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comparison blobtoolkit.xml @ 1:840822c1e84a draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955
author bgruening
date Mon, 20 Mar 2023 16:37:54 +0000
parents 7d9ee8cd14b8
children 53dd00a4ab68
comparison
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0:7d9ee8cd14b8 1:840822c1e84a
37 #if $mode_conditional.blast_input.selector == 'enabled' 37 #if $mode_conditional.blast_input.selector == 'enabled'
38 ln -s '$mode_conditional.blast_input.hits' './blast_results.tab' && 38 ln -s '$mode_conditional.blast_input.hits' './blast_results.tab' &&
39 #end if 39 #end if
40 #if $mode_conditional.cov 40 #if $mode_conditional.cov
41 ln -s '$mode_conditional.cov' './input.bam' && 41 ln -s '$mode_conditional.cov' './input.bam' &&
42 ln -s '$mode_conditional.cov.metadata.bam_index' './input.bam.bai' &&
43 #end if 42 #end if
44 #if $mode_conditional.bed 43 #if $mode_conditional.bed
45 mkdir -p './bed_files' && 44 mkdir -p './bed_files' &&
46 #import re 45 #import re
47 #for $i, $input in enumerate($mode_conditional.bed): 46 #for $i, $input in enumerate($mode_conditional.bed):
97 $mode_conditional.advanced_options.replace 96 $mode_conditional.advanced_options.replace
98 './Blobdir' 97 './Blobdir'
99 && tar -zcf './Blobdir.tgz' './Blobdir' 98 && tar -zcf './Blobdir.tgz' './Blobdir'
100 99
101 #else if $mode_conditional.selector == 'filter' 100 #else if $mode_conditional.selector == 'filter'
101 #if $mode_conditional.filter_options.list
102 echo $mode_conditional.filter_options.list > id_list.txt &&
103 #end if
102 #if $mode_conditional.blobdir.is_of_type("tgz") 104 #if $mode_conditional.blobdir.is_of_type("tgz")
103 tar -zxf '${mode_conditional.blobdir}' -C './' && 105 tar -zxf '${mode_conditional.blobdir}' -C './' &&
104 #else 106 #else
105 tar -xf '${mode_conditional.blobdir}' -C './' && 107 tar -xf '${mode_conditional.blobdir}' -C './' &&
106 #end if 108 #end if
107 #if $mode_conditional.filter_options.fasta 109 #if $mode_conditional.filter_options.fasta
108 ln -s '${mode_conditional.filter_options.fasta}' './input.fasta' && 110 ln -s '${mode_conditional.filter_options.fasta}' './input.fasta' &&
109 #end if 111 #end if
110 #if $mode_conditional.filter_options.fastq_filter.selector == 'enabled' 112 #if $mode_conditional.filter_options.fastq_filter.selector == 'enabled'
111 ln -s '${mode_conditional.filter_options.fastq}' './input.fastq' && 113 ln -s '${mode_conditional.filter_options.fastq_filter.fastq}' './input.fastq' &&
112 ln -s '$mode_conditional.filter_options.cov' './input.bam' && 114 ln -s '$mode_conditional.filter_options.fastq_filter.cov' './input.bam' &&
113 ln -s '$mode_conditional.filter_options.cov.metadata.bam_index' './input.bam.csi' &&
114 #end if 115 #end if
115 blobtools filter 116 blobtools filter
116 #if $mode_conditional.filter_options.param 117 #if $mode_conditional.filter_options.param
117 --param $mode_conditional.filter_options.param 118 --param $mode_conditional.filter_options.param
118 #end if 119 #end if
119 #if $mode_conditional.filter_options.json 120 #if $mode_conditional.filter_options.json
120 --json $mode_conditional.filter_options.json 121 --json $mode_conditional.filter_options.json
121 #end if 122 #end if
122 #if $mode_conditional.filter_options.list 123 #if $mode_conditional.filter_options.list
123 --list $mode_conditional.filter_options.list 124 --list id_list.txt
124 #end if 125 #end if
125 $mode_conditional.filter_options.invert 126 $mode_conditional.filter_options.invert
126 #if $mode_conditional.filter_options.fasta 127 #if $mode_conditional.filter_options.fasta
127 --fasta './input.fasta' 128 --fasta './input.fasta'
128 #end if 129 #end if
349 <param name="fasta" value="assembly.fasta.gz"/> 350 <param name="fasta" value="assembly.fasta.gz"/>
350 <param name="meta" value="assembly.yaml"/> 351 <param name="meta" value="assembly.yaml"/>
351 <param name="taxid" value="801"/> 352 <param name="taxid" value="801"/>
352 <param name="taxdump" value="small_taxdump.tar.gz"/> 353 <param name="taxdump" value="small_taxdump.tar.gz"/>
353 </conditional> 354 </conditional>
354 <output name="blobdir" file="test01_blobdir.tar.gz" compare="sim_size" delta="1000"/> 355 <output name="blobdir" file="test01_blobdir.tar.gz" compare="sim_size" delta="1500"/>
355 </test> 356 </test>
356 <test expect_num_outputs="1"> 357 <test expect_num_outputs="1">
357 <conditional name="mode_conditional"> 358 <conditional name="mode_conditional">
358 <param name="selector" value="add"/> 359 <param name="selector" value="add"/>
359 <param name="blobdir" value="test01_blobdir.tar.gz"/> 360 <param name="blobdir" value="test01_blobdir.tar.gz"/>
371 <param name="bitscore" value="1"/> 372 <param name="bitscore" value="1"/>
372 <param name="hit_count" value="10"/> 373 <param name="hit_count" value="10"/>
373 <param name="hits_cols" value="1=qseqid,2=staxids,3=bitscore,5=sseqid,10=qstart,11=qend,14=evalue"/> 374 <param name="hits_cols" value="1=qseqid,2=staxids,3=bitscore,5=sseqid,10=qstart,11=qend,14=evalue"/>
374 </conditional> 375 </conditional>
375 </conditional> 376 </conditional>
376 <output name="blobdir" file="test02_blobdir.tar.gz" compare="sim_size" delta="1000"/> 377 <output name="blobdir" file="test02_blobdir.tar.gz" compare="sim_size" delta="1500"/>
377 </test> 378 </test>
378 <test expect_num_outputs="1"> 379 <test expect_num_outputs="1">
379 <conditional name="mode_conditional"> 380 <conditional name="mode_conditional">
380 <param name="selector" value="filter"/> 381 <param name="selector" value="filter"/>
381 <param name="blobdir" value="test02_blobdir.tar.gz"/> 382 <param name="blobdir" value="test02_blobdir.tar.gz"/>
388 <param name="remove_selector" value="--all"/> 389 <param name="remove_selector" value="--all"/>
389 </section> 390 </section>
390 </conditional> 391 </conditional>
391 <output name="blobdir"> 392 <output name="blobdir">
392 <assert_contents> 393 <assert_contents>
393 <has_size value="672428" delta="1000"/> 394 <has_size value="672500" delta="1000"/>
394 </assert_contents> 395 </assert_contents>
395 </output> 396 </output>
396 </test> 397 </test>
397 <test expect_num_outputs="3"> 398 <test expect_num_outputs="3">
398 <conditional name="mode_conditional"> 399 <conditional name="mode_conditional">
402 </conditional> 403 </conditional>
403 <output name="plot_circle" file="test04_circle.png" ftype="png"/> 404 <output name="plot_circle" file="test04_circle.png" ftype="png"/>
404 <output name="plot_cumulative" file="test04_cumulative.png" ftype="png"/> 405 <output name="plot_cumulative" file="test04_cumulative.png" ftype="png"/>
405 <output name="plot_snail" file="test04_snail.png" ftype="png"/> 406 <output name="plot_snail" file="test04_snail.png" ftype="png"/>
406 </test> 407 </test>
408 <test expect_num_outputs="1">
409 <conditional name="mode_conditional">
410 <param name="selector" value="filter"/>
411 <param name="blobdir" value="test02_blobdir.tar.gz"/>
412 <section name="filter_options">
413 <param name="list" value="801 802"/>
414 <param name="fasta" value="contig.fasta"/>
415 </section>
416 <section name="remove_options">
417 <param name="remove_selector" value="--all"/>
418 </section>
419 </conditional>
420 <output name="blobdir">
421 <assert_contents>
422 <has_size value="672497" delta="1000"/>
423 </assert_contents>
424 </output>
425 </test>
407 </tests> 426 </tests>
408 <help><![CDATA[ 427 <help><![CDATA[
409 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, 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,
410 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. 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.
411 ]]></help> 430 ]]></help>