changeset 11:37b497aa133f (2023-07-02) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 8c6730485b00a47419ebe86278e4bd669377e3e2" |
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modified:
lastz.xml lastz_d.xml lastz_macros.xml |
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| diff -r 2ff111fac1d7 -r 3e1ea2facca6 lastz.xml --- a/lastz.xml Fri Apr 02 17:18:40 2021 +0000 +++ b/lastz.xml Sat Nov 27 10:41:24 2021 +0000 |
| [ |
| @@ -1,16 +1,22 @@ -<tool id="lastz_wrapper_2" name="LASTZ" version="1.3.3"> +<tool id="lastz_wrapper_2" name="LASTZ" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>: align long sequences</description> <macros> <import>lastz_macros.xml</import> </macros> + <expand macro="bio_tools"/> <requirements> - <requirement type="package" version="@LASTZ_CONDA_VERSION@">lastz</requirement> - <requirement type="package" version="1.7">samtools</requirement> - <requirement type="package" version="3.4.2">r-base</requirement> - <requirement type="package" version="1.0.6">bzip2</requirement> + <requirement type="package" version="@TOOL_VERSION@">lastz</requirement> + <requirement type="package" version="1.14">samtools</requirement> + <requirement type="package" version="3.6.3">r-base</requirement> + <requirement type="package" version="1.0.8">bzip2</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ - lastz + #if $lastz_32: + lastz_32 + #else: + lastz + #end if + @TARGET_INPUT_COMMAND_LINE@ ## If --self is set: perform self alignment and ignore the query #if $where_to_look.self: @@ -291,7 +297,7 @@ <inputs> <expand macro="target_input"/> <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"/> - + <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"/> <section name="where_to_look" expanded="False" title="Where to look"> <param name="strand" type="select" display="radio" label="which strand to search" argument="--strand" help="Search both strands or choose plus or minus"> <option value="--strand=both" selected="True">Both</option> @@ -645,6 +651,7 @@ <param name="ref_source" value="history" /> <param name="target" ftype="fasta.gz" value="chrM_human.fa.gz" /> <param name="query" ftype="fastq" value="chrM_mouse.fq" /> + <param name="lastz_32" value="true" /> <param name="strand" value="--strand=both" /> <param name="format" value="blastn" /> <output name="output" value="test5.out" /> |
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| diff -r 2ff111fac1d7 -r 3e1ea2facca6 lastz_d.xml --- a/lastz_d.xml Fri Apr 02 17:18:40 2021 +0000 +++ b/lastz_d.xml Sat Nov 27 10:41:24 2021 +0000 |
| [ |
| @@ -1,11 +1,12 @@ -<tool id="lastz_d_wrapper" name="LASTZ_D" version="1.3.2"> +<tool id="lastz_d_wrapper" name="LASTZ_D" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>: estimate substitution scores matrix</description> <macros> <import>lastz_macros.xml</import> </macros> + <expand macro="bio_tools"/> <requirements> - <requirement type="package" version="@LASTZ_CONDA_VERSION@">lastz</requirement> - <requirement type="package" version="1.0.6">bzip2</requirement> + <requirement type="package" version="@TOOL_VERSION@">lastz</requirement> + <requirement type="package" version="1.0.8">bzip2</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ lastz_D |
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| diff -r 2ff111fac1d7 -r 3e1ea2facca6 lastz_macros.xml --- a/lastz_macros.xml Fri Apr 02 17:18:40 2021 +0000 +++ b/lastz_macros.xml Sat Nov 27 10:41:24 2021 +0000 |
| [ |
| @@ -1,5 +1,6 @@ <macros> - <token name="@LASTZ_CONDA_VERSION@">1.0.4</token> + <token name="@TOOL_VERSION@">1.04.15</token> + <token name="@VERSION_SUFFIX@">0</token> <token name="@TARGET_INPUT_COMMAND_LINE@"><![CDATA[ #if $source.ref_source=="history": #if $source.target.is_of_type('fasta.gz'): @@ -22,6 +23,11 @@ #end if ]]> </token> + <xml name="bio_tools"> + <xrefs> + <xref type="bio.tools">lastz</xref> + </xrefs> + </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"> |