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comparison proteinortho.xml @ 1:26abc7846e6f draft

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"planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5"
author iuc
date Tue, 14 Sep 2021 11:39:10 +0000
parents 4850f0d15f01
children a8addd4fb60a
comparison
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0:4850f0d15f01 1:26abc7846e6f
1 <tool id="proteinortho" name="Proteinortho" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@"> 1 <tool id="proteinortho" name="Proteinortho" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" profile="@PROFILE@">
2 <description>detects orthologous proteins/genes within different species</description> 2 <description>detects orthologous proteins/genes within different species</description>
3 <macros> 3 <macros>
4 <import>proteinortho_macros.xml</import> 4 <import>proteinortho_macros.xml</import>
5 <xml name="test_outputs">
6 <output name="proteinortho">
7 <assert_contents>
8 <has_line_matching expression="# Species\tGenes\tAlg\.-Conn\.\t.*"/>
9 <has_line_matching expression="[0-9]+\t[0-9]+\t.*"/>
10 <has_line_matching expression=".*(C|C2|E|L|M)_[0-9]+.*"/>
11 </assert_contents>
12 </output>
13 <output name="blastgraph">
14 <assert_contents>
15 <has_line_matching expression="# file_a\tfile_b"/>
16 <has_line_matching expression="# a\tb\tevalue_ab\tbitscore_ab\tevalue_ba\tbitscore_ba"/>
17 <has_line_matching expression="# (C|C2|E|L|M)\.fasta\t(C|C2|E|L|M)\.fasta"/>
18 <has_line_matching expression=".*(C|C2|E|L|M)_[0-9]+\t(C|C2|E|L|M)_[0-9]+.*"/>
19 </assert_contents>
20 </output>
21 <output name="proteinorthograph">
22 <assert_contents>
23 <has_line_matching expression="# file_a\tfile_b"/>
24 <has_line_matching expression="# a\tb\tevalue_ab\tbitscore_ab\tevalue_ba\tbitscore_ba(\tsame_strand\tsimscore)?"/>
25 <has_line_matching expression="# (C|C2|E|L|M)\.fasta\t(C|C2|E|L|M)\.fasta"/>
26 <has_line_matching expression=".*(C|C2|E|L|M)_[0-9]+\t(C|C2|E|L|M)_[0-9]+.*"/>
27 </assert_contents>
28 </output>
29 </xml>
5 </macros> 30 </macros>
6 <expand macro="requirements"/> 31 <expand macro="requirements"/>
7 <expand macro="version_command"/> 32 <expand macro="version_command"/>
8 <command detect_errors="exit_code"><![CDATA[ 33 <command detect_errors="exit_code"><![CDATA[
9 ## the following ln-action is necessary, since the file names are used by proteinortho (output contains filenames => species names) 34 ## the following ln-action is necessary, since the file names are used by proteinortho (output contains filenames => species names)
109 <data name="proteinorthograph" format="tabular" label="${tool.name} on ${on_string}: orthology-pairs" from_work_dir="result.proteinortho-graph"/> 134 <data name="proteinorthograph" format="tabular" label="${tool.name} on ${on_string}: orthology-pairs" from_work_dir="result.proteinortho-graph"/>
110 </outputs> 135 </outputs>
111 <tests> 136 <tests>
112 <test expect_num_outputs="3"> <!-- test normal --> 137 <test expect_num_outputs="3"> <!-- test normal -->
113 <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/> 138 <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/>
114 <output name="proteinortho"> 139 <expand macro="test_outputs"/>
115 <assert_contents> 140 <assert_command>
116 <has_text text="# Species&#009;Genes&#009;Alg.-Conn."/> 141 <has_text text="--p=diamond"/>
117 <has_text text="2&#009;5&#009;0.16"/> 142 </assert_command>
118 <has_text text="M_640,M_642,M_649"/>
119 </assert_contents>
120 </output>
121 <output name="blastgraph">
122 <assert_contents>
123 <has_text text="L_10&#009;E_10&#009;"/>
124 </assert_contents>
125 </output>
126 <output name="proteinorthograph">
127 <assert_contents>
128 <has_text text="L_11&#009;E_11&#009;"/>
129 </assert_contents>
130 </output>
131 </test> 143 </test>
132 <test expect_num_outputs="3"> <!-- various parameter --> 144 <test expect_num_outputs="3"> <!-- various parameter -->
133 <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/> 145 <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/>
134 <param name="evalue" value="1"/> 146 <param name="evalue" value="1"/>
135 <param name="conn" value="1"/> 147 <param name="conn" value="1"/>
136 <param name="cov" value="42"/> 148 <param name="cov" value="42"/>
137 <param name="sim" value="42"/> 149 <param name="sim" value="42"/>
138 <param name="identity" value="42"/> 150 <param name="identity" value="42"/>
139 <param name="selfblast" value="true"/> 151 <param name="selfblast" value="true"/>
140 <param name="singles" value="true"/> 152 <param name="singles" value="true"/>
141 <output name="proteinortho"> 153 <expand macro="test_outputs"/>
142 <assert_contents> 154 <assert_command>
143 <has_text text="# Species&#009;Genes&#009;Alg.-Conn."/> 155 <has_text text="--p=diamond"/>
144 <has_text text="1&#009;1&#009;0"/> 156 </assert_command>
145 <has_text text="&#009;C_177&#009;"/>
146 </assert_contents>
147 </output>
148 <output name="blastgraph">
149 <assert_contents>
150 <has_text text="C_1&#009;C_1&#009;"/>
151 </assert_contents>
152 </output>
153 <output name="proteinorthograph">
154 <assert_contents>
155 <has_text text="C_12&#009;C_21&#009;"/>
156 </assert_contents>
157 </output>
158 </test> 157 </test>
159 <test expect_num_outputs="3"> <!-- synteny --> 158 <test expect_num_outputs="3"> <!-- synteny -->
160 <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/> 159 <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/>
161 <param name="input_files_syn" value="L.gff,C.gff,C2.gff,E.gff,M.gff"/> 160 <param name="input_files_syn" value="L.gff,C.gff,C2.gff,E.gff,M.gff"/>
162 <param name="synteny_options" value="specified"/> 161 <param name="synteny_options" value="specified"/>
163 <output name="proteinortho"> 162 <expand macro="test_outputs"/>
164 <assert_contents> 163 <assert_command>
165 <has_text text="# Species&#009;Genes&#009;Alg.-Conn."/> 164 <has_text text="--p=diamond"/>
166 <has_text text="4&#009;5&#009;0.144"/> 165 </assert_command>
167 <has_text text="E_313,E_315"/>
168 </assert_contents>
169 </output>
170 <output name="proteinorthograph">
171 <assert_contents>
172 <has_text text="M_313&#009;L_313&#009;"/>
173 </assert_contents>
174 </output>
175 </test> 166 </test>
176 <test expect_num_outputs="3"> <!-- blast --> 167 <test expect_num_outputs="3"> <!-- blast -->
177 <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/> 168 <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/>
178 <param name="--p" value="blastp"/> 169 <param name="p" value="blastp"/>
179 <output name="proteinortho"> 170 <expand macro="test_outputs"/>
180 <assert_contents> 171 <assert_command>
181 <has_text text="# Species&#009;Genes&#009;Alg.-Conn."/> 172 <has_text text="--p=blastp"/>
182 <has_text text="2&#009;5&#009;0.16"/> 173 </assert_command>
183 <has_text text="M_640,M_642,M_649"/>
184 </assert_contents>
185 </output>
186 <output name="blastgraph">
187 <assert_contents>
188 <has_text text="M_3&#009;L_3&#009;"/>
189 </assert_contents>
190 </output>
191 <output name="proteinorthograph">
192 <assert_contents>
193 <has_text text="M_317&#009;L_317&#009;"/>
194 </assert_contents>
195 </output>
196 </test> 174 </test>
197 <test expect_num_outputs="3"> <!-- auto blast --> 175 <test expect_num_outputs="3"> <!-- auto blast -->
198 <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/> 176 <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/>
199 <param name="--p" value="autoblast"/> 177 <param name="p" value="autoblast"/>
200 <output name="proteinortho"> 178 <expand macro="test_outputs"/>
201 <assert_contents> 179 <assert_command>
202 <has_text text="# Species&#009;Genes&#009;Alg.-Conn."/> 180 <has_text text="--p=autoblast"/>
203 <has_text text="2&#009;5&#009;0.16"/> 181 </assert_command>
204 <has_text text="M_640,M_642,M_649"/>
205 </assert_contents>
206 </output>
207 <output name="blastgraph">
208 <assert_contents>
209 <has_text text="M_3&#009;L_3&#009;"/>
210 </assert_contents>
211 </output>
212 <output name="proteinorthograph">
213 <assert_contents>
214 <has_text text="M_317&#009;L_317&#009;"/>
215 </assert_contents>
216 </output>
217 </test> 182 </test>
218 <test expect_num_outputs="3"> <!-- last --> 183 <test expect_num_outputs="3"> <!-- last -->
219 <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/> 184 <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/>
220 <param name="--p" value="lastp"/> 185 <param name="p" value="lastp"/>
221 <output name="proteinortho"> 186 <expand macro="test_outputs"/>
222 <assert_contents> 187 <assert_command>
223 <has_text text="# Species&#009;Genes&#009;Alg.-Conn."/> 188 <has_text text="--p=lastp"/>
224 <has_text text="2&#009;5&#009;0.16"/> 189 </assert_command>
225 <has_text text="M_640,M_642,M_649"/>
226 </assert_contents>
227 </output>
228 <output name="blastgraph">
229 <assert_contents>
230 <has_text text="M_636&#009;E_317&#009;"/>
231 </assert_contents>
232 </output>
233 <output name="proteinorthograph">
234 <assert_contents>
235 <has_text text="E_11&#009;C_11&#009;"/>
236 </assert_contents>
237 </output>
238 </test> 190 </test>
239 <test expect_num_outputs="3"> <!-- blat --> 191 <test expect_num_outputs="3"> <!-- blat -->
240 <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/> 192 <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/>
241 <param name="--p" value="blastp"/> 193 <param name="p" value="blastp"/>
242 <output name="proteinortho"> 194 <expand macro="test_outputs"/>
243 <assert_contents> 195 <assert_command>
244 <has_text text="# Species&#009;Genes&#009;Alg.-Conn."/> 196 <has_text text="--p=blastp"/>
245 <has_text text="2&#009;5&#009;0.16"/> 197 </assert_command>
246 <has_text text="M_640,M_642,M_649"/>
247 </assert_contents>
248 </output>
249 <output name="blastgraph">
250 <assert_contents>
251 <has_text text="E_10&#009;C_10&#009;"/>
252 </assert_contents>
253 </output>
254 <output name="proteinorthograph">
255 <assert_contents>
256 <has_text text="E_10&#009;C_10&#009;"/>
257 </assert_contents>
258 </output>
259 </test> 198 </test>
260 </tests> 199 </tests>
261 <help><![CDATA[Proteinortho with POFF - An orthology detection tool 200 <help><![CDATA[Proteinortho with POFF - An orthology detection tool
262 201
263 **What it does** 202 **What it does**