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comparison lastdb.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 bf30030e5265
children f5a5a2b39ff2
comparison
equal deleted inserted replaced
3:3de2195f32c0 4:8705e0d74a0f
1 <tool id="last_db" name="LASTdb" version="@LAST_CONDA_VERSION@+galaxy1" profile="18.01"> 1 <tool id="last_db" name="LASTdb" version="@LAST_CONDA_VERSION@+galaxy0" profile="20.01">
2 2
3 <description>prepares sequences for subsequent comparison and alignment using lastal.</description> 3 <description>prepares sequences for subsequent comparison and alignment using lastal.</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 lastdb 14 set -e -o pipefail;
15 15
16 #if $input_files.ext == 'fasta' 16 #if $input_files.ext.endswith('.gz')
17 zcat
18 #else
19 cat
20 #end if
21 '$input_files' | lastdb
22
23 #if $input_files.ext.startswith('fasta')
17 -Q 0 24 -Q 0
18 #else if $input_files.ext == 'fastqsanger' 25 #else if $input_files.ext.startswith('fastqsanger')
19 -Q 1 26 -Q 1
20 #else if $input_files.ext == 'fastqsolexa' 27 #else if $input_files.ext.startswith('fastqsolexa')
21 -Q 2 28 -Q 2
22 #else if $input_files.ext == 'fastqillumina' 29 #else if $input_files.ext.startswith('fastqillumina')
23 -Q 3 30 -Q 3
24 #end if 31 #end if
25 $lastdb.sequences_type.protein 32 $lastdb.sequences_type.protein
26 -a $lastdb.sequences_type.a 33 -a $lastdb.sequences_type.a
27 -R $lastdb.repeats.uppercase$lastdb.repeats.simple_repeat 34 -R $lastdb.repeats.uppercase$lastdb.repeats.simple_repeat
28 $lastdb.repeats.sm_lower 35 $lastdb.repeats.sm_lower
29 -S $lastdb.lastdb_advanced.S 36 -S $lastdb.lastdb_advanced.S
30 -u $lastdb.lastdb_advanced.seeds.u 37 -u $lastdb.lastdb_advanced.seeds.u
31 -w $lastdb.lastdb_advanced.seeds.w 38 -w $lastdb.lastdb_advanced.seeds.w
32 -W $lastdb.lastdb_advanced.seeds.W 39 #if $lastdb.lastdb_advanced.seeds.W
40 -W $lastdb.lastdb_advanced.seeds.W
41 #end if
33 -m $lastdb.lastdb_advanced.seeds.m 42 -m $lastdb.lastdb_advanced.seeds.m
34 -i $lastdb.lastdb_advanced.i 43 -i $lastdb.lastdb_advanced.i
35 -C $lastdb.lastdb_advanced.C 44 -C $lastdb.lastdb_advanced.C
36 -s \${GALAXY_MEMORY_MB:-2G} 45 -s \${GALAXY_MEMORY_MB:-2G}
37 -P \${GALAXY_SLOTS:-1} 46 -P \${GALAXY_SLOTS:-1}
38 'lastdb' 47 'lastdb'
39 '$input_files' 48
40 49
41 && 50 &&
42 51
43 mkdir '$outfile.files_path' && 52 mkdir '$outfile.files_path' &&
44 mv lastdb* '$outfile.files_path' 53 mv lastdb* '$outfile.files_path'
45 ]]></command> 54 ]]></command>
46 55
47 <inputs> 56 <inputs>
48 <param name="input_files" type="data" format="fasta,fastqsanger,fastqsolexa,fastqillumina" label="Reference(s) input files" /> 57 <param name="input_files" type="data" format="fasta,fasta.gz,fastq,fastq.gz" label="Reference(s) input files" />
49 <section name="lastdb" title="Lastdb arguments" expanded="true"> 58 <section name="lastdb" title="Lastdb arguments" expanded="true">
50 <conditional name="sequences_type"> 59 <conditional name="sequences_type">
51 <param name="protein" type="select" multiple="false" label="The sequences are :"> 60 <param name="protein" type="select" multiple="false" label="The sequences are :">
52 <option value="" selected="true">DNA</option> 61 <option value="" selected="true">DNA</option>
53 <option value="-p">Proteins (-p)</option> 62 <option value="-p">Proteins (-p)</option>
79 <option value="1" selected="true">Forward</option> 88 <option value="1" selected="true">Forward</option>
80 <option value="2">Both</option> 89 <option value="2">Both</option>
81 </param> 90 </param>
82 91
83 <conditional name="seeds"> 92 <conditional name="seeds">
84 <param argument="-u" type="select" multiple="false" label="Specify a seeding scheme."> 93 <param argument="-u" type="select" multiple="false" optional="true" label="Specify a seeding scheme.">
85 <option value="BISF">BISF</option> 94 <option value="BISF">BISF</option>
86 <option value="BISR">BISR</option> 95 <option value="BISR">BISR</option>
87 <option value="MAM4">MAM4</option> 96 <option value="MAM4">MAM4</option>
88 <option value="MAM8">MAM8</option> 97 <option value="MAM8">MAM8</option>
89 <option value="MURPHY10">MURPHY10</option> 98 <option value="MURPHY10">MURPHY10</option>
132 </data> 141 </data>
133 </outputs> 142 </outputs>
134 143
135 <tests> 144 <tests>
136 <test> 145 <test>
137 <param name="input_files" value="humanMito.fa" ftype="fasta"/> 146 <param name="input_files" value="humanMito.fa.gz" ftype="fasta.gz"/>
138 <section name="lastdb"> 147 <section name="lastdb">
139 <section name="repeats"> 148 <section name="repeats">
140 <param name="uppercase" value="0"/> 149 <param name="uppercase" value="0"/>
141 <param name="simple_repeat" value="1"/> 150 <param name="simple_repeat" value="1"/>
142 <param name="sm_lower" value="true"/> 151 <param name="sm_lower" value="true"/>
143 </section> 152 </section>
144 </section> 153 </section>
145 <output name="outfile" compare="contains" file="humdb.lastdb" ftype="lastdb"> 154 <output name="outfile" compare="contains" file="humdb.lastdb" ftype="lastdb">
146 <extra_files type="file" value="humdb.bck" name="lastdb.bck" compare="sim_size" delta="1"/> 155 <extra_files type="file" value="humdb.bck" name="lastdb.bck" compare="sim_size" delta="1"/>
147 <extra_files type="file" value="humdb.des" name="lastdb.des"/> 156 <extra_files type="file" value="humdb.des" name="lastdb.des"/>
148 <extra_files type="file" value="humdb.prj" name="lastdb.prj"/> 157 <extra_files type="file" value="humdb.prj" name="lastdb.prj" compare="sim_size" delta="2"/>
149 <extra_files type="file" value="humdb.sds" name="lastdb.sds"/> 158 <extra_files type="file" value="humdb.sds" name="lastdb.sds"/>
150 <extra_files type="file" value="humdb.ssp" name="lastdb.ssp" compare="sim_size" delta="1"/> 159 <extra_files type="file" value="humdb.ssp" name="lastdb.ssp" compare="sim_size" delta="1"/>
151 <extra_files type="file" value="humdb.suf" name="lastdb.suf" compare="sim_size" delta="1"/> 160 <extra_files type="file" value="humdb.suf" name="lastdb.suf" compare="sim_size" delta="1"/>
152 <extra_files type="file" value="humdb.tis" name="lastdb.tis" compare="sim_size" delta="1"/> 161 <extra_files type="file" value="humdb.tis" name="lastdb.tis" compare="sim_size" delta="1"/>
153 </output> 162 </output>
157 <section name="lastdb"> 166 <section name="lastdb">
158 <conditional name="sequences_type"> 167 <conditional name="sequences_type">
159 <param name="protein" value="-p"/> 168 <param name="protein" value="-p"/>
160 </conditional> 169 </conditional>
161 </section> 170 </section>
171 <section name="lastdb_advanced">
172 <conditional name="seeds">
173 <param name="u" value="MURPHY10"/>
174 </section>
162 <output name="outfile" compare="contains" file="hedgdb.lastdb" ftype="lastdb"> 175 <output name="outfile" compare="contains" file="hedgdb.lastdb" ftype="lastdb">
163 <extra_files type="file" value="hedgdb.bck" name="lastdb.bck" compare="sim_size" delta="1"/> 176 <extra_files type="file" value="hedgdb.bck" name="lastdb.bck" compare="sim_size" delta="1"/>
164 <extra_files type="file" value="hedgdb.des" name="lastdb.des"/> 177 <extra_files type="file" value="hedgdb.des" name="lastdb.des"/>
165 <extra_files type="file" value="hedgdb.prj" name="lastdb.prj"/> 178 <extra_files type="file" value="hedgdb.prj" name="lastdb.prj"/>
166 <extra_files type="file" value="hedgdb.sds" name="lastdb.sds"/> 179 <extra_files type="file" value="hedgdb.sds" name="lastdb.sds"/>
168 <extra_files type="file" value="hedgdb.suf" name="lastdb.suf" compare="sim_size" delta="1"/> 181 <extra_files type="file" value="hedgdb.suf" name="lastdb.suf" compare="sim_size" delta="1"/>
169 <extra_files type="file" value="hedgdb.tis" name="lastdb.tis" compare="sim_size" delta="1"/> 182 <extra_files type="file" value="hedgdb.tis" name="lastdb.tis" compare="sim_size" delta="1"/>
170 </output> 183 </output>
171 </test> 184 </test>
172 <test> 185 <test>
173 <param name="input_files" value="humanMito.fq" ftype="fastqsanger"/> 186 <param name="input_files" value="humanMito.fq.gz" ftype="fastqsanger.gz"/>
174 <section name="lastdb"> 187 <section name="lastdb">
175 <param name="Q" value="1"/> 188 <param name="Q" value="1"/>
176 <section name="repeats"> 189 <section name="repeats">
177 <param name="uppercase" value="0"/> 190 <param name="uppercase" value="0"/>
178 <param name="simple_repeat" value="1"/> 191 <param name="simple_repeat" value="1"/>
180 </section> 193 </section>
181 </section> 194 </section>
182 <output name="outfile" compare="contains" file="hedgdb.lastdb" ftype="lastdb"> 195 <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"/> 196 <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"/> 197 <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"/> 198 <extra_files type="file" value="humdb-sanger.prj" name="lastdb.prj" lines_diff="2"/>
186 <extra_files type="file" value="humdb-sanger.sds" name="lastdb.sds"/> 199 <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"/> 200 <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"/> 201 <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"/> 202 <extra_files type="file" value="humdb-sanger.tis" name="lastdb.tis" compare="sim_size" delta="1"/>
190 </output> 203 </output>