Mercurial > repos > jjohnson > contig_annotation_tool
comparison macros.xml @ 2:9a01840eac52 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 6b978e61a7f66160f2577d907f52dd641f103986-dirty
| author | jjohnson |
|---|---|
| date | Mon, 25 Nov 2019 15:09:24 -0500 |
| parents | ad7507073c3f |
| children | 18ece3d5bcde |
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| 1:86cd2e70b0dc | 2:9a01840eac52 |
|---|---|
| 118 <token name="@ADD_NAMES@"><![CDATA[ | 118 <token name="@ADD_NAMES@"><![CDATA[ |
| 119 #if $names.add_names in ['classification','both']: | 119 #if $names.add_names in ['classification','both']: |
| 120 && CAT add_names $names.only_official $names.exclude_scores | 120 && CAT add_names $names.only_official $names.exclude_scores |
| 121 @CAT_TAXONOMY@ | 121 @CAT_TAXONOMY@ |
| 122 #if $bcat == 'CAT' | 122 #if $bcat == 'CAT' |
| 123 -i cat_output.contigs2classification.tsv | 123 -i cat_output.contig2classification.tsv |
| 124 #else | 124 #else |
| 125 -i cat_output.bin2classification.tsv | 125 -i cat_output.bin2classification.tsv |
| 126 #end if | 126 #end if |
| 127 -o classification_names.txt | 127 -o classification_names.txt |
| 128 && @TXT2TSV@ -i classification_names -o $classification_names | 128 && @TXT2TSV@ -i classification_names.txt -o $classification_names |
| 129 #end if | 129 #end if |
| 130 #if $names.add_names in ['orf2lca','both']: | 130 #if $names.add_names in ['orf2lca','both']: |
| 131 && CAT add_names $names.only_official $names.exclude_scores | 131 && CAT add_names $names.only_official $names.exclude_scores |
| 132 @CAT_TAXONOMY@ | 132 @CAT_TAXONOMY@ |
| 133 -i cat_output.ORF2LCA.tsv | 133 -i cat_output.ORF2LCA.tsv |
| 144 <token name="@SUMMARISE@"><![CDATA[ | 144 <token name="@SUMMARISE@"><![CDATA[ |
| 145 #if $summarise in ['classification']: | 145 #if $summarise in ['classification']: |
| 146 #if $names.add_names in ['classification','both'] and $names.only_official: | 146 #if $names.add_names in ['classification','both'] and $names.only_official: |
| 147 #set $summary_input = $classification_names | 147 #set $summary_input = $classification_names |
| 148 #else | 148 #else |
| 149 #set $summary_input = classification_offical_names | 149 #set $summary_input = 'classification_offical_names' |
| 150 && CAT add_names --only_official | 150 && CAT add_names --only_official |
| 151 @CAT_TAXONOMY@ | 151 @CAT_TAXONOMY@ |
| 152 #if $bcat == 'CAT' | 152 #if $bcat == 'CAT' |
| 153 -i cat_output.contigs2classification.tsv | 153 -i cat_output.contig2classification.tsv |
| 154 #else | 154 #else |
| 155 -i cat_output.bin2classification.tsv | 155 -i cat_output.bin2classification.tsv |
| 156 #end if | 156 #end if |
| 157 -o $summary_input | 157 -o $summary_input |
| 158 #end if | 158 #end if |
| 166 #end if | 166 #end if |
| 167 ]]></token> | 167 ]]></token> |
| 168 | 168 |
| 169 <xml name="select_outputs"> | 169 <xml name="select_outputs"> |
| 170 <param name="select_outputs" type="select" multiple="true" optional="false" label="Select outputs"> | 170 <param name="select_outputs" type="select" multiple="true" optional="false" label="Select outputs"> |
| 171 <option value="log" selected="true">CAT.log</option> | 171 <option value="log" selected="true">log</option> |
| 172 <option value="predicted_proteins_faa" selected="true">predicted_proteins.faa</option> | 172 <option value="predicted_proteins_faa" selected="true">predicted_proteins.faa</option> |
| 173 <option value="predicted_proteins_gff">predicted_proteins.gff</option> | 173 <option value="predicted_proteins_gff">predicted_proteins.gff</option> |
| 174 <option value="alignment_diamond">alignment.diamond</option> | 174 <option value="alignment_diamond">alignment.diamond</option> |
| 175 <option value="orf2lca" selected="true">ORF2LCA.txt</option> | 175 <option value="orf2lca" selected="true">ORF2LCA.txt</option> |
| 176 <yield/> | 176 <yield/> |
| 177 </param> | 177 </param> |
| 178 </xml> | 178 </xml> |
| 179 <xml name="select_cat_outputs"> | 179 <xml name="select_cat_outputs"> |
| 180 <param name="bcat" type="hidden" value="CAT"/> | 180 <param name="bcat" type="hidden" value="CAT"/> |
| 181 <param name="seqtype" type="hidden" value="contig"/> | 181 <param name="seqtype" type="hidden" value="contig"/> |
| 182 <param name="sum_titles" type="hidden" value="contigs,number of ORFs,number of positions"/> | |
| 183 <param name="bin_col" type="hidden" value=""/> | |
| 182 <expand macro="select_outputs"> | 184 <expand macro="select_outputs"> |
| 183 <option value="contig2classification" selected="true">contig2classification.txt</option> | 185 <option value="contig2classification" selected="true">contig2classification.txt</option> |
| 184 </expand> | 186 </expand> |
| 185 </xml> | 187 </xml> |
| 186 <xml name="select_bat_outputs"> | 188 <xml name="select_bat_outputs"> |
| 187 <param name="bcat" type="hidden" value="BAT"/> | 189 <param name="bcat" type="hidden" value="BAT"/> |
| 188 <param name="seqtype" type="hidden" value="bin"/> | 190 <param name="seqtype" type="hidden" value="bin"/> |
| 191 <param name="sum_titles" type="hidden" value="bins"/> | |
| 192 <param name="bin_col" type="hidden" value="bin,"/> | |
| 189 <expand macro="select_outputs"> | 193 <expand macro="select_outputs"> |
| 190 <option value="bin2classification" selected="true">bin2classification.txt</option> | 194 <option value="bin2classification" selected="true">bin2classification.txt</option> |
| 191 </expand> | 195 </expand> |
| 192 </xml> | 196 </xml> |
| 193 | 197 |
| 213 </data> | 217 </data> |
| 214 <data name="orf2lca" format="tabular" label="${bcat}.ORF2LCA.txt" from_work_dir="cat_output.ORF2LCA.tsv"> | 218 <data name="orf2lca" format="tabular" label="${bcat}.ORF2LCA.txt" from_work_dir="cat_output.ORF2LCA.tsv"> |
| 215 <filter>'orf2lca' in select_outputs</filter> | 219 <filter>'orf2lca' in select_outputs</filter> |
| 216 <actions> | 220 <actions> |
| 217 <action name="comment_lines" type="metadata" default="1" /> | 221 <action name="comment_lines" type="metadata" default="1" /> |
| 218 <action name="column_names" type="metadata" default="ORF,lineage,bit-score" /> | 222 <action name="column_names" type="metadata" default="ORF,${bin_col}lineage,bit-score" /> |
| 219 </actions> | 223 </actions> |
| 220 </data> | 224 </data> |
| 221 <data name="contig2classification" format="tabular" label="${bcat}.contig2classification.txt" from_work_dir="cat_output.contig2classification.tsv"> | 225 <data name="contig2classification" format="tabular" label="${bcat}.contig2classification.txt" from_work_dir="cat_output.contig2classification.tsv"> |
| 222 <filter>'contig2classification' in select_outputs</filter> | 226 <filter>'contig2classification' in select_outputs</filter> |
| 223 <actions> | 227 <actions> |
| 231 <action name="comment_lines" type="metadata" default="1" /> | 235 <action name="comment_lines" type="metadata" default="1" /> |
| 232 <action name="column_names" type="metadata" default="bin,classification,reason,lineage,lineage scores" /> | 236 <action name="column_names" type="metadata" default="bin,classification,reason,lineage,lineage scores" /> |
| 233 </actions> | 237 </actions> |
| 234 </data> | 238 </data> |
| 235 <data name="orf2lca_names" format="tabular" label="${bcat}.ORF2LCA.names.txt"> | 239 <data name="orf2lca_names" format="tabular" label="${bcat}.ORF2LCA.names.txt"> |
| 236 <filter>'orf2lca' in names.add_names</filter> | 240 <filter>names['add_names'] in ['both','orf2lca']</filter> |
| 237 <actions> | 241 <actions> |
| 238 <action name="comment_lines" type="metadata" default="1" /> | 242 <action name="comment_lines" type="metadata" default="1" /> |
| 239 <action name="column_names" type="metadata" default="ORF,lineage,bit-score,superkingdom,phylum,class,order,family,genus,species" /> | 243 <action name="column_names" type="metadata" default="ORF,${bin_col}lineage,bit-score,superkingdom,phylum,class,order,family,genus,species" /> |
| 240 </actions> | 244 </actions> |
| 241 </data> | 245 </data> |
| 242 <data name="classification_names" format="tabular" label="${bcat}.${seqtype}2classification.names.txt"> | 246 <data name="classification_names" format="tabular" label="${bcat}.${seqtype}2classification.names.txt"> |
| 243 <filter>'classification' in names.add_names</filter> | 247 <filter>names['add_names'] in ['both','classification']</filter> |
| 244 <actions> | 248 <actions> |
| 245 <action name="comment_lines" type="metadata" default="1" /> | 249 <action name="comment_lines" type="metadata" default="1" /> |
| 246 <action name="column_names" type="metadata" default="${seqtype},classification,reason,lineage,lineage scores,superkingdom,phylum,class,order,family,genus,species" /> | 250 <action name="column_names" type="metadata" default="${seqtype},classification,reason,lineage,lineage scores,superkingdom,phylum,class,order,family,genus,species" /> |
| 247 </actions> | 251 </actions> |
| 248 </data> | 252 </data> |
| 249 <data name="classification_summary" format="tabular" label="${bcat}.${seqtype}2classification.summary.txt"> | 253 <data name="classification_summary" format="tabular" label="${bcat}.${seqtype}2classification.summary.txt"> |
| 250 <filter>'classification' in summarise</filter> | 254 <filter>'classification' in summarise</filter> |
| 251 <actions> | 255 <actions> |
| 252 <action name="comment_lines" type="metadata" default="1" /> | 256 <action name="comment_lines" type="metadata" default="4" /> |
| 253 <action name="column_names" type="metadata" default="rank,clade,number of contigs,number of ORFs,number of positions" /> | 257 <action name="column_names" type="metadata" default="rank,clade,number of ${sum_titles}" /> |
| 254 </actions> | 258 </actions> |
| 255 </data> | 259 </data> |
| 256 </xml> | 260 </xml> |
| 257 <token name="@COMMON_HELP@"><![CDATA[ | 261 <token name="@COMMON_HELP@"><![CDATA[ |
| 258 The CAT/BAT workflow is described at: https://github.com/dutilh/CAT | 262 The CAT/BAT workflow is described at: https://github.com/dutilh/CAT |