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comparison lastz.xml @ 7:10aca14c2332 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
author iuc
date Thu, 17 May 2018 04:29:13 -0400
parents b6d7308c3728
children e7f19d6a9af8
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6:b6d7308c3728 7:10aca14c2332
1 <tool id="lastz_wrapper_2" name="LASTZ" version="1.3"> 1 <tool id="lastz_wrapper_2" name="LASTZ" version="1.3.1">
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 <requirements> 6 <requirements>
7 <requirement type="package" version="@LASTZ_CONDA_VERSION@">lastz</requirement> 7 <requirement type="package" version="@LASTZ_CONDA_VERSION@">lastz</requirement>
8 <requirement type="package" version="1.7">samtools</requirement> 8 <requirement type="package" version="1.7">samtools</requirement>
9 <requirement type="package" version="3.4.2">r-base</requirement> 9 <requirement type="package" version="3.4.2">r-base</requirement>
10 <requirement type="package" version="1.0.6">bzip2</requirement>
10 </requirements> 11 </requirements>
11 <command detect_errors="exit_code"><![CDATA[ 12 <command detect_errors="exit_code"><![CDATA[
12 lastz 13 lastz
13 @TARGET_INPUT_COMMAND_LINE@ 14 @TARGET_INPUT_COMMAND_LINE@
14 ## If --self is set: perform self alignment and ignore the query 15 ## If --self is set: perform self alignment and ignore the query
16 '${where_to_look.self}' 17 '${where_to_look.self}'
17 #if $where_to_look.nomirror 18 #if $where_to_look.nomirror
18 '${where_to_look.nomirror}' 19 '${where_to_look.nomirror}'
19 #end if 20 #end if
20 #else: 21 #else:
21 '${query}' 22 @query_input@
22 #end if 23 #end if
23 24
24 ## WHERE TO LOOK -------------------------------- 25 ## WHERE TO LOOK --------------------------------
25 26
26 '${where_to_look.strand}' 27 '${where_to_look.strand}'
277 ]]> 278 ]]>
278 </configfile> 279 </configfile>
279 </configfiles> 280 </configfiles>
280 <inputs> 281 <inputs>
281 <expand macro="target_input"/> 282 <expand macro="target_input"/>
282 <param name="query" format="fasta,fastq" type="data" label="Select QUERY sequence(s)" help="These are the sequences that you are aligning against TARGET"/> 283 <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"/>
283 284
284 <section name="where_to_look" expanded="False" title="Where to look"> 285 <section name="where_to_look" expanded="False" title="Where to look">
285 <param name="strand" type="select" display="radio" label="which strand to search" argument="--strand" help="Search both strands or choose plus or minus"> 286 <param name="strand" type="select" display="radio" label="which strand to search" argument="--strand" help="Search both strands or choose plus or minus">
286 <option value="--strand=both" selected="True">Both</option> 287 <option value="--strand=both" selected="True">Both</option>
287 <option value="--strand=plus">Plus</option> 288 <option value="--strand=plus">Plus</option>
594 <param name="strand" value="--strand=both" /> 595 <param name="strand" value="--strand=both" />
595 <param name="score_file" value="score_file.txt" /> 596 <param name="score_file" value="score_file.txt" />
596 <param name="format" value="general_def" /> 597 <param name="format" value="general_def" />
597 <output name="output" value="test3.out" /> 598 <output name="output" value="test3.out" />
598 </test> 599 </test>
600 <test>
601 <param name="ref_source" value="history" />
602 <param name="target" value="chrM_mouse.fa.gz" />
603 <param name="query" value="chrM_human.fa.gz" />
604 <param name="strand" value="--strand=both" />
605 <param name="format" value="blastn" />
606 <output name="output" value="test4.out" />
607 </test>
608 <test>
609 <param name="ref_source" value="history" />
610 <param name="target" ftype="fasta.gz" value="chrM_human.fa.gz" />
611 <param name="query" ftype="fastq.bz2" value="chrM_mouse.fq.bz2" />
612 <param name="strand" value="--strand=both" />
613 <param name="format" value="blastn" />
614 <output name="output" value="test5.out" />
615 </test>
616 <test>
617 <param name="ref_source" value="history" />
618 <param name="target" ftype="fasta.gz" value="chrM_human.fa.gz" />
619 <param name="query" ftype="fastq.gz" value="chrM_mouse.fq.gz" />
620 <param name="strand" value="--strand=both" />
621 <param name="format" value="blastn" />
622 <output name="output" value="test5.out" />
623 </test>
624 <test>
625 <param name="ref_source" value="history" />
626 <param name="target" ftype="fasta.gz" value="chrM_human.fa.gz" />
627 <param name="query" ftype="fastq" value="chrM_mouse.fq" />
628 <param name="strand" value="--strand=both" />
629 <param name="format" value="blastn" />
630 <output name="output" value="test5.out" />
631 </test>
599 </tests> 632 </tests>
600 633
601 <help><![CDATA[ 634 <help><![CDATA[
602 635
603 **What is does** 636 **What is does**