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comparison data_manager/macros.xml @ 1:2bec6d7877fc draft default tip

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planemo upload commit 68dbaa3df00fe628b7dc0310cd1d19605d0bb307-dirty
author jjohnson
date Tue, 26 Nov 2019 16:11:24 -0500
parents f59e7e242bde
children
comparison
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0:f59e7e242bde 1:2bec6d7877fc
17 <option value="cached">local cached database</option> 17 <option value="cached">local cached database</option>
18 <option value="history">history</option> 18 <option value="history">history</option>
19 </param> 19 </param>
20 <when value="cached"> 20 <when value="cached">
21 <param name="cat_builtin" type="select" label="Use a built-in CAT database" help="If the CAT database of interest is not listed, contact your Galaxy administrator"> 21 <param name="cat_builtin" type="select" label="Use a built-in CAT database" help="If the CAT database of interest is not listed, contact your Galaxy administrator">
22 <options from_data_table="cat_databases"> 22 <options from_data_table="cat_database">
23 <filter type="sort_by" column="2" /> 23 <filter type="sort_by" column="2" />
24 <validator type="no_options" message="No CAT database is available." /> 24 <validator type="no_options" message="No CAT database is available." />
25 </options> 25 </options>
26 </param> 26 </param>
27 </when> 27 </when>
75 --proteins_fasta '$previous.proteins_fasta' 75 --proteins_fasta '$previous.proteins_fasta'
76 --diamond_alignment '$previous.diamond_alignment' 76 --diamond_alignment '$previous.diamond_alignment'
77 #end if 77 #end if
78 --out_prefix 'cat_output' 78 --out_prefix 'cat_output'
79 ]]></token> 79 ]]></token>
80
81 <xml name="custom_settings"> 80 <xml name="custom_settings">
82 <param argument="--range" type="integer" value="10" min="0" max="49" label="range"/> 81 <param argument="--range" type="integer" value="10" min="0" max="49" label="range"/>
83 <param argument="--fraction" type="float" value="0.5" min="0" max="0.99" label="fraction"/> 82 <param argument="--fraction" type="float" value="0.5" min="0" max="0.99" label="fraction"/>
84 </xml> 83 </xml>
85 <token name="@CUSTOM_SETTINGS@"><![CDATA[ 84 <token name="@CUSTOM_SETTINGS@"><![CDATA[
113 <when value="both"> 112 <when value="both">
114 <expand macro="add_names_options"/> 113 <expand macro="add_names_options"/>
115 </when> 114 </when>
116 </conditional> 115 </conditional>
117 </xml> 116 </xml>
117 <token name="@TXT2TSV@">${__tool_directory__}/tabpad.py</token>
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 && ${__tool_directory__}/tabpad.py -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
134 -o orf2lca_names.txt 134 -o orf2lca_names.txt
135 && @TXT2TSV@ -i orf2lca_names.txt -o $orf2lca_names 135 && ${__tool_directory__}/tabpad.py -i orf2lca_names.txt -o $orf2lca_names
136 #end if 136 #end if
137 ]]></token> 137 ]]></token>
138 <xml name="summarise"> 138 <xml name="summarise">
139 <param name="summarise" type="select" label="summarise"> 139 <param name="summarise" type="select" label="summarise">
140 <option value="no">No</option> 140 <option value="no">No</option>
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
160 #if $bcat == 'CAT' 160 #if $bcat == 'CAT'
161 -c $contigs_fasta 161 -c $contigs_fasta
162 #end if 162 #end if
163 -i $summary_input 163 -i $summary_input
164 -o classification_summary.txt 164 -o classification_summary.txt
165 && @TXT2TSV@ -i classification_summary.txt -o $classification_summary 165 && ${__tool_directory__}/tabpad.py -i classification_summary.txt -o $classification_summary
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
194 <token name="@TXT2TSV@"><![CDATA[
195 $__tool_directory__/tabpad.py
196 ]]></token>
197 <xml name="outputs"> 197 <xml name="outputs">
198 <data name="log" format="txt" label="${bcat}.log" from_work_dir="cat_output.log"> 198 <data name="log" format="txt" label="${bcat}.log" from_work_dir="cat_output.log">
199 <filter>'log' in select_outputs or not select_outputs</filter> 199 <filter>'log' in select_outputs or not select_outputs</filter>
200 </data> 200 </data>
201 <data name="predicted_proteins_faa" format="fasta" label="${bcat}.predicted_proteins.faa" from_work_dir="cat_output.predicted_proteins.faa"> 201 <data name="predicted_proteins_faa" format="fasta" label="${bcat}.predicted_proteins.faa" from_work_dir="cat_output.predicted_proteins.faa">
213 </data> 213 </data>
214 <data name="orf2lca" format="tabular" label="${bcat}.ORF2LCA.txt" from_work_dir="cat_output.ORF2LCA.tsv"> 214 <data name="orf2lca" format="tabular" label="${bcat}.ORF2LCA.txt" from_work_dir="cat_output.ORF2LCA.tsv">
215 <filter>'orf2lca' in select_outputs</filter> 215 <filter>'orf2lca' in select_outputs</filter>
216 <actions> 216 <actions>
217 <action name="comment_lines" type="metadata" default="1" /> 217 <action name="comment_lines" type="metadata" default="1" />
218 <action name="column_names" type="metadata" default="ORF,lineage,bit-score" /> 218 <action name="column_names" type="metadata" default="ORF,${bin_col}lineage,bit-score" />
219 </actions> 219 </actions>
220 </data> 220 </data>
221 <data name="contig2classification" format="tabular" label="${bcat}.contig2classification.txt" from_work_dir="cat_output.contig2classification.tsv"> 221 <data name="contig2classification" format="tabular" label="${bcat}.contig2classification.txt" from_work_dir="cat_output.contig2classification.tsv">
222 <filter>'contig2classification' in select_outputs</filter> 222 <filter>'contig2classification' in select_outputs</filter>
223 <actions> 223 <actions>
231 <action name="comment_lines" type="metadata" default="1" /> 231 <action name="comment_lines" type="metadata" default="1" />
232 <action name="column_names" type="metadata" default="bin,classification,reason,lineage,lineage scores" /> 232 <action name="column_names" type="metadata" default="bin,classification,reason,lineage,lineage scores" />
233 </actions> 233 </actions>
234 </data> 234 </data>
235 <data name="orf2lca_names" format="tabular" label="${bcat}.ORF2LCA.names.txt"> 235 <data name="orf2lca_names" format="tabular" label="${bcat}.ORF2LCA.names.txt">
236 <filter>'orf2lca' in names.add_names</filter> 236 <filter>names['add_names'] in ['both','orf2lca']</filter>
237 <actions> 237 <actions>
238 <action name="comment_lines" type="metadata" default="1" /> 238 <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" /> 239 <action name="column_names" type="metadata" default="ORF,${bin_col}lineage,bit-score,superkingdom,phylum,class,order,family,genus,species" />
240 </actions> 240 </actions>
241 </data> 241 </data>
242 <data name="classification_names" format="tabular" label="${bcat}.${seqtype}2classification.names.txt"> 242 <data name="classification_names" format="tabular" label="${bcat}.${seqtype}2classification.names.txt">
243 <filter>'classification' in names.add_names</filter> 243 <filter>names['add_names'] in ['both','classification']</filter>
244 <actions> 244 <actions>
245 <action name="comment_lines" type="metadata" default="1" /> 245 <action name="comment_lines" type="metadata" default="1" />
246 <action name="column_names" type="metadata" default="${seqtype},classification,reason,lineage,lineage scores,superkingdom,phylum,class,order,family,genus,species" /> 246 <action name="column_names" type="metadata" default="${seqtype},classification,reason,lineage,lineage scores,superkingdom,phylum,class,order,family,genus,species" />
247 </actions> 247 </actions>
248 </data> 248 </data>
249 <data name="classification_summary" format="tabular" label="${bcat}.${seqtype}2classification.summary.txt"> 249 <data name="classification_summary" format="tabular" label="${bcat}.${seqtype}2classification.summary.txt">
250 <filter>'classification' in summarise</filter> 250 <filter>'classification' in summarise</filter>
251 <actions> 251 <actions>
252 <action name="comment_lines" type="metadata" default="1" /> 252 <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" /> 253 <action name="column_names" type="metadata" default="rank,clade,number of ${sum_titles}" />
254 </actions> 254 </actions>
255 </data> 255 </data>
256 </xml> 256 </xml>
257 <token name="@COMMON_HELP@"><![CDATA[ 257 <token name="@COMMON_HELP@"><![CDATA[
258 The CAT/BAT workflow is described at: https://github.com/dutilh/CAT 258 The CAT/BAT workflow is described at: https://github.com/dutilh/CAT
259 ]]></token> 259 ]]></token>
260 <xml name="citations"> 260 <xml name="citations">
261 <citations> 261 <citations>
262 <citation type="doi">https://doi.org/10.1101/072868</citation> 262 <citation type="doi">https://doi.org/10.1101/072868</citation>
263 <citation type="doi">https://doi.org/10.1186/s13059-019-1817-x</citation> 263 <citation type="doi">https://doi.org/10.1186/s13059-019-1817-x</citation>
264 <citation type="doi">https://doi.org/10.1038/nmeth.3176</citation>
265 <citation type="doi">https://doi.org/10.1186/1471-2105-11-119</citation>
264 <yield /> 266 <yield />
265 </citations> 267 </citations>
266 </xml> 268 </xml>
267 </macros> 269 </macros>