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comparison intarna.xml @ 9:56f1cef52e96 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
author bgruening
date Wed, 30 Oct 2019 12:30:28 -0400
parents fd067a1143f3
children a3d8b6b2ffd8
comparison
equal deleted inserted replaced
8:0795d6cf0967 9:56f1cef52e96
1 <tool id="intarna" name="IntaRNA" version="3.1.1"> 1 <tool id="intarna" name="IntaRNA" version="3.1.2">
2 <description>Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites.</description> 2 <description>Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites.</description>
3 <macros> 3 <macros>
4 <macro name="query_macro"> 4 <macro name="query_macro">
5 <param argument="--query" format="fasta" help="Sequences have to use IUPAC nucleotide encoding. File must be in FASTA format" label="Query sequence(s)" name="query" type="data" /> 5 <param argument="--query" format="fasta" help="Sequences have to use IUPAC nucleotide encoding. File must be in FASTA format" label="Query sequence(s)" name="query" type="data" />
6 <conditional name="qAcc_cond"> 6 <conditional name="qAcc_cond">
65 <option value="B">in both sequences</option> 65 <option value="B">in both sequences</option>
66 </param> 66 </param>
67 </macro> 67 </macro>
68 </macros> 68 </macros>
69 <requirements> 69 <requirements>
70 <requirement type="package" version="3.1.1">intarna</requirement> 70 <requirement type="package" version="3.1.2">intarna</requirement>
71 </requirements> 71 </requirements>
72 <version_command>IntaRNA --version</version_command> 72 <version_command>IntaRNA --version</version_command>
73 <command detect_errors="exit_code"><![CDATA[ 73 <command detect_errors="exit_code"><![CDATA[
74 74
75 IntaRNA 75 IntaRNA
76 #if $advancedOptions.advancedSelector == "advanced" 76 ## Multithreading
77 --threads "\${GALAXY_SLOTS:-1}"
78 ## basic general parameters
77 ## Query parameters 79 ## Query parameters
78 --query '$advancedOptions.query.query' 80 --query '$advancedOptions.query.query'
79 --qAcc $advancedOptions.query.qAcc_cond.qAcc 81 --qAcc $advancedOptions.query.qAcc_cond.qAcc
80 #if $advancedOptions.query.qAcc_cond.qAcc == "P" or $advancedOptions.query.qAcc_cond.qAcc == "E" 82 #if $advancedOptions.query.qAcc_cond.qAcc == "P" or $advancedOptions.query.qAcc_cond.qAcc == "E"
81 --qAccFile '$advancedOptions.query.qAcc_cond.qAccFile' 83 --qAccFile '$advancedOptions.query.qAcc_cond.qAccFile'
82 #end if 84 #end if
83 --qAccW $advancedOptions.query.qAccW 85 --qAccW $advancedOptions.query.qAccW
84 --qAccL $advancedOptions.query.qAccL 86 --qAccL $advancedOptions.query.qAccL
85 --qIntLoopMax $advancedOptions.query.qIntLoopMax
86 #if $advancedOptions.query.qRegion
87 --qRegion '$advancedOptions.query.qRegion'
88 #end if
89 ## Target param. 87 ## Target param.
90 --target '$advancedOptions.target.target' 88 --target '$advancedOptions.target.target'
91 --tAcc $advancedOptions.target.tAcc_cond.tAcc 89 --tAcc $advancedOptions.target.tAcc_cond.tAcc
92 #if $advancedOptions.target.tAcc_cond.tAcc == "P" or $advancedOptions.target.tAcc_cond.tAcc == "E" 90 #if $advancedOptions.target.tAcc_cond.tAcc == "P" or $advancedOptions.target.tAcc_cond.tAcc == "E"
93 --tAccFile '$advancedOptions.target.tAcc_cond.tAccFile' 91 --tAccFile '$advancedOptions.target.tAcc_cond.tAccFile'
94 #end if 92 #end if
95 --tAccW $advancedOptions.target.tAccW 93 --tAccW $advancedOptions.target.tAccW
96 --tAccL $advancedOptions.target.tAccL 94 --tAccL $advancedOptions.target.tAccL
97 --tIntLoopMax $advancedOptions.target.tIntLoopMax
98 #if $advancedOptions.target.tRegion
99 --tRegion '$advancedOptions.target.tRegion'
100 #end if
101 ## Seed param. 95 ## Seed param.
102 #if $advancedOptions.seed.noSeed 96 #if $advancedOptions.seed.noSeed
103 $advancedOptions.seed.noSeed 97 $advancedOptions.seed.noSeed
104 #else 98 #else
105 --seedBP $advancedOptions.seed.seedBP 99 --seedBP $advancedOptions.seed.seedBP
106 --seedMaxE $advancedOptions.seed.seedMaxE
107 --seedMinPu $advancedOptions.seed.seedMinPu
108 #if $advancedOptions.seed.seedMaxUP > 0 100 #if $advancedOptions.seed.seedMaxUP > 0
109 --seedMaxUP $advancedOptions.seed.seedMaxUP 101 --seedMaxUP $advancedOptions.seed.seedMaxUP
110 #end if 102 #end if
103 #end if
104 ## Prediction param.
105 --mode $advancedOptions.interaction.mode
106 --energy V
107 ## Output param.
108 --out $outfile
109 --outMode C
110 --outSep "`printf "\t"`"
111 --outNumber $advancedOptions.output.outNumber
112 --outOverlap $advancedOptions.output.outOverlap
113 --outCsvCols '$advancedOptions.output.outCsvCols'
114 --outCsvSort '$advancedOptions.output.outCsvSort'
115 #if $advancedOptions.advancedSelector == "advanced"
116 ## Query parameters
117 --qIntLoopMax $advancedOptions.query.qIntLoopMax
118 #if $advancedOptions.query.qRegion
119 --qRegion '$advancedOptions.query.qRegion'
120 #end if
121 ## Target param.
122 --tIntLoopMax $advancedOptions.target.tIntLoopMax
123 #if $advancedOptions.target.tRegion
124 --tRegion '$advancedOptions.target.tRegion'
125 #end if
126 ## Seed param.
127 #if not $advancedOptions.seed.noSeed
128 --seedMaxE $advancedOptions.seed.seedMaxE
129 --seedMinPu $advancedOptions.seed.seedMinPu
111 #if $advancedOptions.seed.seedQMaxUP 130 #if $advancedOptions.seed.seedQMaxUP
112 --seedQMaxUP $advancedOptions.seed.seedQMaxUP 131 --seedQMaxUP $advancedOptions.seed.seedQMaxUP
113 #end if 132 #end if
114 #if $advancedOptions.seed.seedTMaxUP 133 #if $advancedOptions.seed.seedTMaxUP
115 --seedTMaxUP $advancedOptions.seed.seedTMaxUP 134 --seedTMaxUP $advancedOptions.seed.seedTMaxUP
127 #end if 146 #end if
128 #if $advancedOptions.shape.tShape 147 #if $advancedOptions.shape.tShape
129 --tShape '$advancedOptions.shape.tShape' 148 --tShape '$advancedOptions.shape.tShape'
130 #end if 149 #end if
131 ## Prediction param. 150 ## Prediction param.
132 --mode $advancedOptions.interaction.mode
133 --model $advancedOptions.interaction.model 151 --model $advancedOptions.interaction.model
134 --energy V
135 --energyVRNA '$advancedOptions.interaction.energyVRNA' 152 --energyVRNA '$advancedOptions.interaction.energyVRNA'
136 --temperature $advancedOptions.interaction.temperature 153 --temperature $advancedOptions.interaction.temperature
137 #if $advancedOptions.interaction.windowWidth 154 #if $advancedOptions.interaction.windowWidth
138 --windowWidth $advancedOptions.interaction.windowWidth 155 --windowWidth $advancedOptions.interaction.windowWidth
139 --windowOverlap $advancedOptions.interaction.windowOverlap 156 --windowOverlap $advancedOptions.interaction.windowOverlap
140 #end if 157 #end if
141
142 ##Output param. 158 ##Output param.
143 ## create temporary output file to be converted to tab-separated output (see below)
144 --out STDOUT
145 --outMode C
146 --outCsvCols '$advancedOptions.output.outCsvCols'
147 --outCsvSort '$advancedOptions.output.outCsvSort'
148 --outNumber $advancedOptions.output.outNumber
149 --outOverlap $advancedOptions.output.outOverlap
150 --outMaxE $advancedOptions.output.outMaxE 159 --outMaxE $advancedOptions.output.outMaxE
151 --outDeltaE $advancedOptions.output.outDeltaE 160 --outDeltaE $advancedOptions.output.outDeltaE
152 ## add additional output files 161 ## add additional output files
153 #if $advancedOptions.output.add_output_cond.selector == "add" 162 #if $advancedOptions.output.add_output_cond.selector == "add"
154 #if str($advancedOptions.output.add_output_cond.add_output.value) != 'None' 163 #if str($advancedOptions.output.add_output_cond.add_output.value) != 'None'
164 #end if 173 #end if
165 --out '$curOutFile' 174 --out '$curOutFile'
166 #end for 175 #end for
167 #end if 176 #end if
168 #end if 177 #end if
169 #elif $advancedOptions.advancedSelector == "basic"
170 ## Query parameters
171 --query '$advancedOptions.query.query'
172 --qAcc $advancedOptions.query.qAcc_cond.qAcc
173 #if $advancedOptions.query.qAcc_cond.qAcc == "P" or $advancedOptions.query.qAcc_cond.qAcc == "E"
174 --qAccFile '$advancedOptions.query.qAcc_cond.qAccFile'
175 #end if
176 --qAccW $advancedOptions.query.qAccW
177 --qAccL $advancedOptions.query.qAccL
178 ## Target param.
179 --target '$advancedOptions.target.target'
180 --tAcc $advancedOptions.target.tAcc_cond.tAcc
181 #if $advancedOptions.target.tAcc_cond.tAcc == "P" or $advancedOptions.target.tAcc_cond.tAcc == "E"
182 --tAccFile '$advancedOptions.target.tAcc_cond.tAccFile'
183 #end if
184 --tAccW $advancedOptions.target.tAccW
185 --tAccL $advancedOptions.target.tAccL
186 ## Seed param.
187 #if $advancedOptions.seed.noSeed
188 $advancedOptions.seed.noSeed
189 #else
190 --seedBP $advancedOptions.seed.seedBP
191 --seedMaxUP $advancedOptions.seed.seedMaxUP
192 #end if
193 ## Prediction param.
194 --mode $advancedOptions.interaction.mode
195 ## Output param.
196 ## create temporary output file to be converted to tab-separated output (see below)
197 --out STDOUT
198 --outNumber $advancedOptions.output.outNumber
199 --outOverlap $advancedOptions.output.outOverlap
200 --outMode C
201 --outCsvCols '$advancedOptions.output.outCsvCols'
202 --outCsvSort '$advancedOptions.output.outCsvSort'
203 #end if
204
205 ## Multithreading param.
206 --threads "\${GALAXY_SLOTS:-1}"
207 ## convert semicolon-separated output to tab-separated file
208 | sed 's/\t/ /g' | sed 's/;/\t/g' > '$outfile'
209 ## convert additional semicolon-separated output to tab-separated file
210 #if $advancedOptions.advancedSelector == "advanced"
211 #if $advancedOptions.output.add_output_cond.selector == "add"
212 #if str($advancedOptions.output.add_output_cond.add_output.value) != 'None'
213 #for $outFile in $advancedOptions.output.add_output_cond.add_output.value:
214 #if $outFile != 'qAcc' and $outFile != 'tAcc' and $outFile != 'qPu' and $outFile != 'tPu'
215 #set curOutFile = 'intarna_' + str($outFile) + '*.tabular'
216 && sed -i 's/\t/ /g' $curOutFile
217 && sed -i 's/;/\t/g' $curOutFile
218 #end if
219 #end for
220 #end if
221 #end if
222 #end if 178 #end if
223 ]]> 179 ]]>
224 </command> 180 </command>
225 <inputs> 181 <inputs>
226 <conditional name="advancedOptions"> 182 <conditional name="advancedOptions">