Mercurial > repos > bgruening > bionano_scaffold

comparison bionano_scaffold.xml @ 10:22286dab5aa1 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit bf9f16e7144d2a619863c84a4aede8c9ef520d0e
author bgruening
date Wed, 18 Jan 2023 15:22:13 +0000
parents faee8629b460
children 3371c5bdc17a
comparison
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9:faee8629b460 10:22286dab5aa1
57 -o ./ 57 -o ./
58 #if $trim_cut_sites 58 #if $trim_cut_sites
59 && export PATH=/opt/conda/bin/:\$PATH 59 && export PATH=/opt/conda/bin/:\$PATH
60 && python '$__tool_directory__/remove_fake_cut_sites.py' $output_file_NCBI 'SCAFFOLD_NCBI_trimmed.fasta' 'output.log' 60 && python '$__tool_directory__/remove_fake_cut_sites.py' $output_file_NCBI 'SCAFFOLD_NCBI_trimmed.fasta' 'output.log'
61 && python '$__tool_directory__/remove_fake_cut_sites.py' $output_file_not_scaffolded 'NOT_SCAFFOLDED_trimmed.fasta' 'output.log' 61 && python '$__tool_directory__/remove_fake_cut_sites.py' $output_file_not_scaffolded 'NOT_SCAFFOLDED_trimmed.fasta' 'output.log'
62 #end if 62 #end if
63 && echo >> hybrid_scaffolds/*cut.txt
64 && mv hybrid_scaffolds/*cut.txt hybrid_scaffolds/keys.txt
63 ]]> </command> 65 ]]> </command>
64 <configfiles> 66 <configfiles>
65 <configfile name="vgp_mode"><![CDATA[ 67 <configfile name="vgp_mode"><![CDATA[
66 #if $configuration_options.configuration == 'vgp' 68 #if $configuration_options.configuration == 'vgp'
67 <hybridScaffold> 69 <hybridScaffold>
386 <param name="conflict_filter_sequence" argument="-N" type="select" label="Sequences conflict filter" help="Conflict filter level for sequences [required if not using -M option]"> 388 <param name="conflict_filter_sequence" argument="-N" type="select" label="Sequences conflict filter" help="Conflict filter level for sequences [required if not using -M option]">
387 <option value="1">No filter</option> 389 <option value="1">No filter</option>
388 <option value="2">Cut contig at conflict</option> 390 <option value="2">Cut contig at conflict</option>
389 <option value="3">Exclude conflicting contig</option> 391 <option value="3">Exclude conflicting contig</option>
390 </param> 392 </param>
391 <param name="all_files" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Provide all files" help="Generate a collection with the files contained in the hybrid_scaffolds folder" /> 393 <param name="all_files" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Provide BisCot required files" help="Generate a collection with the files contained in the hybrid_scaffolds folder" />
392 <param name="zip_file" argument="-z" type="boolean" truevalue="-z results.zip" falsevalue="" checked="false" label="Generate an output package in ZIP format" help="The hybrid scaffold output package (.zip) can be imported into Access for visualization" /> 394 <param name="zip_file" argument="-z" type="boolean" truevalue="-z results.zip" falsevalue="" checked="false" label="Generate an output package in ZIP format" help="The hybrid scaffold output package (.zip) can be imported into Access for visualization" />
393 <param name="trim_cut_sites" type="boolean" checked="true" label="Remove BioNano cut sites" help="This option removes the spurious BioNano cut sites that are inserted into gaps in some assemblies, replacing them with Ns." /> 395 <param name="trim_cut_sites" type="boolean" checked="true" label="Remove BioNano cut sites" help="This option removes the spurious BioNano cut sites that are inserted into gaps in some assemblies, replacing them with Ns." />
394 <!-- 396 <!--
395 397
396 Those options have been disabled because the Docker container doesn't include the required packages 398 Those options have been disabled because the Docker container doesn't include the required packages
438 <data name="conflicts" format="txt" from_work_dir="hybrid_scaffolds/conflicts.txt" label="${tool.name} on ${on_string}: conflicts"/> 440 <data name="conflicts" format="txt" from_work_dir="hybrid_scaffolds/conflicts.txt" label="${tool.name} on ${on_string}: conflicts"/>
439 <data name="results" format="zip" from_work_dir="results.zip" label="${tool.name} on ${on_string}: results"> 441 <data name="results" format="zip" from_work_dir="results.zip" label="${tool.name} on ${on_string}: results">
440 <filter>zip_file</filter> 442 <filter>zip_file</filter>
441 </data> 443 </data>
442 <data name="ngs_contigs_scaffold_agp" format="agp" from_work_dir="hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD.agp" label="${tool.name} on ${on_string}: AGP file"/> 444 <data name="ngs_contigs_scaffold_agp" format="agp" from_work_dir="hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD.agp" label="${tool.name} on ${on_string}: AGP file"/>
443 <collection name="allfiles" type="list" label="${tool.name} on ${on_string}: hybrid scaffolds files"> 445
444 <discover_datasets pattern="__name_and_ext__" directory="hybrid_scaffolds" /> 446 <data name="query_file" format="cmap" from_work_dir="hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_BNGcontigs_HYBRID_SCAFFOLD_q.cmap" label="${tool.name} on ${on_string}: query CMAP">
445 <filter>all_files</filter> 447 <filter>all_files</filter>
446 </collection> 448 </data>
449 <data name="reference_file" format="cmap" from_work_dir="hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_BNGcontigs_HYBRID_SCAFFOLD_r.cmap" label="${tool.name} on ${on_string}: reference CMAP">
450 <filter>all_files</filter>
451 </data>
452 <data name="xmap_file" format="xml" from_work_dir="hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD.xmap" label="${tool.name} on ${on_string}: XMAP configuration">
453 <filter>all_files</filter>
454 </data>
455 <data name="key_file" format="tabular" from_work_dir="hybrid_scaffolds/keys.txt" label="${tool.name} on ${on_string}: Bionano key file">
456 <filter>all_files</filter>
457 </data>
447 </outputs> 458 </outputs>
448 <tests> 459 <tests>
449 <test expect_num_outputs="6"> 460 <test expect_num_outputs="6">
450 <param name="ngs_fasta" value="assembly.fasta.gz"/> 461 <param name="ngs_fasta" value="assembly.fasta.gz"/>
451 <param name="bionano_cmap" value="colormap_assembly.cmap"/> 462 <param name="bionano_cmap" value="colormap_assembly.cmap"/>
646 <has_text_matching expression='attr="insertThreads" val0="\d+"'/> 657 <has_text_matching expression='attr="insertThreads" val0="\d+"'/>
647 <has_text_matching expression='attr="maxvirtmem" val0="\d+"'/> 658 <has_text_matching expression='attr="maxvirtmem" val0="\d+"'/>
648 <has_text text="hybridScaffold"/> 659 <has_text text="hybridScaffold"/>
649 </assert_stdout> 660 </assert_stdout>
650 </test> 661 </test>
651 <test expect_num_outputs="6"> 662 <test expect_num_outputs="9">
652 <param name="ngs_fasta" value="assembly.fasta.gz"/> 663 <param name="ngs_fasta" value="assembly.fasta.gz"/>
653 <param name="bionano_cmap" value="colormap_assembly.cmap"/> 664 <param name="bionano_cmap" value="colormap_assembly.cmap"/>
654 <param name="conflict_filter_genome" value="3"/> 665 <param name="conflict_filter_genome" value="3"/>
655 <param name="conflict_filter_sequence" value="3"/> 666 <param name="conflict_filter_sequence" value="3"/>
656 <param name="all_files" value="true"/> 667 <param name="all_files" value="true"/>
677 <has_size value="311" delta="20" /> 688 <has_size value="311" delta="20" />
678 <has_text text="##agp-version"/> 689 <has_text text="##agp-version"/>
679 <has_n_lines n="9"/> 690 <has_n_lines n="9"/>
680 </assert_contents> 691 </assert_contents>
681 </output> 692 </output>
682 <output_collection name="allfiles" type="list" count="21"> 693 <output name="query_file" ftype="cmap">
683 <element name="BSPQI_bionano_bppAdjust_cmap_ngs_fasta_BNGcontigs_NGScontigs_q"> 694 <assert_contents>
684 <assert_contents> 695 <has_text text="3879935.1"/>
685 <has_text text="Number of Consensus Maps"/> 696 <has_text text="Coverage refer to the interval between current site and next site"/>
686 <has_n_lines n="534" delta="50"/> 697 </assert_contents>
687 </assert_contents> 698 </output>
688 </element> 699 <output name="reference_file" ftype="cmap">
689 </output_collection> 700 <assert_contents>
701 <has_text text="4753350.0"/>
702 <has_text text=" StdDev refers to the interval between the current site and the next site"/>
703 </assert_contents>
704 </output>
705 <output name="xmap_file" ftype="xml">
706 <assert_contents>
707 <has_text text="XMAP File Version"/>
708 <has_text text="(7,7)(8,8)(9,9)(10,10)(11,11)(12,12)(13,13)"/>
709 </assert_contents>
710 </output>
690 <assert_stdout> 711 <assert_stdout>
691 <has_text_matching expression='attr="maxmem" val0="\d+"'/> 712 <has_text_matching expression='attr="maxmem" val0="\d+"'/>
692 <has_text_matching expression='attr="maxthreads" val0="\d+"'/> 713 <has_text_matching expression='attr="maxthreads" val0="\d+"'/>
693 <has_text_matching expression='attr="insertThreads" val0="\d+"'/> 714 <has_text_matching expression='attr="insertThreads" val0="\d+"'/>
694 <has_text_matching expression='attr="maxvirtmem" val0="\d+"'/> 715 <has_text_matching expression='attr="maxvirtmem" val0="\d+"'/>