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comparison mitos.xml @ 0:39b6485e2d34 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
author iuc
date Fri, 27 Mar 2020 17:53:04 -0400
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children 1f4933f5a323
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-1:000000000000 0:39b6485e2d34
1 <tool id="mitos" name="@MITOS_NAME@" version="@MITOS_VERSION@" profile="20.01">
2 <description>de-novo annotation of metazoan mitochondrial genomes</description>
3 <macros>
4 <import>macros.xml</import>
5 <token name="@MITOS_NAME@">MITOS</token>
6 <token name="@MITOS_VERSION@">1.0.5</token>
7 </macros>
8 <requirements>
9 <requirement type="package" version="@MITOS_VERSION@">mitos</requirement>
10 <requirement type="package">zip</requirement>
11 </requirements>
12 <version_command>python -c "import mitos; print(mitos.__version__)"</version_command>
13 <command detect_errors="aggressive"><![CDATA[
14 mkdir outdir &&
15
16 runmitos.py
17 --input '$input'
18 --code $code
19 --outdir outdir
20 --refdir '$refdir.fields.path'
21 #for tpe in ["prot", "trna", "rrna"]
22 #if not $tpe in str($advanced.featuretypes).split(',')
23 --no$tpe
24 #end if
25 #end for
26 --finovl $advanced.finovl
27 --evalue $advanced_prot.evalue
28 --cutoff $advanced_prot.cutoff
29 #set maxovl=float($advanced_prot.maxovl)/100.0
30 --maxovl $maxovl
31 --clipfac $advanced_prot.clipfac
32 #set fragovl=float($advanced_prot.fragovl)/100.0
33 --fragovl $fragovl
34 --fragfac $advanced_prot.fragfac
35 --ststrange $advanced_prot.ststrange
36
37 #if "raw" in str($addoutputs).split(','):
38 && zip -9 -y -r output.zip outdir/ > /dev/null
39 #end if
40 ]]></command>
41 <inputs>
42 <param argument="--input" label="sequence" type="data" format="fasta" help="a single sequence in fasta formated sequence">
43 <options options_filter_attribute="metadata.sequences">
44 <filter type="add_value" value="1"/>
45 </options>
46 </param>
47 <param argument="--code" label="Genetic code" type="select">
48 <option value="2">Vertebrate (2)</option>
49 <option value="4">Mold, Protozoan, Coelenteral (4)</option>
50 <option value="5">Invertebrate (5)</option>
51 <option value="9">Echinoderm, Flatworm (9)</option>
52 <option value="13">Ascidian (13)</option>
53 <option value="14">Alternative Flatworm (14)</option>
54 </param>
55 <param argument="--refdir" label="Reference data" type="select" help="contact the administrator of this Galaxy instance if you miss reference data">
56 <options from_data_table="mitos">
57 <filter type="static_value" value="mitos" column="2"/>
58 </options>
59 <validator message="No reference annotation is available for MITOS" type="no_options" />
60 </param>
61 <param name="addoutputs" type="select" multiple="true" label="Outputs">
62 <option value="bed" selected="true">BED</option>
63 <option value="mito" selected="false">mito</option>
64 <option value="gff" selected="false">GFF file</option>
65 <option value="seq" selected="false">SEQ</option>
66 <option value="fas" selected="false">nucleotide FASTA</option>
67 <option value="faa" selected="false">protein FASTA</option>
68 <option value="geneorder" selected="false">geneorder</option>
69 <option value="protein_plot" selected="false">Protein prediction plot</option>
70 <option value="ncRNA_plot" selected="false">ncRNA prediction plot</option>
71 <!--<option value="ncRNA_structure_ps_plots" selected="false">ncRNA structure plots - postscript</option>-->
72 <option value="ncRNA_structure_svg_plots" selected="false">ncRNA structure plots - svg</option>
73 <option value="raw" selected="false">zipped raw results</option>
74 </param>
75 <section name="advanced" title="Advanced options">
76 <param name="featuretypes" label="Feature types" help="Feature types that should be predicted by MITOS (--noprot,--notrna,--norrna)" type="select" multiple="true">
77 <option value="prot" selected="true">Protein coding genes</option>
78 <option value="trna" selected="true">tRNAs</option>
79 <option value="rrna" selected="true">rRNAs</option>
80 </param>
81 <param argument="--finovl" label="Final overlap (nt)" help="Maximum number of nucleotides by which genes of different types may overlap" type="integer" value="35" min="0"/>
82 </section>
83 <section name="advanced_prot" title="Advanced options for protein coding gene prediction">
84 <param argument="--evalue" label="BLAST E-value Exponent" help="Negation of the exponent of the E-value threshold used by BLAST, i.e. a value X gives an E-value of 10^(-X)" type="float" value="2" min="0"/>
85 <param argument="--cutoff" label="Quality cutoff" help="Minimum allowed quality in % of the maximum quality value per reading frame" type="integer" value="50" min="0" max="100"/>
86 <param argument="--maxovl" label="Maximum overlap" help="Maximum allowed overlap of proteins in percent of the smaller feature " type="integer" value="20" min="0" max="100"/>
87 <param argument="--clipfac" label="Clipping factor" help="Clip overlapping proteins with the same name that differ by less than the specified factor" type="float" value="10" min="0"/>
88 <param argument="--fragovl" label="Fragment overlap" help="Maximum allowed overlap of proteins in the query (in percent of the shorter query range) for two hits to be counted as fragments of the same gene" type="integer" value="20" min="0" max="100"/>
89 <param argument="--fragfac" label="Fragment quality factor" help="Maximum factor by which fragments of the same protein may differ in their quality" type="float" value="10"/>
90 <param argument="--ststrange" label="Start/stop range" help="Number of aminoacids searched for start and stop codon of proteins" type="integer" value="6"/>
91 </section>
92 </inputs>
93 <outputs>
94 <data name="bedout" format="bed" from_work_dir="outdir/result.bed">
95 <filter>"bed" in str(addoutputs)</filter>
96 </data>
97 <data name="mitoout" format="tabular" from_work_dir="outdir/result" label="${tool.name} on ${on_string}: mito">
98 <filter>"mito" in str(addoutputs)</filter>
99 </data>
100 <data name="gffout" format="gff" from_work_dir="outdir/result.gff" label="${tool.name} on ${on_string}: GFF">
101 <filter>"gff" in str(addoutputs)</filter>
102 </data>
103 <data name="seqout" format="txt" from_work_dir="outdir/result.seq" label="${tool.name} on ${on_string}: TBL">
104 <filter>"seq" in str(addoutputs)</filter>
105 </data>
106 <data name="fasout" format="fasta" from_work_dir="outdir/result.fas" label="${tool.name} on ${on_string}: nt FASTA">
107 <filter>"fas" in str(addoutputs)</filter>
108 </data>
109 <data name="faaout" format="fasta" from_work_dir="outdir/result.faa" label="${tool.name} on ${on_string}: aa FASTA">
110 <filter>"faa" in str(addoutputs)</filter>
111 </data>
112 <data name="geneorderout" format="fasta" from_work_dir="outdir/result.geneorder" label="${tool.name} on ${on_string}: geneorder">
113 <filter>"geneorder" in str(addoutputs)</filter>
114 </data>
115 <data name="protein_plot_out" format="pdf" from_work_dir="outdir/plots/prot.pdf" label="${tool.name} on ${on_string}: Protein prediction plot">
116 <filter>"protein_plot" in str(addoutputs)</filter>
117 </data>
118 <data name="ncRNA_plot_out" format="pdf" from_work_dir="outdir/plots/rna.pdf" label="${tool.name} on ${on_string}: ncRNA prediction plot">
119 <filter>"protein_plot" in str(addoutputs)</filter>
120 </data>
121 <!--<collection name="ncRNA_structure_plot_ps_out" type="list" label="${tool.name} on ${on_string}: ncRNA postscript structure plots">
122 <discover_datasets pattern="(?P&lt;name&gt;.+)\.ps" format="ps" directory="outdir/plots" />
123 <filter>"ncRNA_structure_ps_plots" in str(addoutputs)</filter>
124 </collection>-->
125 <collection name="ncRNA_structure_plot_svg_out" type="list" label="${tool.name} on ${on_string}: ncRNA svg structure plots">
126 <discover_datasets pattern="(?P&lt;name&gt;.+)\.svg" format="svg" directory="outdir/plots" />
127 <filter>"ncRNA_structure_svg_plots" in str(addoutputs)</filter>
128 </collection>
129 <data name="rawout" format="zip" from_work_dir="output.zip" label="${tool.name} on ${on_string}: raw data">
130 <filter>"raw" in str(addoutputs)</filter>
131 </data>
132 </outputs>
133 <tests>
134 <!-- default options -->
135 <test expect_num_outputs="1">
136 <param name="input" value="NC_012920.fasta"/>
137 <param name="code" value="2"/>
138 <param name="refdir" value="mitos1-refdata" />
139 <output name="bedout" file="NC_012920.bed" ftype="bed"/>
140 <assert_command>
141 <has_text text="--code 2"/>
142 <has_text text="--finovl 35"/>
143 <has_text text="--evalue 2.0"/>
144 <has_text text="--cutoff 50"/>
145 <has_text text="--maxovl 0.2"/>
146 <has_text text="--clipfac 10.0"/>
147 <has_text text="--fragovl 0.2"/>
148 <has_text text="--fragfac 10.0"/>
149 <has_text text="--ststrange 6"/>
150 </assert_command>
151 </test>
152 <!-- default options, add outputs -->
153 <test expect_num_outputs="11">
154 <param name="input" value="NC_012920.fasta"/>
155 <param name="code" value="2"/>
156 <param name="refdir" value="mitos1-refdata" />
157 <param name="addoutputs" value="bed,mito,gff,seq,fas,faa,raw,geneorder,protein_plot,ncRNA_plot,ncRNA_structure_svg_plots"/>
158 <output name="bedout" file="NC_012920.bed" ftype="bed"/>
159 <output name="mitoout" file="NC_012920.mito" ftype="tabular" />
160 <output name="gffout" file="NC_012920.gff" ftype="gff" />
161 <output name="seqout" file="NC_012920.seq" ftype="txt" />
162 <output name="fasout" file="NC_012920.fas" ftype="fasta" />
163 <output name="faaout" file="NC_012920.faa" ftype="fasta" />
164 <output name="rawout" ftype="zip">
165 <assert_contents>
166 <has_archive_member path=".*/result.bed"/>
167 </assert_contents>
168 </output>
169 <output name="geneorderout" file="NC_012920.geneorder" ftype="fasta" />
170 <output name="protein_plot_out" file="NC_012920_prot.pdf" ftype="pdf" compare="sim_size"/>
171 <output name="ncRNA_plot_out" file="NC_012920_ncrna.pdf" ftype="pdf" compare="sim_size"/>
172 <output_collection name="ncRNA_structure_plot_svg_out" type="list" count="24">
173 <element name="trnA-5586-5654" file="NC_012920_trnA.svg" ftype="svg" />
174 </output_collection>
175 <assert_command>
176 <has_text text="--code 2"/>
177 <has_text text="--finovl 35"/>
178 <has_text text="--evalue 2.0"/>
179 <has_text text="--cutoff 50"/>
180 <has_text text="--maxovl 0.2"/>
181 <has_text text="--clipfac 10.0"/>
182 <has_text text="--fragovl 0.2"/>
183 <has_text text="--fragfac 10.0"/>
184 <has_text text="--ststrange 6"/>
185 </assert_command>
186 </test>
187 <!-- no rRNA, and advanced options -->
188 <test expect_num_outputs="1">
189 <param name="input" value="NC_012920.fasta"/>
190 <param name="code" value="2"/>
191 <param name="refdir" value="mitos1-refdata" />
192 <param name="advanced|featuretypes" value="prot,trna" />
193 <param name="advanced|finovl" value="50" />
194 <output name="bedout" file="NC_012920.bed" ftype="bed" compare="sim_size"/>
195 <assert_command>
196 <has_text text="--code 2"/>
197 <has_text text="--norrna"/>
198 <has_text text="--finovl 50"/>
199 </assert_command>
200 </test>
201 <!-- no rRNA, no tRNA; advanced protein options -->
202 <test expect_num_outputs="1">
203 <param name="input" value="NC_012920.fasta"/>
204 <param name="code" value="5"/>
205 <param name="refdir" value="mitos1-refdata" />
206 <param name="advanced|featuretypes" value="prot" />
207 <param name="advanced_prot|evalue" value="3"/>
208 <param name="advanced_prot|cutoff" value="40"/>
209 <param name="advanced_prot|maxovl" value="30"/>
210 <param name="advanced_prot|clipfac" value="5"/>
211 <param name="advanced_prot|fragovl" value="15"/>
212 <param name="advanced_prot|fragfac" value="11"/>
213 <param name="advanced_prot|ststrange" value="12"/>
214 <param name="addoutputs" value="bed"/>
215 <output name="bedout" file="NC_012920.bed" ftype="bed" compare="sim_size"/>
216 <assert_command>
217 <has_text text="--code 5"/>
218 <has_text text="--evalue 3"/>
219 <has_text text="--cutoff 40"/>
220 <has_text text="--maxovl 0.3"/>
221 <has_text text="--clipfac 5.0"/>
222 <has_text text="--fragovl 0.15"/>
223 <has_text text="--fragfac 11.0"/>
224 <has_text text="--ststrange 12"/>
225 </assert_command>
226 </test>
227 </tests>
228 <help>
229 @COMMON_HELP@
230 <![CDATA[
231 ]]></help>
232 <citations>
233 <citation type="doi">10.1016/j.ympev.2012.08.023</citation>
234 </citations>
235 </tool>
236