comparison kofamscan.xml @ 3:c3c46f14c7a4 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
author iuc
date Mon, 22 Apr 2024 14:41:54 +0000
parents 95c71179a054
children 2eb7932e91a3
comparison
equal deleted inserted replaced
2:95c71179a054 3:c3c46f14c7a4
1 <tool id="kofamscan" name="KofamScan" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="kofamscan" name="KofamScan" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>gene function annotation based on KEGG orthology and HMM</description> 2 <description>gene function annotation based on KEGG orthology and HMM</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">1.3.0</token> 4 <token name="@TOOL_VERSION@">1.3.0</token>
5 <token name="@VERSION_SUFFIX@">1</token> 5 <token name="@VERSION_SUFFIX@">2</token>
6 <xml name="reportannotation" token_selected=""> 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?"/> 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> 8 </xml>
9 </macros> 9 </macros>
10 <xrefs> 10 <xrefs>
12 </xrefs> 12 </xrefs>
13 <requirements> 13 <requirements>
14 <requirement type="package" version="@TOOL_VERSION@">kofamscan</requirement> 14 <requirement type="package" version="@TOOL_VERSION@">kofamscan</requirement>
15 <requirement type="package" version="3.0">zip</requirement> 15 <requirement type="package" version="3.0">zip</requirement>
16 </requirements> 16 </requirements>
17 <version_command><![CDATA[sansa -v | grep "Sansa " | cut -d "v" -f 3]]></version_command> 17 <version_command><![CDATA[exec_annotation --version | cut -d " " -f 2]]></version_command>
18 <command detect_errors="exit_code"><![CDATA[ 18 <command detect_errors="exit_code"><![CDATA[
19 ## preprocessing 19 #if $p_cond.p_sel != "cached"
20 mkdir ./profile && 20 ## preprocessing
21 mkdir ./temp_extract && 21 mkdir ./profile &&
22 #if $p_cond.p_sel == 'compressed' 22 mkdir ./temp_extract &&
23 tar -xf '${p_cond.p}' -C temp_extract && 23 #if $p_cond.p_sel == 'compressed'
24 find ./temp_extract/ -name '*.hmm' -exec mv {} ./profile \; && 24 tar -xf '${p_cond.p}' -C temp_extract &&
25 find ./temp_extract/ -name '*.hal' -exec mv {} ./profile \; && 25 find ./temp_extract/ -name '*.hmm' -exec mv {} ./profile \; &&
26 #elif $p_cond.p_sel == 'hmm' 26 find ./temp_extract/ -name '*.hal' -exec mv {} ./profile \; &&
27 ## input files require prefix 'K' and file extension '.hmm' 27 #elif $p_cond.p_sel == 'hmm'
28 #for $i, $current in enumerate($p_cond.p) 28 ## input files require prefix 'K' and file extension '.hmm'
29 ln -s '$current' 'profile/K${i}.hmm' && 29 #for $i, $current in enumerate($p_cond.p)
30 #end for 30 ln -s '$current' 'profile/K${i}.hmm' &&
31 #end for
32 #end if
31 #end if 33 #end if
32 34
33 ## run 35 ## run
34 exec_annotation 36 exec_annotation
35 -p 'profile' 37
38 #if $p_cond.p_sel != "cached"
39 -p 'profile'
40 -k '$p_cond.k'
41 #else
42 -p '$p_cond.kofam.fields.profile_dir/#if $p_cond.kofam_subset then $p_cond.kofam_subset else ""#'
43 -k '$p_cond.kofam.fields.ko_list'
44 #end if
36 -o 'result.txt' 45 -o 'result.txt'
37 -k '$k'
38 --cpu \${GALAXY_SLOTS:-4} 46 --cpu \${GALAXY_SLOTS:-4}
39 -E $E 47 -E $E
40 -T $ap.T 48 -T $ap.T
41 -f '$ap.f_cond.f_sel' 49 -f '$ap.f_cond.f_sel'
42 $ap.f_cond.reportannotation 50 $ap.f_cond.reportannotation
52 ]]></command> 60 ]]></command>
53 <inputs> 61 <inputs>
54 <param name="query" type="data" format="fasta" label="Select query sequence file" help="Nucleotide sequences are not accepted."/> 62 <param name="query" type="data" format="fasta" label="Select query sequence file" help="Nucleotide sequences are not accepted."/>
55 <conditional name="p_cond"> 63 <conditional name="p_cond">
56 <param name="p_sel" type="select" label="Select profile database format"> 64 <param name="p_sel" type="select" label="Select profile database format">
57 <option value="compressed" selected="true">Compressed set of HMM and HAL file(s)</option> 65 <option value="cached" selected="true">Cached</option>
66 <option value="compressed">Compressed set of HMM and HAL file(s)</option>
58 <option value="hmm">HMM file(s)</option> 67 <option value="hmm">HMM file(s)</option>
59 </param> 68 </param>
69 <when value="cached">
70 <param name="kofam" type="select">
71 <options from_data_table="kofam"/>
72 </param>
73 <param name="kofam_subset" type="select" optional="true">
74 <options from_data_table="kofam_subset">
75 <filter type="param_value" column="2" ref="kofam"/>
76 <filter type="sort_by" column="1"/>
77 <filter type="unique_value" column="1"/>
78 <column name="name" index="1"/>
79 <column name="value" index="0"/>
80 </options>
81 <validator type="no_options" message="No option available for this input"/>
82 </param>
83 </when>
60 <when value="compressed"> 84 <when value="compressed">
61 <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/)."/> 85 <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/)."/>
86 <param argument="-k" type="data" format="tabular" label="Select KO list file"/>
62 </when> 87 </when>
63 <when value="hmm"> 88 <when value="hmm">
64 <param argument="-p" type="data" format="hmm3" multiple="true" label="Select profile HMM file(s)"/> 89 <param argument="-p" type="data" format="hmm3" multiple="true" label="Select profile HMM file(s)"/>
90 <param argument="-k" type="data" format="tabular" label="Select KO list file"/>
65 </when> 91 </when>
66 </conditional> 92 </conditional>
67 <param argument="-k" type="data" format="tabular" label="Select KO list file"/>
68 <param argument="-E" type="float" min="0.0" max="1.0" value="0.01" label="Set E-value threshold"/> 93 <param argument="-E" type="float" min="0.0" max="1.0" value="0.01" label="Set E-value threshold"/>
69 <section name="ap" title="Advanced parameters" expanded="true"> 94 <section name="ap" title="Advanced parameters" expanded="true">
70 <param argument="-T" type="integer" value="1" label="Set threshold scale" help="The score thresholds will be multiplied by this value."/> 95 <param argument="-T" type="integer" value="1" label="Set threshold scale" help="The score thresholds will be multiplied by this value."/>
71 <conditional name="f_cond"> 96 <conditional name="f_cond">
72 <param name="f_sel" type="select" label="Select output format"> 97 <param name="f_sel" type="select" label="Select output format">
95 <option value="tabular">HMMER tabular summary</option> 120 <option value="tabular">HMMER tabular summary</option>
96 </param> 121 </param>
97 </section> 122 </section>
98 </inputs> 123 </inputs>
99 <outputs> 124 <outputs>
125 <data name="out_result" format="txt" from_work_dir="result.txt" label="${tool.name} on ${on_string}: Results">
126 <filter>'result' in ap['out']</filter>
127 <change_format>
128 <when input='ap.f_cond.f_sel' value="detail-tsv" format="tabular" />
129 </change_format>
130 </data>
100 <data name="out_alignments" format="zip" from_work_dir="tmp/alignments.zip" label="${tool.name} on ${on_string}: HMMER alignments"> 131 <data name="out_alignments" format="zip" from_work_dir="tmp/alignments.zip" label="${tool.name} on ${on_string}: HMMER alignments">
101 <filter>'alignments' in ap['out']</filter> 132 <filter>'alignments' in ap['out']</filter>
102 </data> 133 </data>
103 <data name="out_output" format="txt" from_work_dir="tmp/output/output.txt" label="${tool.name} on ${on_string}: HMMER output"> 134 <data name="out_output" format="txt" from_work_dir="tmp/output/output.txt" label="${tool.name} on ${on_string}: HMMER output">
104 <filter>'output' in ap['out']</filter> 135 <filter>'output' in ap['out']</filter>
105 </data>
106 <data name="out_result" format="txt" from_work_dir="result.txt" label="${tool.name} on ${on_string}: Results">
107 <filter>'result' in ap['out']</filter>
108 </data> 136 </data>
109 <data name="out_tabular" format="txt" from_work_dir="tmp/tabular/tabular.txt" label="${tool.name} on ${on_string}: HMMER tabular"> 137 <data name="out_tabular" format="txt" from_work_dir="tmp/tabular/tabular.txt" label="${tool.name} on ${on_string}: HMMER tabular">
110 <filter>'tabular' in ap['out']</filter> 138 <filter>'tabular' in ap['out']</filter>
111 </data> 139 </data>
112 </outputs> 140 </outputs>
129 <!-- #2 --> 157 <!-- #2 -->
130 <test expect_num_outputs="4"> 158 <test expect_num_outputs="4">
131 <param name="query" value="query.fasta"/> 159 <param name="query" value="query.fasta"/>
132 <conditional name="p_cond"> 160 <conditional name="p_cond">
133 <param name="p_sel" value="hmm"/> 161 <param name="p_sel" value="hmm"/>
134 <param name="p" value="K00001.hmm,K00002.hmm,K00003.hmm"/> 162 <param name="p" value="profiles/K00001.hmm,profiles/K00002.hmm,profiles/K00003.hmm"/>
135 </conditional> 163 </conditional>
136 <param name="k" value="ko"/> 164 <param name="k" value="ko"/>
137 <param name="E" value="0.02"/> 165 <param name="E" value="0.02"/>
138 <section name="ap"> 166 <section name="ap">
139 <param name="T" value="2"/> 167 <param name="T" value="2"/>
152 <assert_contents> 180 <assert_contents>
153 <has_n_lines n="224"/> 181 <has_n_lines n="224"/>
154 <has_line line="Internal pipeline statistics summary:"/> 182 <has_line line="Internal pipeline statistics summary:"/>
155 </assert_contents> 183 </assert_contents>
156 </output> 184 </output>
157 <output name="out_result"> 185 <output name="out_result" ftype="tabular">
158 <assert_contents> 186 <assert_contents>
159 <has_n_lines n="9"/> 187 <has_n_lines n="9"/>
160 <has_text_matching expression=".+sp\|P19858\|LDHA_BOVIN"/> 188 <has_text_matching expression=".+sp\|P19858\|LDHA_BOVIN"/>
161 </assert_contents> 189 </assert_contents>
162 </output> 190 </output>
170 <!-- #3 --> 198 <!-- #3 -->
171 <test expect_num_outputs="1"> 199 <test expect_num_outputs="1">
172 <param name="query" value="query.fasta"/> 200 <param name="query" value="query.fasta"/>
173 <conditional name="p_cond"> 201 <conditional name="p_cond">
174 <param name="p_sel" value="hmm"/> 202 <param name="p_sel" value="hmm"/>
175 <param name="p" value="K00001.hmm,K00002.hmm,K00003.hmm"/> 203 <param name="p" value="profiles/K00001.hmm,profiles/K00002.hmm,profiles/K00003.hmm"/>
176 </conditional> 204 </conditional>
177 <param name="k" value="ko"/> 205 <param name="k" value="ko"/>
178 <section name="ap"> 206 <section name="ap">
179 <conditional name="f_cond"> 207 <conditional name="f_cond">
180 <param name="f_sel" value="mapper"/> 208 <param name="f_sel" value="mapper"/>
181 </conditional> 209 </conditional>
182 </section> 210 </section>
183 <output name="out_result"> 211 <output name="out_result" ftype="txt">
184 <assert_contents> 212 <assert_contents>
185 <has_n_lines n="7"/> 213 <has_n_lines n="7"/>
186 <has_line line="sp|P19858|LDHA_BOVIN"/> 214 <has_line line="sp|P19858|LDHA_BOVIN"/>
187 </assert_contents> 215 </assert_contents>
188 </output> 216 </output>
190 <!-- #4 --> 218 <!-- #4 -->
191 <test expect_num_outputs="1"> 219 <test expect_num_outputs="1">
192 <param name="query" value="query.fasta"/> 220 <param name="query" value="query.fasta"/>
193 <conditional name="p_cond"> 221 <conditional name="p_cond">
194 <param name="p_sel" value="hmm"/> 222 <param name="p_sel" value="hmm"/>
195 <param name="p" value="K00001.hmm,K00002.hmm,K00003.hmm"/> 223 <param name="p" value="profiles/K00001.hmm,profiles/K00002.hmm,profiles/K00003.hmm"/>
196 </conditional> 224 </conditional>
197 <param name="k" value="ko"/> 225 <param name="k" value="ko"/>
198 <section name="ap"> 226 <section name="ap">
199 <conditional name="f_cond"> 227 <conditional name="f_cond">
200 <param name="f_sel" value="mapper-one-line"/> 228 <param name="f_sel" value="mapper-one-line"/>
217 <param name="k" value="ko"/> 245 <param name="k" value="ko"/>
218 <output name="out_result"> 246 <output name="out_result">
219 <assert_contents> 247 <assert_contents>
220 <has_n_lines n="5"/> 248 <has_n_lines n="5"/>
221 <has_text_matching expression=".+sp\|P00329\|ADH1_MOUSE.+"/> 249 <has_text_matching expression=".+sp\|P00329\|ADH1_MOUSE.+"/>
250 </assert_contents>
251 </output>
252 </test>
253 <!-- #6 test with cached data -->
254 <test expect_num_outputs="1">
255 <param name="query" value="query.fasta"/>
256 <conditional name="p_cond">
257 <param name="p_sel" value="cached"/>
258 <param name="kofam" value="test_value"/>
259 </conditional>
260 <param name="k" value="ko"/>
261 <section name="ap">
262 <conditional name="f_cond">
263 <param name="f_sel" value="mapper-one-line"/>
264 </conditional>
265 </section>
266 <output name="out_result" ftype="txt">
267 <assert_contents>
268 <has_n_lines n="7"/>
269 <has_line line="sp|P19858|LDHA_BOVIN"/>
270 </assert_contents>
271 </output>
272 </test>
273 <!-- #6 test with cached data + subset -->
274 <test expect_num_outputs="1">
275 <param name="query" value="query.fasta"/>
276 <conditional name="p_cond">
277 <param name="p_sel" value="cached"/>
278 <param name="kofam" value="test_value"/>
279 <param name="kofam_subset" value="SUBSET"/>
280 </conditional>
281 <param name="k" value="ko"/>
282 <section name="ap">
283 <conditional name="f_cond">
284 <param name="f_sel" value="mapper-one-line"/>
285 </conditional>
286 </section>
287 <output name="out_result" ftype="txt">
288 <assert_contents>
289 <has_n_lines n="7"/>
290 <has_line line="sp|P19858|LDHA_BOVIN"/>
222 </assert_contents> 291 </assert_contents>
223 </output> 292 </output>
224 </test> 293 </test>
225 </tests> 294 </tests>
226 <help><![CDATA[ 295 <help><![CDATA[