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comparison lastz.xml @ 10:3e1ea2facca6 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 8c6730485b00a47419ebe86278e4bd669377e3e2"
author iuc
date Sat, 27 Nov 2021 10:41:24 +0000
parents 2ff111fac1d7
children 37b497aa133f
comparison
equal deleted inserted replaced
9:2ff111fac1d7 10:3e1ea2facca6
1 <tool id="lastz_wrapper_2" name="LASTZ" version="1.3.3"> 1 <tool id="lastz_wrapper_2" name="LASTZ" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>: align long sequences</description> 2 <description>: align long sequences</description>
3 <macros> 3 <macros>
4 <import>lastz_macros.xml</import> 4 <import>lastz_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="bio_tools"/>
6 <requirements> 7 <requirements>
7 <requirement type="package" version="@LASTZ_CONDA_VERSION@">lastz</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">lastz</requirement>
8 <requirement type="package" version="1.7">samtools</requirement> 9 <requirement type="package" version="1.14">samtools</requirement>
9 <requirement type="package" version="3.4.2">r-base</requirement> 10 <requirement type="package" version="3.6.3">r-base</requirement>
10 <requirement type="package" version="1.0.6">bzip2</requirement> 11 <requirement type="package" version="1.0.8">bzip2</requirement>
11 </requirements> 12 </requirements>
12 <command detect_errors="exit_code"><![CDATA[ 13 <command detect_errors="exit_code"><![CDATA[
13 lastz 14 #if $lastz_32:
15 lastz_32
16 #else:
17 lastz
18 #end if
19
14 @TARGET_INPUT_COMMAND_LINE@ 20 @TARGET_INPUT_COMMAND_LINE@
15 ## If --self is set: perform self alignment and ignore the query 21 ## If --self is set: perform self alignment and ignore the query
16 #if $where_to_look.self: 22 #if $where_to_look.self:
17 '${where_to_look.self}' 23 '${where_to_look.self}'
18 #if $where_to_look.nomirror 24 #if $where_to_look.nomirror
289 </configfile> 295 </configfile>
290 </configfiles> 296 </configfiles>
291 <inputs> 297 <inputs>
292 <expand macro="target_input"/> 298 <expand macro="target_input"/>
293 <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"/> 299 <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"/>
294 300 <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"/>
295 <section name="where_to_look" expanded="False" title="Where to look"> 301 <section name="where_to_look" expanded="False" title="Where to look">
296 <param name="strand" type="select" display="radio" label="which strand to search" argument="--strand" help="Search both strands or choose plus or minus"> 302 <param name="strand" type="select" display="radio" label="which strand to search" argument="--strand" help="Search both strands or choose plus or minus">
297 <option value="--strand=both" selected="True">Both</option> 303 <option value="--strand=both" selected="True">Both</option>
298 <option value="--strand=plus">Plus</option> 304 <option value="--strand=plus">Plus</option>
299 <option value="--strand=minus">Minus</option> 305 <option value="--strand=minus">Minus</option>
643 </test> 649 </test>
644 <test> 650 <test>
645 <param name="ref_source" value="history" /> 651 <param name="ref_source" value="history" />
646 <param name="target" ftype="fasta.gz" value="chrM_human.fa.gz" /> 652 <param name="target" ftype="fasta.gz" value="chrM_human.fa.gz" />
647 <param name="query" ftype="fastq" value="chrM_mouse.fq" /> 653 <param name="query" ftype="fastq" value="chrM_mouse.fq" />
654 <param name="lastz_32" value="true" />
648 <param name="strand" value="--strand=both" /> 655 <param name="strand" value="--strand=both" />
649 <param name="format" value="blastn" /> 656 <param name="format" value="blastn" />
650 <output name="output" value="test5.out" /> 657 <output name="output" value="test5.out" />
651 </test> 658 </test>
652 <test> 659 <test>