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comparison merqury.xml @ 2:589078edd230 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
author iuc
date Mon, 25 Apr 2022 11:20:41 +0000
parents 39edec572bae
children f8113c25bc6b
comparison
equal deleted inserted replaced
1:39edec572bae 2:589078edd230
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 ${on_string}: BED files">
151 <discover_datasets pattern="(?P&lt;name&gt;.+)\.bed" format="bed" directory="output_files"/> 165 <discover_datasets pattern="(?P&lt;name&gt;.+)\.bed" format="bed" directory="output_files"/>
169 </collection> 183 </collection>
170 <collection name="stats_files" type="list" label="${tool.name} on ${on_string}: stats"> 184 <collection name="stats_files" type="list" label="${tool.name} on ${on_string}: stats">
171 <discover_datasets pattern="(?P&lt;name&gt;.+)\.stats" format="tabular" directory="output_files"/> 185 <discover_datasets pattern="(?P&lt;name&gt;.+)\.stats" format="tabular" directory="output_files"/>
172 <filter>"stats" in output_selector</filter> 186 <filter>"stats" in output_selector</filter>
173 </collection> 187 </collection>
188 <data name="log_file" format="txt" label="${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**