Mercurial > repos > iuc > merqury
comparison merqury.xml @ 2:589078edd230 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
author | iuc |
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date | Mon, 25 Apr 2022 11:20:41 +0000 |
parents | 39edec572bae |
children | f8113c25bc6b |
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1:39edec572bae | 2:589078edd230 |
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15 #if $mode.assembly_options.assembly_01.ext.endswith(".gz") | 15 #if $mode.assembly_options.assembly_01.ext.endswith(".gz") |
16 && gunzip -c $mode.assembly_options.assembly_01 > assembly.fasta | 16 && gunzip -c $mode.assembly_options.assembly_01 > assembly.fasta |
17 #else | 17 #else |
18 && ln -s '$mode.assembly_options.assembly_01' assembly.fasta | 18 && ln -s '$mode.assembly_options.assembly_01' assembly.fasta |
19 #end if | 19 #end if |
20 && merqury.sh read-db.meryl assembly.fasta ${label} | 20 && merqury.sh read-db.meryl assembly.fasta ${label} |
21 #if 'log' in $output_selector | |
22 &> $log_file | |
23 #end if | |
21 && mv ${label}* output_files | 24 && mv ${label}* output_files |
22 && find . -maxdepth 1 -name 'assembly_only*' -type f -print0 | xargs -0r mv -t output_files | 25 && find . -maxdepth 1 -name 'assembly_only*' -type f -print0 | xargs -0r mv -t output_files |
23 #else | 26 #else |
24 #if $mode.assembly_options.assembly_01.ext.endswith(".gz") | 27 #if $mode.assembly_options.assembly_01.ext.endswith(".gz") |
25 && gunzip -c $mode.assembly_options.assembly_01 > assembly_01.fasta | 28 && gunzip -c $mode.assembly_options.assembly_01 > assembly_01.fasta |
30 && gunzip -c $mode.assembly_options.assembly_02 > assembly_02.fasta | 33 && gunzip -c $mode.assembly_options.assembly_02 > assembly_02.fasta |
31 #else | 34 #else |
32 && ln -s '$mode.assembly_options.assembly_02' assembly_02.fasta | 35 && ln -s '$mode.assembly_options.assembly_02' assembly_02.fasta |
33 #end if | 36 #end if |
34 && merqury.sh read-db.meryl assembly_01.fasta assembly_02.fasta ${label} | 37 && merqury.sh read-db.meryl assembly_01.fasta assembly_02.fasta ${label} |
38 #if 'log' in $output_selector | |
39 &> $log_file | |
40 #end if | |
35 && mv ${label}* output_files | 41 && mv ${label}* output_files |
36 && find . -maxdepth 1 -name 'assembly_only*' -type f -print0 | xargs -0r mv -t output_files | 42 && find . -maxdepth 1 -name 'assembly_only*' -type f -print0 | xargs -0r mv -t output_files |
37 #end if | 43 #end if |
38 #else | 44 #else |
39 && mkdir -p read-db.meryl pat.meryl mat.meryl | 45 && mkdir -p read-db.meryl pat.meryl mat.meryl |
45 && gunzip -c $mode.assembly_options.assembly_01 > assembly.fasta | 51 && gunzip -c $mode.assembly_options.assembly_01 > assembly.fasta |
46 #else | 52 #else |
47 && ln -s '$mode.assembly_options.assembly_01' assembly.fasta | 53 && ln -s '$mode.assembly_options.assembly_01' assembly.fasta |
48 #end if | 54 #end if |
49 && merqury.sh read-db.meryl pat.meryl mat.meryl assembly.fasta ${label} | 55 && merqury.sh read-db.meryl pat.meryl mat.meryl assembly.fasta ${label} |
56 #if 'log' in $output_selector | |
57 &> $log_file | |
58 #end if | |
50 && mv ${label}* output_files | 59 && mv ${label}* output_files |
51 && find . -maxdepth 1 -name 'assembly_only*' -type f -print0 | xargs -0r mv -t output_files | 60 && find . -maxdepth 1 -name 'assembly_only*' -type f -print0 | xargs -0r mv -t output_files |
52 #else | 61 #else |
53 #if $mode.assembly_options.assembly_01.ext.endswith(".gz") | 62 #if $mode.assembly_options.assembly_01.ext.endswith(".gz") |
54 && gunzip -c $mode.assembly_options.assembly_01 > assembly_01.fasta | 63 && gunzip -c $mode.assembly_options.assembly_01 > assembly_01.fasta |
59 && gunzip -c $mode.assembly_options.assembly_02 > assembly_02.fasta | 68 && gunzip -c $mode.assembly_options.assembly_02 > assembly_02.fasta |
60 #else | 69 #else |
61 && ln -s '$mode.assembly_options.assembly_02' assembly_02.fasta | 70 && ln -s '$mode.assembly_options.assembly_02' assembly_02.fasta |
62 #end if | 71 #end if |
63 && merqury.sh read-db.meryl pat.meryl mat.meryl assembly_01.fasta assembly_02.fasta ${label} | 72 && merqury.sh read-db.meryl pat.meryl mat.meryl assembly_01.fasta assembly_02.fasta ${label} |
73 #if 'log' in $output_selector | |
74 &> $log_file | |
75 #end if | |
64 && mv ${label}* output_files | 76 && mv ${label}* output_files |
65 && find . -maxdepth 1 -name 'assembly_only*' -type f -print0 | xargs -0r mv -t output_files | 77 && find . -maxdepth 1 -name 'assembly_only*' -type f -print0 | xargs -0r mv -t output_files |
66 #end if | 78 #end if |
67 #end if | 79 #end if |
80 | |
68 ]]> </command> | 81 ]]> </command> |
69 <inputs> | 82 <inputs> |
70 <conditional name="mode"> | 83 <conditional name="mode"> |
71 <param name="options" type="select" | 84 <param name="options" type="select" |
72 label="Evaluation mode" help="Merqury allows two operational modes: default and trio mode."> | 85 label="Evaluation mode" help="Merqury allows two operational modes: default and trio mode."> |
142 <option value="plots" selected="true">Plots</option> | 155 <option value="plots" selected="true">Plots</option> |
143 <option value="sizes">Size files</option> | 156 <option value="sizes">Size files</option> |
144 <option value="stats" selected="true">Stats file</option> | 157 <option value="stats" selected="true">Stats file</option> |
145 <option value="bed">BED: hap-mer tracks</option> | 158 <option value="bed">BED: hap-mer tracks</option> |
146 <option value="wig">WIG: hap-mer tracks</option> | 159 <option value="wig">WIG: hap-mer tracks</option> |
160 <option value="log">Log file</option> | |
147 </param> | 161 </param> |
148 </inputs> | 162 </inputs> |
149 <outputs> | 163 <outputs> |
150 <collection name="bed_files" type="list" label="${tool.name} on ${on_string}: BED files"> | 164 <collection name="bed_files" type="list" label="${tool.name} on ${on_string}: BED files"> |
151 <discover_datasets pattern="(?P<name>.+)\.bed" format="bed" directory="output_files"/> | 165 <discover_datasets pattern="(?P<name>.+)\.bed" format="bed" directory="output_files"/> |
169 </collection> | 183 </collection> |
170 <collection name="stats_files" type="list" label="${tool.name} on ${on_string}: stats"> | 184 <collection name="stats_files" type="list" label="${tool.name} on ${on_string}: stats"> |
171 <discover_datasets pattern="(?P<name>.+)\.stats" format="tabular" directory="output_files"/> | 185 <discover_datasets pattern="(?P<name>.+)\.stats" format="tabular" directory="output_files"/> |
172 <filter>"stats" in output_selector</filter> | 186 <filter>"stats" in output_selector</filter> |
173 </collection> | 187 </collection> |
188 <data name="log_file" format="txt" label="${tool.name} on ${on_string}: log file"> | |
189 <filter>"log" in output_selector</filter> | |
190 </data> | |
174 </outputs> | 191 </outputs> |
175 <tests> | 192 <tests> |
176 <!--Test 01: trio mode--> | 193 <!--Test 01: trio mode--> |
177 <test expect_num_outputs="2"> | 194 <test expect_num_outputs="2"> |
178 <conditional name="mode"> | 195 <conditional name="mode"> |
298 <param name="output_selector" value="qv"/> | 315 <param name="output_selector" value="qv"/> |
299 <output_collection name="qv_files" type="list" count="1"> | 316 <output_collection name="qv_files" type="list" count="1"> |
300 <element name="output_04" file="output_04_qv.tabular" ftype="tabular"/> | 317 <element name="output_04" file="output_04_qv.tabular" ftype="tabular"/> |
301 </output_collection> | 318 </output_collection> |
302 </test> | 319 </test> |
320 <!--Test 05: log file--> | |
321 <test expect_num_outputs="2"> | |
322 <conditional name="mode"> | |
323 <param name="options" value="trio"/> | |
324 <param name="meryldb_F1" value="child.meryldb" ftype="meryldb"/> | |
325 <param name="meryldb_PAT" value="pat.meryldb" ftype="meryldb"/> | |
326 <param name="meryldb_MAT" value="mat.meryldb" ftype="meryldb"/> | |
327 <conditional name="assembly_options"> | |
328 <param name="number_assemblies" value="two"/> | |
329 <param name="assembly_01" value="assembly.fasta.gz" ftype="fasta.gz"/> | |
330 <param name="assembly_02" value="assembly_02.fasta.gz" ftype="fasta.gz"/> | |
331 </conditional> | |
332 </conditional> | |
333 <param name="label" value="output_05"/> | |
334 <param name="output_selector" value="qv,log"/> | |
335 <output_collection name="qv_files" type="list" count="1"> | |
336 <element name="output_05" file="output_04_qv.tabular" ftype="tabular"/> | |
337 </output_collection> | |
338 <output name="log_file" file="output_05_log.txt" ftype="txt" lines_diff='4'/> | |
339 </test> | |
303 </tests> | 340 </tests> |
304 <help><![CDATA[ | 341 <help><![CDATA[ |
305 .. class:: infomark | 342 .. class:: infomark |
306 | 343 |
307 **Purpose** | 344 **Purpose** |