Mercurial > repos > abims-sbr > mutcount
comparison MutCount.xml @ 4:5766f80370e7 draft
planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 17acd02c547bd1f7661a846661aa99de9743efe9
| author | abims-sbr |
|---|---|
| date | Tue, 27 Feb 2018 08:43:50 -0500 |
| parents | 263caa68d7bb |
| children | 0ba551449008 |
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| 3:263caa68d7bb | 4:5766f80370e7 |
|---|---|
| 87 <filter>(method['method_run']=='concat')</filter> | 87 <filter>(method['method_run']=='concat')</filter> |
| 88 </data> | 88 </data> |
| 89 <data format="csv" name="aatypes_counts" label="aatypes_counts.csv" from_work_dir="aatypes_counts.csv" > | 89 <data format="csv" name="aatypes_counts" label="aatypes_counts.csv" from_work_dir="aatypes_counts.csv" > |
| 90 <filter>(method['method_run']=='concat')</filter> | 90 <filter>(method['method_run']=='concat')</filter> |
| 91 </data> | 91 </data> |
| 92 <data format="csv" name="gc_counts" label="codons_counts.csv" from_work_dir="gc_counts.csv" > | 92 <data format="csv" name="gc_counts" label="gc_counts.csv" from_work_dir="gc_counts.csv" > |
| 93 <filter>(method['method_run']=='concat')</filter> | 93 <filter>(method['method_run']=='concat')</filter> |
| 94 </data> | 94 </data> |
| 95 <data format="csv" name="aa_transitions" label="aa_transitions.csv" from_work_dir="aa_transitions.csv" > | 95 <data format="csv" name="aa_transitions" label="aa_transitions.csv" from_work_dir="aa_transitions.csv" > |
| 96 <filter>(method['method_run']=='concat')</filter> | 96 <filter>(method['method_run']=='concat')</filter> |
| 97 </data> | 97 </data> |
| 178 <param name="method_run" value="separated" /> | 178 <param name="method_run" value="separated" /> |
| 179 <param name="format_run" value="nucleic" /> | 179 <param name="format_run" value="nucleic" /> |
| 180 <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/locus1_sp6_sp6.fasta,sep_nuc/locus1_sp8_sp8.fasta,sep_nuc/locus2_sp6_sp6.fasta" /> |
| 181 <param name="concat_phy" ftype="fasta" value="phylogeny_concat.fasta" /> | 181 <param name="concat_phy" ftype="fasta" value="phylogeny_concat.fasta" /> |
| 182 </conditional> | 182 </conditional> |
| 183 <output name="nuc_comp" value="OUT_nuc/nuc_compositions.csv" lines_diff="2"/> | 183 <output name="nuc_comp"> |
| 184 <output name="percent_gc" value="OUT_nuc/percent_GC.csv" lines_diff="2"/> | 184 <assert_contents> |
| 185 <output name="percent_pur" value="OUT_nuc/percent_purine.csv" lines_diff="2"/> | 185 <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"/> |
| 186 <output name="purine_load" value="OUT_nuc/Purine_Load_Indice.csv" lines_diff="2"/> | 186 </assert_contents> |
| 187 </output> | |
| 188 <output name="percent_gc"> | |
| 189 <assert_contents> | |
| 190 <has_line line="locus2_sp6_sp6.fasta,45.83333,42.70833,NA,45.31250,NA,42.70833,45.83333,NA,NA,42.70833" /> | |
| 191 </assert_contents> | |
| 192 </output> | |
| 193 <output name="percent_pur"> | |
| 194 <assert_contents> | |
| 195 <has_line line="locus2_sp6_sp6.fasta,56.25000,54.16667,NA,55.72917,NA,56.77083,57.81250,NA,NA,56.77083" /> | |
| 196 </assert_contents> | |
| 197 </output> | |
| 198 <output name="purine_load"> | |
| 199 <assert_contents> | |
| 200 <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" /> | |
| 201 </assert_contents> | |
| 202 </output> | |
| 187 </test> | 203 </test> |
| 188 | 204 |
| 189 <test> | 205 <test> |
| 190 <conditional name="method" > | 206 <conditional name="method" > |
| 191 <param name="method_run" value="separated" /> | 207 <param name="method_run" value="separated" /> |
| 192 <param name="format_run" value="proteic" /> | 208 <param name="format_run" value="proteic" /> |
| 193 <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/locus1_sp6_sp6.fasta,sep_aa/locus1_sp8_sp8.fasta,sep_aa/locus2_sp6_sp6.fasta" /> |
| 194 <param name="concat_phy" ftype="fasta" value="phylogeny_concat.fasta" /> | 210 <param name="concat_phy" ftype="fasta" value="phylogeny_concat.fasta" /> |
| 195 </conditional> | 211 </conditional> |
| 196 <output name="ivywrel" value="OUT_aa/IVYWREL.csv" lines_diff="2"/> | 212 <output name="ivywrel"> |
| 197 <output name="rhkde" value="OUT_aa/RHKDE.csv" lines_diff="2"/> | 213 <assert_contents> |
| 198 <output name="payre_mvgds" value="OUT_aa/PAYRE-MVGDS.csv" lines_diff="2"/> | 214 <has_line line="locus2_sp6_sp6.fasta,21.00000,0.32812,23.00000,0.35938,NA,NA,23.00000,0.35938,NA,NA,22.00000,0.34375,23.00000,0.35938,NA,NA,NA,NA,22.00000,0.34375" /> |
| 199 <output name="avlimfyw" value="OUT_aa/AVLIMFYW.csv" lines_diff="2"/> | 215 </assert_contents> |
| 216 </output> | |
| 217 <output name="rhkde"> | |
| 218 <assert_contents> | |
| 219 <has_line line="locus1_sp8_sp8.fasta,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,14.00000,0.18182,4.00000,0.05195,10.00000,0.12987,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,16.00000,0.20779,5.00000,0.06494,11.00000,0.14286,15.00000,0.19481,4.00000,0.05195,11.00000,0.14286,14.00000,0.18182,2.00000,0.02597,12.00000,0.15584,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,13.00000,0.19697,2.00000,0.03030,11.00000,0.16667,15.00000,0.19481,4.00000,0.05195,11.00000,0.14286"/> | |
| 220 </assert_contents> | |
| 221 </output> | |
| 222 <output name="payre_mvgds"> | |
| 223 <assert_contents> | |
| 224 <has_line line="locus2_sp6_sp6.fasta,18.00000,0.28125,6.00000,0.09375,20.00000,0.31250,0.90000,0.30000,18.00000,0.28125,6.00000,0.09375,21.00000,0.32812,0.85714,0.28571,NA,NA,NA,NA,NA,NA,NA,NA,18.00000,0.28125,6.00000,0.09375,20.00000,0.31250,0.90000,0.30000,NA,NA,NA,NA,NA,NA,NA,NA,17.00000,0.26562,6.00000,0.09375,20.00000,0.31250,0.85000,0.30000,20.00000,0.31250,8.00000,0.12500,19.00000,0.29688,1.05263,0.42105,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,17.00000,0.26562,6.00000,0.09375,20.00000,0.31250,0.85000,0.30000"/> | |
| 225 </assert_contents> | |
| 226 </output> | |
| 227 <output name="avlimfyw"> | |
| 228 <assert_contents> | |
| 229 <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"/> | |
| 230 </assert_contents> | |
| 231 </output> | |
| 200 </test> | 232 </test> |
| 201 </tests> | 233 </tests> |
| 202 | 234 |
| 203 <help> | 235 <help> |
| 204 | 236 |