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comparison lastdb.xml @ 2:bf30030e5265 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit d48fa8fc8724e2a1c659dde00cad9d6db3e710db"
author iuc
date Thu, 10 Sep 2020 16:08:15 +0000
parents 86206f93fb13
children 8705e0d74a0f
comparison
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1:86206f93fb13 2:bf30030e5265
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 lastdb 14 lastdb
15 -Q $lastdb.Q 15
16 #if $input_files.ext == 'fasta'
17 -Q 0
18 #else if $input_files.ext == 'fastqsanger'
19 -Q 1
20 #else if $input_files.ext == 'fastqsolexa'
21 -Q 2
22 #else if $input_files.ext == 'fastqillumina'
23 -Q 3
24 #end if
16 $lastdb.sequences_type.protein 25 $lastdb.sequences_type.protein
17 -a $lastdb.sequences_type.a 26 -a $lastdb.sequences_type.a
18 -R $lastdb.repeats.uppercase$lastdb.repeats.simple_repeat 27 -R $lastdb.repeats.uppercase$lastdb.repeats.simple_repeat
19 $lastdb.repeats.sm_lower 28 $lastdb.repeats.sm_lower
20 -S $lastdb.lastdb_advanced.S 29 -S $lastdb.lastdb_advanced.S
30 '$input_files' 39 '$input_files'
31 40
32 && 41 &&
33 42
34 mkdir '$outfile.files_path' && 43 mkdir '$outfile.files_path' &&
35 mv lastdb.* '$outfile.files_path' 44 mv lastdb* '$outfile.files_path'
36 ]]></command> 45 ]]></command>
37 46
38 <inputs> 47 <inputs>
39 <param name="input_files" type="data" format="fasta,fastqsanger,fastqsolexa,fastqillumina" label="Reference(s) input files" /> 48 <param name="input_files" type="data" format="fasta,fastqsanger,fastqsolexa,fastqillumina" label="Reference(s) input files" />
40 <section name="lastdb" title="Lastdb arguments" expanded="true"> 49 <section name="lastdb" title="Lastdb arguments" expanded="true">
41 <param argument="-Q" type="select" multiple="false" label="Input format">
42 <option value="0" selected="true">FASTA</option>
43 <option value="1">fastq-sanger</option>
44 <option value="2">fastq-solexa</option>
45 <option value="3">fastq-illumina</option>
46 </param>
47
48 <conditional name="sequences_type"> 50 <conditional name="sequences_type">
49 <param name="protein" type="select" multiple="false" label="The sequences are :"> 51 <param name="protein" type="select" multiple="false" label="The sequences are :">
50 <option value="" selected="true">DNA</option> 52 <option value="" selected="true">DNA</option>
51 <option value="-p">Proteins (-p)</option> 53 <option value="-p">Proteins (-p)</option>
52 </param> 54 </param>
165 <extra_files type="file" value="hedgdb.ssp" name="lastdb.ssp" compare="sim_size" delta="1"/> 167 <extra_files type="file" value="hedgdb.ssp" name="lastdb.ssp" compare="sim_size" delta="1"/>
166 <extra_files type="file" value="hedgdb.suf" name="lastdb.suf" compare="sim_size" delta="1"/> 168 <extra_files type="file" value="hedgdb.suf" name="lastdb.suf" compare="sim_size" delta="1"/>
167 <extra_files type="file" value="hedgdb.tis" name="lastdb.tis" compare="sim_size" delta="1"/> 169 <extra_files type="file" value="hedgdb.tis" name="lastdb.tis" compare="sim_size" delta="1"/>
168 </output> 170 </output>
169 </test> 171 </test>
172 <test>
173 <param name="input_files" value="humanMito.fq" ftype="fastqsanger"/>
174 <section name="lastdb">
175 <param name="Q" value="1"/>
176 <section name="repeats">
177 <param name="uppercase" value="0"/>
178 <param name="simple_repeat" value="1"/>
179 <param name="sm_lower" value="true"/>
180 </section>
181 </section>
182 <output name="outfile" compare="contains" file="hedgdb.lastdb" ftype="lastdb">
183 <extra_files type="file" value="humdb-sanger.bck" name="lastdb.bck" compare="sim_size" delta="1"/>
184 <extra_files type="file" value="humdb-sanger.des" name="lastdb.des"/>
185 <extra_files type="file" value="humdb-sanger.prj" name="lastdb.prj" lines_diff="1"/>
186 <extra_files type="file" value="humdb-sanger.sds" name="lastdb.sds"/>
187 <extra_files type="file" value="humdb-sanger.ssp" name="lastdb.ssp" compare="sim_size" delta="1"/>
188 <extra_files type="file" value="humdb-sanger.suf" name="lastdb.suf" compare="sim_size" delta="1"/>
189 <extra_files type="file" value="humdb-sanger.tis" name="lastdb.tis" compare="sim_size" delta="1"/>
190 </output>
191 </test>
170 </tests> 192 </tests>
171 193
172 <help>@LAST_HELP@</help> 194 <help>@LAST_HELP@</help>
173 <citations><expand macro="citations"/></citations> 195 <citations><expand macro="citations"/></citations>
174 </tool> 196 </tool>