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comparison blobtoolkit.xml @ 2:a4e7a0877d0c draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 5078c7010ec46fd01fec2057dd4486781c958c37
author bgruening
date Tue, 28 Mar 2023 15:17:06 +0000
parents cbcbcb47b798
children f6cc3378ec15
comparison
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1:cbcbcb47b798 2:a4e7a0877d0c
20 --meta 'assembly.yaml' 20 --meta 'assembly.yaml'
21 #end if 21 #end if
22 --taxid $mode_conditional.taxid 22 --taxid $mode_conditional.taxid
23 --taxdump './taxdump' 23 --taxdump './taxdump'
24 './Blobdir' 24 './Blobdir'
25 && cp -r './taxdump' './Blobdir/' 25 && tar -C ./Blobdir -zcvf Blobdir.tgz .
26 && tar -zcf './Blobdir.tgz' './Blobdir'
27
28 #else if $mode_conditional.selector == 'add' 26 #else if $mode_conditional.selector == 'add'
27 mkdir -p './Blobdir' &&
28 mkdir -p './taxdump' &&
29 ln -s '${mode_conditional.taxdump}' 'taxdump.tar' &&
30 tar -xf 'taxdump.tar' -C './taxdump' &&
29 #if $mode_conditional.blobdir.is_of_type("tgz") 31 #if $mode_conditional.blobdir.is_of_type("tgz")
30 tar -zxf '${mode_conditional.blobdir}' -C './' && 32 tar -zxf '${mode_conditional.blobdir}' -C './Blobdir' &&
31 #else 33 #else
32 tar -xf '${mode_conditional.blobdir}' -C './' && 34 tar -xf '${mode_conditional.blobdir}' -C './Blobdir' &&
33 #end if 35 #end if
34 #if $mode_conditional.busco 36 #if $mode_conditional.busco
35 ln -s '${mode_conditional.busco}' './busco_results.tab' && 37 ln -s '${mode_conditional.busco}' './busco_results.tab' &&
36 #end if 38 #end if
37 #if $mode_conditional.blast_input.selector == 'enabled' 39 #if $mode_conditional.blast_input.selector == 'enabled'
48 ln -sf '${input}' './bed_files/${safename}.bed' && 50 ln -sf '${input}' './bed_files/${safename}.bed' &&
49 #end for 51 #end for
50 #end if 52 #end if
51 blobtools add 53 blobtools add
52 --threads \${GALAXY_SLOTS:-8} 54 --threads \${GALAXY_SLOTS:-8}
53 --taxdump './Blobdir/taxdump' 55 --taxdump './taxdump'
54 #if $mode_conditional.busco 56 #if $mode_conditional.busco
55 --busco './busco_results.tab' 57 --busco './busco_results.tab'
56 #end if 58 #end if
57 #if $mode_conditional.blast_input.selector == 'enabled' 59 #if $mode_conditional.blast_input.selector == 'enabled'
58 --hits './blast_results.tab' 60 --hits './blast_results.tab'
93 #if $mode_conditional.advanced_options.pileup_args 95 #if $mode_conditional.advanced_options.pileup_args
94 --pileup-args '${mode_conditional.advanced_options.pileup_args}' 96 --pileup-args '${mode_conditional.advanced_options.pileup_args}'
95 #end if 97 #end if
96 $mode_conditional.advanced_options.replace 98 $mode_conditional.advanced_options.replace
97 './Blobdir' 99 './Blobdir'
98 && tar -zcf './Blobdir.tgz' './Blobdir' 100 && tar -C ./Blobdir -zcvf Blobdir.tgz .
99 101
100 #else if $mode_conditional.selector == 'filter' 102 #else if $mode_conditional.selector == 'filter'
103 mkdir -p './Blobdir' &&
104 #if $mode_conditional.blobdir.is_of_type("tgz")
105 tar -zxf '${mode_conditional.blobdir}' -C './Blobdir' &&
106 #else
107 tar -xf '${mode_conditional.blobdir}' -C './Blobdir' &&
108 #end if
101 #if $mode_conditional.filter_options.list 109 #if $mode_conditional.filter_options.list
102 echo $mode_conditional.filter_options.list > id_list.txt && 110 echo $mode_conditional.filter_options.list > id_list.txt &&
103 #end if 111 #end if
104 #if $mode_conditional.blobdir.is_of_type("tgz") 112 #if $mode_conditional.blobdir.is_of_type("tgz")
105 tar -zxf '${mode_conditional.blobdir}' -C './' && 113 tar -zxf '${mode_conditional.blobdir}' -C './' &&
146 #if $mode_conditional.remove_options.field 154 #if $mode_conditional.remove_options.field
147 --field $mode_conditional.remove_options.field 155 --field $mode_conditional.remove_options.field
148 #end if 156 #end if
149 ./Blobdir 157 ./Blobdir
150 #end if 158 #end if
151 && tar -zcf './Blobdir.tgz' './Blobdir' 159 && tar -C ./Blobdir -zcvf Blobdir.tgz .
152
153 #else if $mode_conditional.selector == 'plots'
154 #if $mode_conditional.blobdir.is_of_type("tgz")
155 tar -zxf '${mode_conditional.blobdir}' -C './' &&
156 #else
157 tar -xf '${mode_conditional.blobdir}' -C './' &&
158 #end if
159 blobtools view
160 --format $mode_conditional.format
161 --view 'blob'
162 ./Blobdir
163 && mv ./Blobdir.blob.circle* ./Blobdir.blob.circle
164 && blobtools view
165 --format $mode_conditional.format
166 --view 'cumulative'
167 ./Blobdir
168 && mv ./Blobdir.cumulative* Blobdir.cumulative
169 && blobtools view
170 --format $mode_conditional.format
171 --view 'snail'
172 ./Blobdir
173 && mv ./Blobdir.snail* Blobdir.snail
174 #end if 160 #end if
175 ]]></command> 161 ]]></command>
176 <inputs> 162 <inputs>
177 <conditional name="mode_conditional"> 163 <conditional name="mode_conditional">
178 <param name="selector" type="select" label="Select mode" help="Select a BlobToolKit module"> 164 <param name="selector" type="select" label="Select mode" help="Select a BlobToolKit module">
179 <option value="create">Create a BlobToolKit dataset</option> 165 <option value="create">Create a BlobToolKit dataset</option>
180 <option value="add">Add data to a BlobToolKit dataset</option> 166 <option value="add">Add data to a BlobToolKit dataset</option>
181 <option value="filter">Edit a BlobToolKit dataset</option> 167 <option value="filter">Edit a BlobToolKit dataset</option>
182 <option value="plots">Generate plots</option>
183 </param> 168 </param>
184 <when value="create"> 169 <when value="create">
185 <param argument="--fasta" type="data" format="fasta" label="Genome assembly file" help="FASTA sequence file" /> 170 <param argument="--fasta" type="data" format="fasta" label="Genome assembly file" help="FASTA sequence file" />
186 <param argument="--meta" type="data" format="yaml" label="Metadata file" optional="true" help="Optional metadata dataset"/> 171 <param argument="--meta" type="data" format="yaml" label="Metadata file" optional="true" help="Optional metadata dataset"/>
187 <param argument="--taxid" type="integer" value="" label="NCBI taxonomy ID" help="Add ranks to metadata for a taxid"/> 172 <param argument="--taxid" type="integer" value="" label="NCBI taxonomy ID" help="Add ranks to metadata for a taxid"/>
188 <param argument="--taxdump" type="data" format="tar,tgz,gz" label="NCBI taxdump directory" help="It should be compressed in tar.gz format"/> 173 <expand macro="macro_taxdump"/>
189 </when> 174 </when>
190 <when value="add"> 175 <when value="add">
191 <param name="blobdir" type="data" format="tgz" label="Blobdir.tgz file" help="This file should be generated by Blobtool create" /> 176 <param name="blobdir" type="data" format="tgz" label="Blobdir.tgz file" help="This file should be generated by Blobtool create" />
177 <expand macro="macro_taxdump"/>
192 <param argument="--busco" type="data" format="tsv,tabular,txt" optional="true" label="BUSCO full table file"/> 178 <param argument="--busco" type="data" format="tsv,tabular,txt" optional="true" label="BUSCO full table file"/>
193 <conditional name="blast_input"> 179 <conditional name="blast_input">
194 <param name="selector" type="select" label="BLAST/Diamond hits"> 180 <param name="selector" type="select" label="BLAST/Diamond hits">
195 <option value="enabled">Enabled</option> 181 <option value="enabled">Enabled</option>
196 <option value="disabled" selected="true">Disabled</option> 182 <option value="disabled" selected="true">Disabled</option>
308 </sanitizer> 294 </sanitizer>
309 <validator type="regex">[0-9a-zA-Z]+</validator> 295 <validator type="regex">[0-9a-zA-Z]+</validator>
310 </param> 296 </param>
311 </section> 297 </section>
312 </when> 298 </when>
313 <when value="plots">
314 <param name="blobdir" type="data" format="tgz" label="Blobdir file" help="This file should be generated by the moudule create" />
315 <param argument="--format" type="select" label="Image format">
316 <option value="png">PNG</option>
317 <option value="svg">SVG</option>
318 </param>
319 <param argument="--param" type="text" optional="true" label="Query parameter" help="Query string parameter."/>
320 </when>
321 </conditional> 299 </conditional>
322 </inputs> 300 </inputs>
323 <outputs> 301 <outputs>
324 <data name="blobdir" format="tgz" from_work_dir="./Blobdir.tgz" label="${tool.name} on ${on_string}: Blobdir.tgz"> 302 <data name="blobdir" format="tgz" from_work_dir="./Blobdir.tgz" label="${tool.name} on ${on_string}: Blobdir.tgz">
325 <filter>mode_conditional['selector'] == 'create' or mode_conditional['selector'] == 'add' or mode_conditional['selector'] == 'filter'</filter> 303 <filter>mode_conditional['selector'] == 'create' or mode_conditional['selector'] == 'add' or mode_conditional['selector'] == 'filter'</filter>
326 </data>
327 <data name="plot_circle" format="png" from_work_dir="./Blobdir.blob.circle" label="${tool.name} on ${on_string}: blob plot">
328 <filter>mode_conditional['selector'] == 'plots'</filter>
329 <change_format>
330 <when input="$mode_conditional.format" value="svg" format="svg"/>
331 </change_format>
332 </data>
333 <data name="plot_cumulative" format="png" from_work_dir="./Blobdir.cumulative" label="${tool.name} on ${on_string}: cumulative plot">
334 <filter>mode_conditional['selector'] == 'plots'</filter>
335 <change_format>
336 <when input="$mode_conditional.format" value="svg" format="svg"/>
337 </change_format>
338 </data>
339 <data name="plot_snail" format="png" from_work_dir="./Blobdir.snail" label="${tool.name} on ${on_string}: snail plot">
340 <filter>mode_conditional['selector'] == 'plots'</filter>
341 <change_format>
342 <when input="$mode_conditional.format" value="svg" format="svg"/>
343 </change_format>
344 </data> 304 </data>
345 </outputs> 305 </outputs>
346 <tests> 306 <tests>
347 <test expect_num_outputs="1"> 307 <test expect_num_outputs="1">
348 <conditional name="mode_conditional"> 308 <conditional name="mode_conditional">
350 <param name="fasta" value="assembly.fasta.gz"/> 310 <param name="fasta" value="assembly.fasta.gz"/>
351 <param name="meta" value="assembly.yaml"/> 311 <param name="meta" value="assembly.yaml"/>
352 <param name="taxid" value="801"/> 312 <param name="taxid" value="801"/>
353 <param name="taxdump" value="small_taxdump.tar.gz"/> 313 <param name="taxdump" value="small_taxdump.tar.gz"/>
354 </conditional> 314 </conditional>
355 <output name="blobdir" file="test01_blobdir.tar.gz" compare="sim_size" delta="1500"/> 315 <output name="blobdir" file="test01_blobdir.tar.gz" compare="sim_size" delta="100"/>
356 </test> 316 </test>
357 <test expect_num_outputs="1"> 317 <test expect_num_outputs="1">
358 <conditional name="mode_conditional"> 318 <conditional name="mode_conditional">
359 <param name="selector" value="add"/> 319 <param name="selector" value="add"/>
360 <param name="blobdir" value="test01_blobdir.tar.gz"/> 320 <param name="blobdir" value="test01_blobdir.tar.gz"/>
321 <param name="taxdump" value="small_taxdump.tar.gz"/>
361 <param name="busco" value="busco_full_table.tabular"/> 322 <param name="busco" value="busco_full_table.tabular"/>
362 <param name="cov" value="bam_file.bam"/> 323 <param name="cov" value="bam_file.bam"/>
363 <param name="fasta" value="contig.fasta"/> 324 <param name="fasta" value="contig.fasta"/>
364 <section name="advanced_options"> 325 <section name="advanced_options">
365 <param name="update_plot" value="false"/> 326 <param name="update_plot" value="false"/>
372 <param name="bitscore" value="1"/> 333 <param name="bitscore" value="1"/>
373 <param name="hit_count" value="10"/> 334 <param name="hit_count" value="10"/>
374 <param name="hits_cols" value="1=qseqid,2=staxids,3=bitscore,5=sseqid,10=qstart,11=qend,14=evalue"/> 335 <param name="hits_cols" value="1=qseqid,2=staxids,3=bitscore,5=sseqid,10=qstart,11=qend,14=evalue"/>
375 </conditional> 336 </conditional>
376 </conditional> 337 </conditional>
377 <output name="blobdir" file="test02_blobdir.tar.gz" compare="sim_size" delta="1500"/> 338 <output name="blobdir" file="test02_blobdir.tar.gz" compare="sim_size" delta="100"/>
378 </test> 339 </test>
379 <test expect_num_outputs="1"> 340 <test expect_num_outputs="1">
380 <conditional name="mode_conditional"> 341 <conditional name="mode_conditional">
381 <param name="selector" value="filter"/> 342 <param name="selector" value="filter"/>
382 <param name="blobdir" value="test02_blobdir.tar.gz"/> 343 <param name="blobdir" value="test02_blobdir.tar.gz"/>
389 <param name="remove_selector" value="--all"/> 350 <param name="remove_selector" value="--all"/>
390 </section> 351 </section>
391 </conditional> 352 </conditional>
392 <output name="blobdir"> 353 <output name="blobdir">
393 <assert_contents> 354 <assert_contents>
394 <has_size value="672500" delta="1000"/> 355 <has_size value="620" delta="50"/>
395 </assert_contents> 356 </assert_contents>
396 </output> 357 </output>
397 </test>
398 <test expect_num_outputs="3">
399 <conditional name="mode_conditional">
400 <param name="selector" value="plots"/>
401 <param name="blobdir" value="test02_blobdir.tar.gz"/>
402 <param name="format" value="png"/>
403 </conditional>
404 <output name="plot_circle" file="test04_circle.png" ftype="png"/>
405 <output name="plot_cumulative" file="test04_cumulative.png" ftype="png"/>
406 <output name="plot_snail" file="test04_snail.png" ftype="png"/>
407 </test> 358 </test>
408 <test expect_num_outputs="1"> 359 <test expect_num_outputs="1">
409 <conditional name="mode_conditional"> 360 <conditional name="mode_conditional">
410 <param name="selector" value="filter"/> 361 <param name="selector" value="filter"/>
411 <param name="blobdir" value="test02_blobdir.tar.gz"/> 362 <param name="blobdir" value="test02_blobdir.tar.gz"/>
417 <param name="remove_selector" value="--all"/> 368 <param name="remove_selector" value="--all"/>
418 </section> 369 </section>
419 </conditional> 370 </conditional>
420 <output name="blobdir"> 371 <output name="blobdir">
421 <assert_contents> 372 <assert_contents>
422 <has_size value="672497" delta="1000"/> 373 <has_size value="620" delta="50"/>
423 </assert_contents> 374 </assert_contents>
424 </output> 375 </output>
425 </test> 376 </test>
426 </tests> 377 </tests>
427 <help><![CDATA[ 378 <help><![CDATA[
428 BlobToolKit is a software suite to aid researchers in identifying and isolating non-target data in draft and publicly available genome assemblies. It can be used to process assembly, 379 BlobToolKit is a software suite to aid researchers in identifying and isolating non-target data in draft and publicly available genome assemblies. It can be used to process assembly,
429 read and analysis files for fully reproducible interactive exploration in the browser-based Viewer. BlobToolKit can be used during assembly to filter non-target DNA, helping researchers produce assemblies with high biological credibility. 380 read and analysis files for fully reproducible interactive exploration in the browser-based Viewer. BlobToolKit can be used during assembly to filter non-target DNA, helping researchers produce assemblies with high biological credibility.
381
382 .. class:: infomark
383
384 **NCBI taxdump directory**
385
386 The taxdump database, provided by NCBI, includes the taxonomic lineage of taxa, information on type strains and material, and host information. The file **new_taxdump.tar.gz** can be downloaded from the taxonomy directory on the `FTP site <ftp.ncbi.nlm.nih.gov/pub/taxonomy/new_taxdump/>`_.
387
430 ]]></help> 388 ]]></help>
431 <expand macro="citations"/> 389 <expand macro="citations"/>
432 </tool> 390 </tool>