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comparison lasttrain.xml @ 4:8705e0d74a0f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 6b601baaf89634bc8d110ea06e3e64c7a585f3ba"
author iuc
date Wed, 24 Mar 2021 22:36:50 +0000
parents 3de2195f32c0
children 19c265784f35
comparison
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3:3de2195f32c0 4:8705e0d74a0f
1 <tool id="last_train" name="LAST-train" version="@LAST_CONDA_VERSION@+galaxy2" profile="18.01"> 1 <tool id="last_train" name="LAST-train" version="@LAST_CONDA_VERSION@+galaxy0" profile="20.01">
2 2
3 <description>finds the rates (probabilities) of insertion, deletion, and substitutions between two sets of sequences.</description> 3 <description>finds the rates (probabilities) of insertion, deletion, and substitutions between two sets of sequences.</description>
4 4
5 <macros> 5 <macros>
6 <import>macros_last.xml</import> 6 <import>macros_last.xml</import>
9 <requirements> 9 <requirements>
10 <requirement type="package" version="@LAST_CONDA_VERSION@">last</requirement> 10 <requirement type="package" version="@LAST_CONDA_VERSION@">last</requirement>
11 </requirements> 11 </requirements>
12 12
13 <command detect_errors="exit_code"><![CDATA[ 13 <command detect_errors="exit_code"><![CDATA[
14 set -e -o pipefail;
14 #if $db_opts.db_opts_input == 'lastdb' 15 #if $db_opts.db_opts_input == 'lastdb'
15 ln -s '$db_opts.lastdatabase.extra_files_path' './db_files' && 16 ln -s '$db_opts.lastdatabase.extra_files_path' './db_files' &&
16 #end if 17 #end if
17 18 #if $query_fasta.ext.endswith('.gz')
18 last-train 19 zcat
20 #else
21 cat
22 #end if
23 '$query_fasta' | last-train
19 24
20 -Q $init_options.Q 25 -Q $init_options.Q
21 -r $init_options.r 26 -r $init_options.r
22 -q $init_options.q 27 -q $init_options.q
23 -a $init_options.cost_opt.a 28 -a $init_options.cost_opt.a
41 '${"' '".join(str($db_opts.database.fields.path).split(","))}' 46 '${"' '".join(str($db_opts.database.fields.path).split(","))}'
42 #else if $db_opts.db_opts_input == 'lastdb' 47 #else if $db_opts.db_opts_input == 'lastdb'
43 'db_files/lastdb' 48 'db_files/lastdb'
44 #end if 49 #end if
45 50
46 '$query_fasta'
47
48 >'$outfile' 51 >'$outfile'
49 52
50 ]]></command> 53 ]]></command>
51 54
52 <inputs> 55 <inputs>
53 <expand macro="input_db" /> 56 <expand macro="input_db" />
54 <param name="query_fasta" type="data" format="fasta,fastqsanger" label="Queries input files" /> 57 <param name="query_fasta" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" label="Queries input files" />
55 <conditional name="init_options"> 58 <conditional name="init_options">
56 <param argument="-Q" type="select" multiple="false" label="Query input format"> 59 <param argument="-Q" type="select" multiple="false" label="Query input format">
57 <option value="0" selected="true">FASTA</option> 60 <option value="0" selected="true">FASTA</option>
58 <option value="1">Fastq-sanger</option> 61 <option value="1">Fastq-sanger</option>
59 </param> 62 </param>
113 <section name="last_train_opt"> 116 <section name="last_train_opt">
114 <section name="align_opt"> 117 <section name="align_opt">
115 <param name="E" value="10"/> 118 <param name="E" value="10"/>
116 </section> 119 </section>
117 </section> 120 </section>
118 <param name="query_fasta" value="fuguMito.fa"/> 121 <param name="query_fasta" value="fuguMito.fa.gz" ftype="fasta.gz"/>
119 <output name="outfile" file="last_train_E.txt" ftype="txt" lines_diff="22"/> 122 <output name="outfile" file="last_train_E.txt" ftype="txt" lines_diff="28"/>
120 </test> 123 </test>
121 <test> 124 <test>
122 <conditional name="db_opts"> 125 <conditional name="db_opts">
123 <param name="db_opts_input" value="db"/> 126 <param name="db_opts_input" value="db"/>
124 <param name="database" value="humdb"/> 127 <param name="database" value="humdb"/>
125 </conditional> 128 </conditional>
126 <param name="query_fasta" value="fuguMito.fa"/> 129 <param name="query_fasta" value="fuguMito.fq.gz" ftype="fastqsanger.gz"/>
127 <output name="outfile" file="last_train.txt" ftype="txt" lines_diff="22"/> 130 <output name="outfile" file="last_train.txt" ftype="txt" lines_diff="22"/>
128 </test> 131 </test>
129 </tests> 132 </tests>
130 133
131 <help>@LAST_HELP@</help> 134 <help>@LAST_HELP@</help>