Mercurial > repos > abims-sbr > mutcount

comparison MutCount.xml @ 9:04a9ada73cc4 draft

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planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit f1ba8d136e0129f3e8435b25a95f70f697d51464-dirty
author abims-sbr
date Tue, 03 Jul 2018 10:55:46 -0400
parents 705a7bf4c311
children f62c76aab669
comparison
equal deleted inserted replaced
8:705a7bf4c311 9:04a9ada73cc4
23 #if str($method.method_run) == "concat" : 23 #if str($method.method_run) == "concat" :
24 python '$__tool_directory__/scripts/S01a_codons_counting.py' ${method.concat_nuc} '$method.list_species' '$method.list_species_boot' $method.num_iter $method.num_sampled > ${log} 24 python '$__tool_directory__/scripts/S01a_codons_counting.py' ${method.concat_nuc} '$method.list_species' '$method.list_species_boot' $method.num_iter $method.num_sampled > ${log}
25 #end if 25 #end if
26 26
27 #if str($method.method_run) == "separated" : 27 #if str($method.method_run) == "separated" :
28 #set $infiles = ""
29 #for $input in $method.sep_file 28 #for $input in $method.sep_file
30 ln -s '$input' '$input.element_identifier'; 29 ln -s '$input' '$input.element_identifier';
31 #set $infiles = $infiles + $input.element_identifier + "," 30 echo '$input.element_identifier' >> list_files;
32 #end for 31 #end for
33 #set $infiles = $infiles[:-1]
34 32
35 #if str($method.format_run)== "nucleic" : 33 #if str($method.format_run)== "nucleic" :
36 python '$__tool_directory__/scripts/S02b_study_seq_composition_nuc.py' '$infiles' ${method.concat_phy} 34 python '$__tool_directory__/scripts/S02b_study_seq_composition_nuc.py' ${method.concat_phy} list_files
37 #end if 35 #end if
38 36
39 #if str($method.format_run)== "proteic" : 37 #if str($method.format_run)== "proteic" :
40 cp '$__tool_directory__/scripts/amino_acid_properties.csv' . 38 cp '$__tool_directory__/scripts/amino_acid_properties.csv' .
41 && 39 &&
42 python '$__tool_directory__/scripts/S01b_study_seq_composition_aa.py' '$infiles' ${method.concat_phy} 40 python '$__tool_directory__/scripts/S01b_study_seq_composition_aa.py' ${method.concat_phy} list_files
43 #end if 41 #end if
44 #end if 42 #end if
45 43
46 ]]> 44 ]]>
47 </command> 45 </command>
155 </data> 153 </data>
156 154
157 </outputs> 155 </outputs>
158 156
159 <tests> 157 <tests>
160
161 <test> 158 <test>
162 <conditional name="method" > 159 <conditional name="method" >
163 <param name="method_run" value="concat" /> 160 <param name="method_run" value="concat" />
164 <param name="concat_nuc" ftype="fasta" value="concatenation.fasta" /> 161 <param name="concat_nuc" ftype="fasta" value="concatenation.fasta" />
165 <param name="list_species" ftype="text" value="Ps,Pp,Pu,Ac,Ap,Pf,Pg,Ph,Pi" /> 162 <param name="list_species" ftype="text" value="Ps,Pp,Pu,Ac,Ap,Pf,Pg,Ph,Pi" />
174 <output name="gc_and_others_freqs" value="OUT_concat/gc_and_others_freqs.csv"/> 171 <output name="gc_and_others_freqs" value="OUT_concat/gc_and_others_freqs.csv"/>
175 <output name="codons_transitions_freqs" value="OUT_concat/codons_transitions_freqs.csv" lines_diff="72"/> 172 <output name="codons_transitions_freqs" value="OUT_concat/codons_transitions_freqs.csv" lines_diff="72"/>
176 <output name="aa_transitions_freqs" value="OUT_concat/aa_transitions_freqs.csv" lines_diff="72"/> 173 <output name="aa_transitions_freqs" value="OUT_concat/aa_transitions_freqs.csv" lines_diff="72"/>
177 <output name="aatypes_transitions_freqs" value="OUT_concat/aatypes_transitions_freqs.csv" lines_diff="72"/> 174 <output name="aatypes_transitions_freqs" value="OUT_concat/aatypes_transitions_freqs.csv" lines_diff="72"/>
178 </test> 175 </test>
179
180 <test> 176 <test>
181 <conditional name="method" > 177 <conditional name="method" >
182 <param name="method_run" value="separated" /> 178 <param name="method_run" value="separated" />
183 <param name="format_run" value="nucleic" /> 179 <param name="format_run" value="nucleic" />
184 <param name="sep_file" ftype="fasta" value="sep_nuc/locus1_sp6_sp6.fasta,sep_nuc/locus1_sp8_sp8.fasta,sep_nuc/locus2_sp6_sp6.fasta" /> 180 <param name="sep_file" ftype="fasta" value="sep_nuc/orthogroup_1_sp6_sp6.fasta,sep_nuc/orthogroup_1_sp8_sp8.fasta,sep_nuc/orthogroup_2_sp6_sp6.fasta" />
185 <param name="concat_phy" ftype="fasta" value="phylogeny_concat.fasta" /> 181 <param name="concat_phy" ftype="fasta" value="phylogeny_concat.fasta" />
186 </conditional> 182 </conditional>
187 <output name="nuc_comp"> 183 <output name="nuc_comp">
188 <assert_contents> 184 <assert_contents>
189 <has_line line="locus2_sp6_sp6.fasta,0.30208,0.23958,0.19792,0.26042,0.29688,0.27604,0.18229,0.24479,NA,NA,NA,NA,0.30208,0.24479,0.19792,0.25521,NA,NA,NA,NA,0.31250,0.26042,0.17188,0.25521,0.32292,0.21875,0.20312,0.25521,NA,NA,NA,NA,NA,NA,NA,NA,0.31771,0.25521,0.17708,0.25000"/> 185 <has_line line="orthogroup_2_sp6_sp6.fasta,0.30208,0.23958,0.19792,0.26042,0.29688,0.27604,0.18229,0.24479,NA,NA,NA,NA,0.30208,0.24479,0.19792,0.25521,NA,NA,NA,NA,0.31250,0.26042,0.17188,0.25521,0.32292,0.21875,0.20312,0.25521,NA,NA,NA,NA,NA,NA,NA,NA,0.31771,0.25521,0.17708,0.25000"/>
190 </assert_contents> 186 </assert_contents>
191 </output> 187 </output>
192 <output name="percent_gc"> 188 <output name="percent_gc">
193 <assert_contents> 189 <assert_contents>
194 <has_line line="locus2_sp6_sp6.fasta,45.83333,42.70833,NA,45.31250,NA,42.70833,45.83333,NA,NA,42.70833" /> 190 <has_line line="orthogroup_2_sp6_sp6.fasta,45.83333,42.70833,NA,45.31250,NA,42.70833,45.83333,NA,NA,42.70833" />
195 </assert_contents> 191 </assert_contents>
196 </output> 192 </output>
197 <output name="percent_pur"> 193 <output name="percent_pur">
198 <assert_contents> 194 <assert_contents>
199 <has_line line="locus2_sp6_sp6.fasta,56.25000,54.16667,NA,55.72917,NA,56.77083,57.81250,NA,NA,56.77083" /> 195 <has_line line="orthogroup_2_sp6_sp6.fasta,56.25000,54.16667,NA,55.72917,NA,56.77083,57.81250,NA,NA,56.77083" />
200 </assert_contents> 196 </assert_contents>
201 </output> 197 </output>
202 <output name="purine_load"> 198 <output name="purine_load">
203 <assert_contents> 199 <assert_contents>
204 <has_line line="locus2_sp6_sp6.fasta,192,12,12,62.50000,62.50000,192,12,4,62.50000,20.83333,NA,NA,NA,NA,NA,192,11,11,57.29167,57.29167,NA,NA,NA,NA,NA,192,16,10,83.33333,52.08333,192,10,20,52.08333,104.16667,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,192,14,12,72.91667,62.50000" /> 200 <has_line line="orthogroup_2_sp6_sp6.fasta,192,12,12,62.50000,62.50000,192,12,4,62.50000,20.83333,NA,NA,NA,NA,NA,192,11,11,57.29167,57.29167,NA,NA,NA,NA,NA,192,16,10,83.33333,52.08333,192,10,20,52.08333,104.16667,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,192,14,12,72.91667,62.50000" />
205 </assert_contents> 201 </assert_contents>
206 </output> 202 </output>
207 </test> 203 </test>
208 204
209 <test> 205 <test>
210 <conditional name="method" > 206 <conditional name="method" >
211 <param name="method_run" value="separated" /> 207 <param name="method_run" value="separated" />
212 <param name="format_run" value="proteic" /> 208 <param name="format_run" value="proteic" />
213 <param name="sep_file" ftype="fasta" value="sep_aa/locus1_sp6_sp6.fasta,sep_aa/locus1_sp8_sp8.fasta,sep_aa/locus2_sp6_sp6.fasta" /> 209 <param name="sep_file" ftype="fasta" value="sep_aa/orthogroup_1_sp6_sp6.fasta,sep_aa/orthogroup_1_sp8_sp8.fasta,sep_aa/orthogroup_2_sp6_sp6.fasta" />
214 <param name="concat_phy" ftype="fasta" value="phylogeny_concat.fasta" /> 210 <param name="concat_phy" ftype="fasta" value="phylogeny_concat.fasta" />
215 </conditional> 211 </conditional>
216 <output name="ivywrel"> 212 <output name="ivywrel">
217 <assert_contents> 213 <assert_contents>
218 <has_line line="locus1_sp8_sp8.fasta,25.00000,0.36765,28.00000,0.36364,NA,NA,NA,NA,27.00000,0.35065,27.00000,0.35065,28.00000,0.36364,0.00000,0.00000,27.00000,0.40909,27.00000,0.35065" /> 214 <has_line line="orthogroup_1_sp8_sp8.fasta,25.00000,0.36765,28.00000,0.36364,NA,NA,NA,NA,27.00000,0.35065,27.00000,0.35065,28.00000,0.36364,0.00000,0.00000,27.00000,0.40909,27.00000,0.35065" />
219 </assert_contents> 215 </assert_contents>
220 </output> 216 </output>
221 <output name="rhkde"> 217 <output name="rhkde">
222 <assert_contents> 218 <assert_contents>
223 <has_line line="locus1_sp6_sp6.fasta,28.00000,0.35897,14.00000,0.17949,14.00000,0.17949,30.00000,0.38462,16.00000,0.20513,14.00000,0.17949,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,30.00000,0.38462,16.00000,0.20513,14.00000,0.17949,30.00000,0.38462,16.00000,0.20513,14.00000,0.17949,30.00000,0.38462,16.00000,0.20513,14.00000,0.17949,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,30.00000,0.38462,16.00000,0.20513,14.00000,0.17949"/> 219 <has_line line="orthogroup_1_sp6_sp6.fasta,28.00000,0.35897,14.00000,0.17949,14.00000,0.17949,30.00000,0.38462,16.00000,0.20513,14.00000,0.17949,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,30.00000,0.38462,16.00000,0.20513,14.00000,0.17949,30.00000,0.38462,16.00000,0.20513,14.00000,0.17949,30.00000,0.38462,16.00000,0.20513,14.00000,0.17949,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,30.00000,0.38462,16.00000,0.20513,14.00000,0.17949"/>
224 </assert_contents> 220 </assert_contents>
225 </output> 221 </output>
226 <output name="payre_mvgds"> 222 <output name="payre_mvgds">
227 <assert_contents> 223 <assert_contents>
228 <has_line line="locus1_sp8_sp8.fasta,16.00000,0.23529,3.00000,0.04412,27.00000,0.39706,0.59259,0.11111,18.00000,0.23377,4.00000,0.05195,29.00000,0.37662,0.62069,0.13793,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,19.00000,0.24675,6.00000,0.07792,30.00000,0.38961,0.63333,0.20000,20.00000,0.25974,7.00000,0.09091,32.00000,0.41558,0.62500,0.21875,20.00000,0.25974,5.00000,0.06494,29.00000,0.37662,0.68966,0.17241,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,14.00000,0.21212,2.00000,0.03030,26.00000,0.39394,0.53846,0.07692,19.00000,0.24675,6.00000,0.07792,32.00000,0.41558,0.59375,0.18750"/> 224 <has_line line="orthogroup_1_sp8_sp8.fasta,16.00000,0.23529,3.00000,0.04412,27.00000,0.39706,0.59259,0.11111,18.00000,0.23377,4.00000,0.05195,29.00000,0.37662,0.62069,0.13793,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,19.00000,0.24675,6.00000,0.07792,30.00000,0.38961,0.63333,0.20000,20.00000,0.25974,7.00000,0.09091,32.00000,0.41558,0.62500,0.21875,20.00000,0.25974,5.00000,0.06494,29.00000,0.37662,0.68966,0.17241,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,14.00000,0.21212,2.00000,0.03030,26.00000,0.39394,0.53846,0.07692,19.00000,0.24675,6.00000,0.07792,32.00000,0.41558,0.59375,0.18750"/>
229 </assert_contents> 225 </assert_contents>
230 </output> 226 </output>
231 <output name="avlimfyw"> 227 <output name="avlimfyw">
232 <assert_contents> 228 <assert_contents>
233 <has_line line="locus2_sp6_sp6.fasta,27.00000,0.42188,21.00000,0.32812,6.00000,0.09375,28.00000,0.43750,22.00000,0.34375,6.00000,0.09375,NA,NA,NA,NA,NA,NA,28.00000,0.43750,22.00000,0.34375,6.00000,0.09375,NA,NA,NA,NA,NA,NA,28.00000,0.43750,22.00000,0.34375,6.00000,0.09375,30.00000,0.46875,24.00000,0.37500,6.00000,0.09375,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,28.00000,0.43750,22.00000,0.34375,6.00000,0.09375"/> 229 <has_line line="orthogroup_2_sp6_sp6.fasta,27.00000,0.42188,21.00000,0.32812,6.00000,0.09375,28.00000,0.43750,22.00000,0.34375,6.00000,0.09375,NA,NA,NA,NA,NA,NA,28.00000,0.43750,22.00000,0.34375,6.00000,0.09375,NA,NA,NA,NA,NA,NA,28.00000,0.43750,22.00000,0.34375,6.00000,0.09375,30.00000,0.46875,24.00000,0.37500,6.00000,0.09375,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,28.00000,0.43750,22.00000,0.34375,6.00000,0.09375"/>
234 </assert_contents> 230 </assert_contents>
235 </output> 231 </output>
236 </test> 232 </test>
233
237 </tests> 234 </tests>
238 235
239 <help> 236 <help>
240 237
241 @HELP_AUTHORS@ 238 @HELP_AUTHORS@