Mercurial > repos > bgruening > bionano_scaffold
changeset 9:faee8629b460 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit 37549c604916ef256e82a3f89ab95b40759bc158
| author | bgruening |
|---|---|
| date | Tue, 13 Dec 2022 09:26:04 +0000 |
| parents | 5258e18bbe23 |
| children | 22286dab5aa1 |
| files | bionano_scaffold.xml macros.xml |
| diffstat | 2 files changed, 54 insertions(+), 66 deletions(-) [+] |
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--- a/bionano_scaffold.xml Sat Feb 05 18:15:29 2022 +0000 +++ b/bionano_scaffold.xml Tue Dec 13 09:26:04 2022 +0000 @@ -374,7 +374,7 @@ </param> </when> <when value="file"> - <param name="configuration_file" type="data" format="xml" label="Configuration file" help="Depending on the complexity of the genome of interest, the values of certain parameters could be adjusted accordingly."/> + <param name="configuration_file" type="data" format="xml,txt" label="Configuration file" help="Depending on the complexity of the genome of interest, the values of certain parameters could be adjusted accordingly."/> </when> </conditional> <param name="conflict_resolution" argument="-M" type="data" format="txt" optional="True" label="Conflict resolution file" help="Input a conflict resolution file indicating which NGS and BioNano conflicting contigs to be cut [optional]"/> @@ -388,6 +388,7 @@ <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="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." /> <!-- @@ -439,6 +440,10 @@ <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" /> + <filter>all_files</filter> + </collection> </outputs> <tests> <test expect_num_outputs="6"> @@ -459,11 +464,6 @@ <has_line line=">Super-Scaffold_1"/> </assert_contents> </output> - <output name="ngs_contigs_not_scaffolded" ftype="fasta"> - <assert_contents> - <has_size value="0"/> - </assert_contents> - </output> <output name="report" file="test_01_report.txt" ftype="txt"/> <output name="ngs_contigs_scaffold_agp" file="test_01.agp" ftype="agp"/> <output name="conflicts" ftype="txt"> @@ -478,17 +478,9 @@ </output> <assert_stdout> <has_text_matching expression='attr="maxmem" val0="\d+"'/> - </assert_stdout> - <assert_stdout> <has_text_matching expression='attr="maxthreads" val0="\d+"'/> - </assert_stdout> - <assert_stdout> <has_text_matching expression='attr="insertThreads" val0="\d+"'/> - </assert_stdout> - <assert_stdout> <has_text_matching expression='attr="maxvirtmem" val0="\d+"'/> - </assert_stdout> - <assert_stdout> <has_text text="hybridScaffold"/> </assert_stdout> </test> @@ -509,11 +501,6 @@ <has_line line=">Super-Scaffold_1"/> </assert_contents> </output> - <output name="ngs_contigs_not_scaffolded" ftype="fasta"> - <assert_contents> - <has_size value="0" /> - </assert_contents> - </output> <output name="report" file="test_02_report.txt" ftype="txt"/> <output name="ngs_contigs_scaffold_agp" ftype="agp"> <assert_contents> @@ -526,19 +513,12 @@ <assert_contents> <has_text text="alignmentOrientation" /> </assert_contents> - </output> <assert_stdout> - <has_text_matching expression='attr="maxmem" val0="\d+"'/> - </assert_stdout> - <assert_stdout> - <has_text_matching expression='attr="maxthreads" val0="\d+"'/> - </assert_stdout> + </output> <assert_stdout> + <has_text_matching expression='attr="maxmem" val0="\d+"'/> + <has_text_matching expression='attr="maxthreads" val0="\d+"'/> <has_text_matching expression='attr="insertThreads" val0="\d+"'/> - </assert_stdout> - <assert_stdout> <has_text_matching expression='attr="maxvirtmem" val0="\d+"'/> - </assert_stdout> - <assert_stdout> <has_text text="hybridScaffold"/> </assert_stdout> </test> @@ -560,11 +540,6 @@ <has_line line=">Super-Scaffold_1"/> </assert_contents> </output> - <output name="ngs_contigs_not_scaffolded" ftype="fasta"> - <assert_contents> - <has_size value="0"/> - </assert_contents> - </output> <output name="report" file="test_03_report.txt" ftype="txt"/> <output name="ngs_contigs_scaffold_agp" ftype="agp"> <assert_contents> @@ -585,17 +560,9 @@ </output> <assert_stdout> <has_text_matching expression='attr="maxmem" val0="\d+"'/> - </assert_stdout> - <assert_stdout> <has_text_matching expression='attr="maxthreads" val0="\d+"'/> - </assert_stdout> - <assert_stdout> <has_text_matching expression='attr="insertThreads" val0="\d+"'/> - </assert_stdout> - <assert_stdout> <has_text_matching expression='attr="maxvirtmem" val0="\d+"'/> - </assert_stdout> - <assert_stdout> <has_text text="hybridScaffold"/> </assert_stdout> </test> @@ -617,11 +584,6 @@ <has_line line=">Super-Scaffold_1"/> </assert_contents> </output> - <output name="ngs_contigs_not_scaffolded" ftype="fasta"> - <assert_contents> - <has_size value="0"/> - </assert_contents> - </output> <output name="report" file="test_04_report.txt" ftype="txt"/> <output name="ngs_contigs_scaffold_agp" ftype="agp"> <assert_contents> @@ -642,17 +604,9 @@ </output> <assert_stdout> <has_text_matching expression='attr="maxmem" val0="\d+"'/> - </assert_stdout> - <assert_stdout> <has_text_matching expression='attr="maxthreads" val0="\d+"'/> - </assert_stdout> - <assert_stdout> <has_text_matching expression='attr="insertThreads" val0="\d+"'/> - </assert_stdout> - <assert_stdout> <has_text_matching expression='attr="maxvirtmem" val0="\d+"'/> - </assert_stdout> - <assert_stdout> <has_text text="hybridScaffold"/> </assert_stdout> </test> @@ -673,9 +627,43 @@ <has_line line=">Super-Scaffold_1"/> </assert_contents> </output> - <output name="ngs_contigs_not_scaffolded_trimmed" ftype="fasta"> + <output name="conflicts" ftype="txt"> + <assert_contents> + <has_text text="alignmentOrientation" /> + </assert_contents> + </output> + <output name="report" file="test_05_report.txt" ftype="txt"/> + <output name="ngs_contigs_scaffold_agp" ftype="agp"> <assert_contents> - <has_size value="0" /> + <has_size value="311" delta="20" /> + <has_text text="##agp-version"/> + <has_n_lines n="9"/> + </assert_contents> + </output> + <assert_stdout> + <has_text_matching expression='attr="maxmem" val0="\d+"'/> + <has_text_matching expression='attr="maxthreads" val0="\d+"'/> + <has_text_matching expression='attr="insertThreads" val0="\d+"'/> + <has_text_matching expression='attr="maxvirtmem" val0="\d+"'/> + <has_text text="hybridScaffold"/> + </assert_stdout> + </test> + <test expect_num_outputs="6"> + <param name="ngs_fasta" value="assembly.fasta.gz"/> + <param name="bionano_cmap" value="colormap_assembly.cmap"/> + <param name="conflict_filter_genome" value="3"/> + <param name="conflict_filter_sequence" value="3"/> + <param name="all_files" value="true"/> + <conditional name="configuration_options"> + <param name="configuration" value="file"/> + <param name="configuration_file" value="configuration.xml"/> + </conditional> + <param name="trim_cut_sites" value="true"/> + <output name="ngs_contigs_scaffold_trimmed" ftype="fasta"> + <assert_contents> + <has_size value="4832591" delta="100" /> + <has_n_lines n="79224"/> + <has_line line=">Super-Scaffold_1"/> </assert_contents> </output> <output name="conflicts" ftype="txt"> @@ -691,19 +679,19 @@ <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> <assert_stdout> <has_text_matching expression='attr="maxmem" val0="\d+"'/> - </assert_stdout> - <assert_stdout> <has_text_matching expression='attr="maxthreads" val0="\d+"'/> - </assert_stdout> - <assert_stdout> <has_text_matching expression='attr="insertThreads" val0="\d+"'/> - </assert_stdout> - <assert_stdout> <has_text_matching expression='attr="maxvirtmem" val0="\d+"'/> - </assert_stdout> - <assert_stdout> <has_text text="hybridScaffold"/> </assert_stdout> </test>
--- a/macros.xml Sat Feb 05 18:15:29 2022 +0000 +++ b/macros.xml Tue Dec 13 09:26:04 2022 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">3.7.0</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</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.