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comparison data_manager/macros.xml @ 0:f59e7e242bde draft

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planemo upload commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
author jjohnson
date Sun, 24 Nov 2019 21:54:57 -0500
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children 2bec6d7877fc
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-1:000000000000 0:f59e7e242bde
1 <macros>
2 <token name="@VERSION@">5.0.3</token>
3 <xml name="requirements">
4 <requirements>
5 <requirement type="package" version="@VERSION@">cat</requirement>
6 <yield/>
7 </requirements>
8 </xml>
9 <xml name="version_command">
10 <version_command>CAT --version</version_command>
11 </xml>
12 <token name="@DATABASE_FOLDER@">CAT_database</token>
13 <token name="@TAXONOMY_FOLDER@">taxonomy</token>
14 <xml name="cat_db">
15 <conditional name="db">
16 <param name="db_src" type="select" label="CAT database from">
17 <option value="cached">local cached database</option>
18 <option value="history">history</option>
19 </param>
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">
22 <options from_data_table="cat_databases">
23 <filter type="sort_by" column="2" />
24 <validator type="no_options" message="No CAT database is available." />
25 </options>
26 </param>
27 </when>
28 <when value="history">
29 <param name="cat_db" type="data" format="txt" label="A history dataset from CAT prepare tool"/>
30 </when>
31 </conditional>
32 </xml>
33 <token name="@CAT_DB@"><![CDATA[
34 #if $db.db_src == 'cached':
35 --database_folder $db.cat_builtin.fields.database_folder
36 --taxonomy_folder $db.cat_builtin.fields.taxonomy_folder
37 #else
38 #import os.path
39 #set $catdb = $db.cat_db.extra_files_path
40 --database_folder '$os.path.join($catdb,"@DATABASE_FOLDER@")'
41 --taxonomy_folder '$os.path.join($catdb,"@TAXONOMY_FOLDER@")'
42 #end if
43 ]]></token>
44 <token name="@CAT_TAXONOMY@"><![CDATA[
45 #if $db.db_src == 'cached':
46 --taxonomy_folder $db.cat_builtin.fields.taxonomy_folder
47 #else
48 #import os.path
49 #set $catdb = $db.cat_db.extra_files_path
50 --taxonomy_folder '$os.path.join($catdb,"@TAXONOMY_FOLDER@")'
51 #end if
52 ]]></token>
53 <xml name="test_catdb">
54 <conditional name="db">
55 <param name="db_src" value="cached"/>
56 <param name="cat_builtin" value="CAT_prepare_test"/>
57 </conditional>
58 </xml>
59
60 <xml name="use_intermediates">
61 <conditional name="previous">
62 <param name="use_previous" type="select" label="Use previous gene prediction and diamond alignment">
63 <option value="no">No</option>
64 <option value="yes">Yes</option>
65 </param>
66 <when value="no"/>
67 <when value="yes">
68 <param argument="--proteins_fasta" type="data" format="fasta" label="predicted proteins fasta"/>
69 <param argument="--diamond_alignment" type="data" format="fasta" label="alignments file"/>
70 </when>
71 </conditional>
72 </xml>
73 <token name="@USE_INTERMEDIATES@"><![CDATA[
74 #if $previous.use_previous == 'yes'
75 --proteins_fasta '$previous.proteins_fasta'
76 --diamond_alignment '$previous.diamond_alignment'
77 #end if
78 --out_prefix 'cat_output'
79 ]]></token>
80
81 <xml name="custom_settings">
82 <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"/>
84 </xml>
85 <token name="@CUSTOM_SETTINGS@"><![CDATA[
86 --range $range
87 --fraction $fraction
88 ]]></token>
89 <xml name="add_names_options">
90 <param argument="--only_official" type="boolean" truevalue="--only_official" falsevalue="" checked="true"
91 label="Only output official level names."/>
92 <param argument="--exclude_scores" type="boolean" truevalue="--exclude_scores" falsevalue="" checked="false"
93 label="Exclude bit-score support scores in the lineage."/>
94 </xml>
95 <token name="@ADD_NAMES_OPTIONS@"><![CDATA[
96 $only_official $exclude_scores
97 ]]></token>
98 <xml name="add_names">
99 <conditional name="names">
100 <param name="add_names" type="select" label="add_names">
101 <option value="no">No</option>
102 <option value="orf2lca">ORF2LCA.txt</option>
103 <option value="classification">classification.txt</option>
104 <option value="both">ORF2LCA.txt and classification.txt</option>
105 </param>
106 <when value="no"/>
107 <when value="orf2lca">
108 <expand macro="add_names_options"/>
109 </when>
110 <when value="classification">
111 <expand macro="add_names_options"/>
112 </when>
113 <when value="both">
114 <expand macro="add_names_options"/>
115 </when>
116 </conditional>
117 </xml>
118 <token name="@ADD_NAMES@"><![CDATA[
119 #if $names.add_names in ['classification','both']:
120 && CAT add_names $names.only_official $names.exclude_scores
121 @CAT_TAXONOMY@
122 #if $bcat == 'CAT'
123 -i cat_output.contigs2classification.tsv
124 #else
125 -i cat_output.bin2classification.tsv
126 #end if
127 -o classification_names.txt
128 && @TXT2TSV@ -i classification_names -o $classification_names
129 #end if
130 #if $names.add_names in ['orf2lca','both']:
131 && CAT add_names $names.only_official $names.exclude_scores
132 @CAT_TAXONOMY@
133 -i cat_output.ORF2LCA.tsv
134 -o orf2lca_names.txt
135 && @TXT2TSV@ -i orf2lca_names.txt -o $orf2lca_names
136 #end if
137 ]]></token>
138 <xml name="summarise">
139 <param name="summarise" type="select" label="summarise">
140 <option value="no">No</option>
141 <option value="classification">classification.txt</option>
142 </param>
143 </xml>
144 <token name="@SUMMARISE@"><![CDATA[
145 #if $summarise in ['classification']:
146 #if $names.add_names in ['classification','both'] and $names.only_official:
147 #set $summary_input = $classification_names
148 #else
149 #set $summary_input = classification_offical_names
150 && CAT add_names --only_official
151 @CAT_TAXONOMY@
152 #if $bcat == 'CAT'
153 -i cat_output.contigs2classification.tsv
154 #else
155 -i cat_output.bin2classification.tsv
156 #end if
157 -o $summary_input
158 #end if
159 && CAT summarise
160 #if $bcat == 'CAT'
161 -c $contigs_fasta
162 #end if
163 -i $summary_input
164 -o classification_summary.txt
165 && @TXT2TSV@ -i classification_summary.txt -o $classification_summary
166 #end if
167 ]]></token>
168
169 <xml name="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>
172 <option value="predicted_proteins_faa" selected="true">predicted_proteins.faa</option>
173 <option value="predicted_proteins_gff">predicted_proteins.gff</option>
174 <option value="alignment_diamond">alignment.diamond</option>
175 <option value="orf2lca" selected="true">ORF2LCA.txt</option>
176 <yield/>
177 </param>
178 </xml>
179 <xml name="select_cat_outputs">
180 <param name="bcat" type="hidden" value="CAT"/>
181 <param name="seqtype" type="hidden" value="contig"/>
182 <expand macro="select_outputs">
183 <option value="contig2classification" selected="true">contig2classification.txt</option>
184 </expand>
185 </xml>
186 <xml name="select_bat_outputs">
187 <param name="bcat" type="hidden" value="BAT"/>
188 <param name="seqtype" type="hidden" value="bin"/>
189 <expand macro="select_outputs">
190 <option value="bin2classification" selected="true">bin2classification.txt</option>
191 </expand>
192 </xml>
193
194 <token name="@TXT2TSV@"><![CDATA[
195 $__tool_directory__/tabpad.py
196 ]]></token>
197 <xml name="outputs">
198 <data name="log" format="txt" label="${bcat}.log" from_work_dir="cat_output.log">
199 <filter>'log' in select_outputs or not select_outputs</filter>
200 </data>
201 <data name="predicted_proteins_faa" format="fasta" label="${bcat}.predicted_proteins.faa" from_work_dir="cat_output.predicted_proteins.faa">
202 <filter>'predicted_proteins_faa' in select_outputs</filter>
203 </data>
204 <data name="predicted_proteins_gff" format="gff" label="${bcat}.predicted_proteins.gff" from_work_dir="cat_output.predicted_proteins.gff">
205 <filter>'predicted_proteins_gff' in select_outputs</filter>
206 </data>
207 <data name="alignment_diamond" format="tabular" label="${bcat}.alignment.diamond" from_work_dir="cat_output.alignment.diamond">
208 <filter>'alignment_diamond' in select_outputs</filter>
209 <actions>
210 <action name="comment_lines" type="metadata" default="1" />
211 <action name="column_names" type="metadata" default="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore" />
212 </actions>
213 </data>
214 <data name="orf2lca" format="tabular" label="${bcat}.ORF2LCA.txt" from_work_dir="cat_output.ORF2LCA.tsv">
215 <filter>'orf2lca' in select_outputs</filter>
216 <actions>
217 <action name="comment_lines" type="metadata" default="1" />
218 <action name="column_names" type="metadata" default="ORF,lineage,bit-score" />
219 </actions>
220 </data>
221 <data name="contig2classification" format="tabular" label="${bcat}.contig2classification.txt" from_work_dir="cat_output.contig2classification.tsv">
222 <filter>'contig2classification' in select_outputs</filter>
223 <actions>
224 <action name="comment_lines" type="metadata" default="1" />
225 <action name="column_names" type="metadata" default="contig,classification,reason,lineage,lineage scores" />
226 </actions>
227 </data>
228 <data name="bin2classification" format="tabular" label="${bcat}.bin2classification.txt" from_work_dir="cat_output.bin2classification.tsv">
229 <filter>'bin2classification' in select_outputs</filter>
230 <actions>
231 <action name="comment_lines" type="metadata" default="1" />
232 <action name="column_names" type="metadata" default="bin,classification,reason,lineage,lineage scores" />
233 </actions>
234 </data>
235 <data name="orf2lca_names" format="tabular" label="${bcat}.ORF2LCA.names.txt">
236 <filter>'orf2lca' in names.add_names</filter>
237 <actions>
238 <action name="comment_lines" type="metadata" default="1" />
239 <action name="column_names" type="metadata" default="ORF,lineage,bit-score,superkingdom,phylum,class,order,family,genus,species" />
240 </actions>
241 </data>
242 <data name="classification_names" format="tabular" label="${bcat}.${seqtype}2classification.names.txt">
243 <filter>'classification' in names.add_names</filter>
244 <actions>
245 <action name="comment_lines" type="metadata" default="1" />
246 <action name="column_names" type="metadata" default="${seqtype},classification,reason,lineage,lineage scores,superkingdom,phylum,class,order,family,genus,species" />
247 </actions>
248 </data>
249 <data name="classification_summary" format="tabular" label="${bcat}.${seqtype}2classification.summary.txt">
250 <filter>'classification' in summarise</filter>
251 <actions>
252 <action name="comment_lines" type="metadata" default="1" />
253 <action name="column_names" type="metadata" default="rank,clade,number of contigs,number of ORFs,number of positions" />
254 </actions>
255 </data>
256 </xml>
257 <token name="@COMMON_HELP@"><![CDATA[
258 The CAT/BAT workflow is described at: https://github.com/dutilh/CAT
259 ]]></token>
260 <xml name="citations">
261 <citations>
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>
264 <yield />
265 </citations>
266 </xml>
267 </macros>