Mercurial > repos > devteam > lastz
changeset 7:86f2c3695694 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 8c6730485b00a47419ebe86278e4bd669377e3e2"
| author | iuc |
|---|---|
| date | Sat, 27 Nov 2021 10:40:44 +0000 |
| parents | ac0ffffa649e |
| children | da6f44d06921 |
| files | lastz.xml lastz_d.xml lastz_macros.xml |
| diffstat | 3 files changed, 20 insertions(+), 13 deletions(-) [+] |
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--- a/lastz.xml Tue Aug 31 09:15:32 2021 +0000 +++ b/lastz.xml Sat Nov 27 10:40:44 2021 +0000 @@ -1,17 +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> - <expand macro="bio_tools"/> <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: @@ -292,7 +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> @@ -646,6 +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" />
--- a/lastz_d.xml Tue Aug 31 09:15:32 2021 +0000 +++ b/lastz_d.xml Sat Nov 27 10:40:44 2021 +0000 @@ -1,12 +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> - <expand macro="bio_tools"/> <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
--- a/lastz_macros.xml Tue Aug 31 09:15:32 2021 +0000 +++ b/lastz_macros.xml Sat Nov 27 10:40:44 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'):