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comparison kofamscan.xml @ 0:24adf43898ec draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit dc0dc99c95658757036bbe7decfd241856e2f412"
author iuc
date Fri, 15 Jan 2021 10:48:52 +0000
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-1:000000000000 0:24adf43898ec
1 <tool id="kofamscan" name="KofamScan" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>gene function annotation based on KEGG orthology and HMM</description>
3 <macros>
4 <token name="@TOOL_VERSION@">1.3.0</token>
5 <token name="@VERSION_SUFFIX@">0</token>
6 <xml name="reportannotation" token_selected="">
7 <param name="reportannotation" type="boolean" truevalue="--report-unannotated" falsevalue="--no-report-unannotated" checked="@SELECTED@" label="Include sequence name to outputs even if no KOs are assigned?"/>
8 </xml>
9 </macros>
10 <requirements>
11 <requirement type="package" version="@TOOL_VERSION@">kofamscan</requirement>
12 <requirement type="package" version="3.0">zip</requirement>
13 </requirements>
14 <version_command><![CDATA[sansa -v | grep "Sansa " | cut -d "v" -f 3]]></version_command>
15 <command detect_errors="exit_code"><![CDATA[
16 ## preprocessing
17 mkdir 'profile' &&
18 #if $p_cond.p_sel == 'compressed'
19 tar -xf '${p_cond.p}' -C 'profile' &&
20 #elif $p_cond.p_sel == 'hmm'
21 ## input files require prefix 'K' and file extension '.hmm'
22 #for $i, $current in enumerate($p_cond.p)
23 ln -s '$current' 'profile/K${i}.hmm' &&
24 #end for
25 #end if
26
27 ## run
28 exec_annotation
29 -p 'profile'
30 -o 'result.txt'
31 -k '$k'
32 --cpu \${GALAXY_SLOTS:-4}
33 -E $E
34 -T $ap.T
35 -f '$ap.f_cond.f_sel'
36 $ap.f_cond.reportannotation
37 #if 'alignments' in $ap.out
38 --create-alignment
39 #end if
40 '$query'
41
42 ## postprocessing
43 #if 'alignments' in $ap.out
44 && test -d 'tmp/alignment' && zip -q -r 'tmp/alignments.zip' tmp/alignment/* || echo 'No alignment files.'
45 #end if
46 ]]></command>
47 <inputs>
48 <param name="query" type="data" format="fasta" label="Select query sequence file" help="Nucleotide sequences are not accepted."/>
49 <conditional name="p_cond">
50 <param name="p_sel" type="select" label="Select profile database format">
51 <option value="compressed" selected="true">Compressed set of HMM and HAL file(s)</option>
52 <option value="hmm">HMM file(s)</option>
53 </param>
54 <when value="compressed">
55 <param argument="-p" type="data" format="tar" label="Select a compressed file with HMM and HAL file(s)" help="Compressed archives are available from KofamKOALA web service (https://www.genome.jp/tools/kofamkoala/)."/>
56 </when>
57 <when value="hmm">
58 <param argument="-p" type="data" format="hmm3" multiple="true" label="Select profile HMM file(s)"/>
59 </when>
60 </conditional>
61 <param argument="-k" type="data" format="tabular" label="Select KO list file"/>
62 <param argument="-E" type="float" min="0.0" max="1.0" value="0.01" label="Set E-value threshold"/>
63 <section name="ap" title="Advanced parameters" expanded="true">
64 <param argument="-T" type="integer" value="1" label="Set threshold scale" help="The score thresholds will be multiplied by this value."/>
65 <conditional name="f_cond">
66 <param name="f_sel" type="select" label="Select output format">
67 <option value="detail" selected="true">Details for each hit (including hits below threshold) (detail)</option>
68 <option value="detail-tsv">Tab separeted values for detail format (detail-tsv)</option>
69 <option value="mapper">KEGG Mapper compatible format (mapper)</option>
70 <option value="mapper-one-line">KEGG Mapper compatible format, but all hit KOs are listed in one line (mapper-oneline)</option>
71 </param>
72 <when value="detail">
73 <expand macro="reportannotation" selected="false"/>
74 </when>
75 <when value="detail-tsv">
76 <expand macro="reportannotation" selected="false"/>
77 </when>
78 <when value="mapper">
79 <expand macro="reportannotation" selected="true"/>
80 </when>
81 <when value="mapper-one-line">
82 <expand macro="reportannotation" selected="true"/>
83 </when>
84 </conditional>
85 <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)" help="Only shown in history if selected here and generated by the specific run.">
86 <option value="result" selected="true">KofamScan Result</option>
87 <option value="alignments">HMMER alignments</option>
88 <option value="output">HMMER run output</option>
89 <option value="tabular">HMMER tabular summary</option>
90 </param>
91 </section>
92 </inputs>
93 <outputs>
94 <data name="out_alignments" format="zip" from_work_dir="tmp/alignments.zip" label="${tool.name} on ${on_string}: HMMER alignments">
95 <filter>'alignments' in ap['out']</filter>
96 </data>
97 <data name="out_output" format="txt" from_work_dir="tmp/output/output.txt" label="${tool.name} on ${on_string}: HMMER output">
98 <filter>'output' in ap['out']</filter>
99 </data>
100 <data name="out_result" format="txt" from_work_dir="result.txt" label="${tool.name} on ${on_string}: Results">
101 <filter>'result' in ap['out']</filter>
102 </data>
103 <data name="out_tabular" format="txt" from_work_dir="tmp/tabular/tabular.txt" label="${tool.name} on ${on_string}: HMMER tabular">
104 <filter>'tabular' in ap['out']</filter>
105 </data>
106 </outputs>
107 <tests>
108 <!-- #1 default -->
109 <test expect_num_outputs="1">
110 <param name="query" value="query.fasta"/>
111 <conditional name="p_cond">
112 <param name="p_sel" value="compressed"/>
113 <param name="p" value="profiles.tar.gz"/>
114 </conditional>
115 <param name="k" value="ko"/>
116 <output name="out_result">
117 <assert_contents>
118 <has_n_lines n="5"/>
119 <has_text_matching expression=".+sp\|P00329\|ADH1_MOUSE.+"/>
120 </assert_contents>
121 </output>
122 </test>
123 <!-- #2 -->
124 <test expect_num_outputs="4">
125 <param name="query" value="query.fasta"/>
126 <conditional name="p_cond">
127 <param name="p_sel" value="hmm"/>
128 <param name="p" value="K00001.hmm,K00002.hmm,K00003.hmm"/>
129 </conditional>
130 <param name="k" value="ko"/>
131 <param name="E" value="0.02"/>
132 <section name="ap">
133 <param name="T" value="2"/>
134 <conditional name="f_cond">
135 <param name="f_sel" value="detail-tsv"/>
136 <param name="reportannotation" value="true"/>
137 </conditional>
138 <param name="out" value="alignments,output,result,tabular"/>
139 </section>
140 <output name="out_alignments">
141 <assert_contents>
142 <has_size value="4099"/>
143 </assert_contents>
144 </output>
145 <output name="out_output">
146 <assert_contents>
147 <has_n_lines n="224"/>
148 <has_line line="Internal pipeline statistics summary:"/>
149 </assert_contents>
150 </output>
151 <output name="out_result">
152 <assert_contents>
153 <has_n_lines n="9"/>
154 <has_text_matching expression=".+sp\|P19858\|LDHA_BOVIN"/>
155 </assert_contents>
156 </output>
157 <output name="out_tabular">
158 <assert_contents>
159 <has_n_lines n="48"/>
160 <has_line line="K1"/>
161 </assert_contents>
162 </output>
163 </test>
164 <!-- #3 -->
165 <test expect_num_outputs="1">
166 <param name="query" value="query.fasta"/>
167 <conditional name="p_cond">
168 <param name="p_sel" value="hmm"/>
169 <param name="p" value="K00001.hmm,K00002.hmm,K00003.hmm"/>
170 </conditional>
171 <param name="k" value="ko"/>
172 <section name="ap">
173 <conditional name="f_cond">
174 <param name="f_sel" value="mapper"/>
175 </conditional>
176 </section>
177 <output name="out_result">
178 <assert_contents>
179 <has_n_lines n="7"/>
180 <has_line line="sp|P19858|LDHA_BOVIN"/>
181 </assert_contents>
182 </output>
183 </test>
184 <!-- #4 -->
185 <test expect_num_outputs="1">
186 <param name="query" value="query.fasta"/>
187 <conditional name="p_cond">
188 <param name="p_sel" value="hmm"/>
189 <param name="p" value="K00001.hmm,K00002.hmm,K00003.hmm"/>
190 </conditional>
191 <param name="k" value="ko"/>
192 <section name="ap">
193 <conditional name="f_cond">
194 <param name="f_sel" value="mapper-one-line"/>
195 </conditional>
196 </section>
197 <output name="out_result">
198 <assert_contents>
199 <has_n_lines n="7"/>
200 <has_line line="sp|P19858|LDHA_BOVIN"/>
201 </assert_contents>
202 </output>
203 </test>
204 </tests>
205 <help><![CDATA[
206 .. class:: infomark
207
208 **What it does**
209
210 KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model.
211
212 KofamScan assigns K numbers to the user's sequence data by HMMER/HMMSEARCH against KOfam (a customized HMM database of KEGG Orthologs (KOs)). K number assignments with scores above the predefined thresholds for individual KOs are more reliable than other proposed assignments. Such high score assignments are highlighted with asterisks '*' in the output. The K number assignments facilitate the interpretation of the annotation results by linking the user's sequence data to the KEGG pathways and EC numbers.
213
214 **Input**
215
216 - a query file in FASTA format with one or more amino acid sequences. Each sequence must have a unique name. A name of a sequence is a string between the header symbol (">") and the first blank character (whitespace, tab, line break, etc.). Do not put a whitespace right after ">".
217
218 ::
219
220 >sp|P00325|ADH1B_HUMAN Alcohol dehydrogenase 1B OS=Homo sapiens GN=ADH1B PE=1 SV=2
221 MSTAGKVIKCKAAVLWEVKKPFSIEDVEVAPPKAYEVRIKMVAVGICRTDDHVVSGNLVT
222
223 - a KO list file of KOfam
224
225 ::
226
227 knum threshold score_type profile_type F-measure nseq nseq_used alen mlen eff_nseq re/pos definition
228 K00001 361.33 domain trim 0.326825 1601 1149 1538 393 13.33 0.590 alcohol dehydrogenase [EC:1.1.1.1]
229
230 - KOfam profile files in HMM3 format or a compressed dataset containing HMM3 profiles and HAL filtering files available `here <ftp://ftp.genome.jp/pub/db/kofam/>`_.
231
232 **Output**
233
234 - KofamScan output
235 - HMMER results as alignments, run output and tabular summary
236
237 .. class:: infomark
238
239 **References**
240
241 More information are available on `GitHub <https://github.com/takaram/kofam_scan>`_ and the `KofamKOALA webserver <https://www.genome.jp/tools/kofamkoala/>`_.
242 ]]></help>
243 <citations>
244 <citation type="doi">10.1093/bioinformatics/btz859</citation>
245 </citations>
246 </tool>