Mercurial > repos > bgruening > bionano_scaffold
changeset 10:22286dab5aa1 draft
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 |
| files | bionano_scaffold.xml macros.xml |
| diffstat | 2 files changed, 36 insertions(+), 15 deletions(-) [+] |
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--- a/bionano_scaffold.xml Tue Dec 13 09:26:04 2022 +0000 +++ b/bionano_scaffold.xml Wed Jan 18 15:22:13 2023 +0000 @@ -59,7 +59,9 @@ && export PATH=/opt/conda/bin/:\$PATH && python '$__tool_directory__/remove_fake_cut_sites.py' $output_file_NCBI 'SCAFFOLD_NCBI_trimmed.fasta' 'output.log' && python '$__tool_directory__/remove_fake_cut_sites.py' $output_file_not_scaffolded 'NOT_SCAFFOLDED_trimmed.fasta' 'output.log' - #end if + #end if + && echo >> hybrid_scaffolds/*cut.txt + && mv hybrid_scaffolds/*cut.txt hybrid_scaffolds/keys.txt ]]> </command> <configfiles> <configfile name="vgp_mode"><![CDATA[ @@ -388,7 +390,7 @@ <option value="2">Cut contig at conflict</option> <option value="3">Exclude conflicting contig</option> </param> - <param name="all_files" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Provide all files" help="Generate a collection with the files contained in the hybrid_scaffolds folder" /> + <param name="all_files" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Provide BisCot required files" help="Generate a collection with the files contained in the hybrid_scaffolds folder" /> <param name="zip_file" argument="-z" type="boolean" truevalue="-z results.zip" falsevalue="" checked="false" label="Generate an output package in ZIP format" help="The hybrid scaffold output package (.zip) can be imported into Access for visualization" /> <param name="trim_cut_sites" type="boolean" checked="true" label="Remove BioNano cut sites" help="This option removes the spurious BioNano cut sites that are inserted into gaps in some assemblies, replacing them with Ns." /> <!-- @@ -440,10 +442,19 @@ <filter>zip_file</filter> </data> <data name="ngs_contigs_scaffold_agp" format="agp" from_work_dir="hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD.agp" label="${tool.name} on ${on_string}: AGP file"/> - <collection name="allfiles" type="list" label="${tool.name} on ${on_string}: hybrid scaffolds files"> - <discover_datasets pattern="__name_and_ext__" directory="hybrid_scaffolds" /> + + <data name="query_file" format="cmap" from_work_dir="hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_BNGcontigs_HYBRID_SCAFFOLD_q.cmap" label="${tool.name} on ${on_string}: query CMAP"> + <filter>all_files</filter> + </data> + <data name="reference_file" format="cmap" from_work_dir="hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_BNGcontigs_HYBRID_SCAFFOLD_r.cmap" label="${tool.name} on ${on_string}: reference CMAP"> <filter>all_files</filter> - </collection> + </data> + <data name="xmap_file" format="xml" from_work_dir="hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD.xmap" label="${tool.name} on ${on_string}: XMAP configuration"> + <filter>all_files</filter> + </data> + <data name="key_file" format="tabular" from_work_dir="hybrid_scaffolds/keys.txt" label="${tool.name} on ${on_string}: Bionano key file"> + <filter>all_files</filter> + </data> </outputs> <tests> <test expect_num_outputs="6"> @@ -648,7 +659,7 @@ <has_text text="hybridScaffold"/> </assert_stdout> </test> - <test expect_num_outputs="6"> + <test expect_num_outputs="9"> <param name="ngs_fasta" value="assembly.fasta.gz"/> <param name="bionano_cmap" value="colormap_assembly.cmap"/> <param name="conflict_filter_genome" value="3"/> @@ -679,14 +690,24 @@ <has_n_lines n="9"/> </assert_contents> </output> - <output_collection name="allfiles" type="list" count="21"> - <element name="BSPQI_bionano_bppAdjust_cmap_ngs_fasta_BNGcontigs_NGScontigs_q"> - <assert_contents> - <has_text text="Number of Consensus Maps"/> - <has_n_lines n="534" delta="50"/> - </assert_contents> - </element> - </output_collection> + <output name="query_file" ftype="cmap"> + <assert_contents> + <has_text text="3879935.1"/> + <has_text text="Coverage refer to the interval between current site and next site"/> + </assert_contents> + </output> + <output name="reference_file" ftype="cmap"> + <assert_contents> + <has_text text="4753350.0"/> + <has_text text=" StdDev refers to the interval between the current site and the next site"/> + </assert_contents> + </output> + <output name="xmap_file" ftype="xml"> + <assert_contents> + <has_text text="XMAP File Version"/> + <has_text text="(7,7)(8,8)(9,9)(10,10)(11,11)(12,12)(13,13)"/> + </assert_contents> + </output> <assert_stdout> <has_text_matching expression='attr="maxmem" val0="\d+"'/> <has_text_matching expression='attr="maxthreads" val0="\d+"'/>
--- a/macros.xml Tue Dec 13 09:26:04 2022 +0000 +++ b/macros.xml Wed Jan 18 15:22:13 2023 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">3.7.0</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">2</token> <token name="@BIONANO_SUPPORT_TEXT@"> Bionano Genomics has agreed to provide the licensed Bionano Solve software to enable the VGP to package the software in a container.