| Previous changeset 8:5258e18bbe23 (2022-02-05) Next changeset 10:22286dab5aa1 (2023-01-18) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit 37549c604916ef256e82a3f89ab95b40759bc158 |
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modified:
bionano_scaffold.xml macros.xml |
| b |
| diff -r 5258e18bbe23 -r faee8629b460 bionano_scaffold.xml --- a/bionano_scaffold.xml Sat Feb 05 18:15:29 2022 +0000 +++ b/bionano_scaffold.xml Tue Dec 13 09:26:04 2022 +0000 |
| [ |
| b'@@ -374,7 +374,7 @@\n </param>\n </when>\n <when value="file">\n- <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."/>\n+ <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."/>\n </when>\n </conditional>\n <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]"/>\n@@ -388,6 +388,7 @@\n <option value="2">Cut contig at conflict</option>\n <option value="3">Exclude conflicting contig</option>\n </param>\n+ <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" />\n <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" />\n <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." />\n <!-- \n@@ -439,6 +440,10 @@\n <filter>zip_file</filter>\n </data>\n <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 ${on_string}: AGP file"/>\n+ <collection name="allfiles" type="list" label="${tool.name} on ${on_string}: hybrid scaffolds files">\n+ <discover_datasets pattern="__name_and_ext__" directory="hybrid_scaffolds" />\n+ <filter>all_files</filter>\n+ </collection>\n </outputs>\n <tests>\n <test expect_num_outputs="6">\n@@ -459,11 +464,6 @@\n <has_line line=">Super-Scaffold_1"/>\n </assert_contents>\n </output>\n- <output name="ngs_contigs_not_scaffolded" ftype="fasta">\n- <assert_contents>\n- <has_size value="0"/>\n- </assert_contents>\n- </output>\n <output name="report" file="test_01_report.txt" ftype="txt"/>\n <output name="ngs_contigs_scaffold_agp" file="test_01.agp" ftype="agp"/>\n <output name="conflicts" ftype="txt">\n@@ -478,17 +478,9 @@\n </output>\n <assert_stdout>\n <has_text_matching expression=\'attr="maxmem" val0="\\d+"\'/>\n- </assert_stdout>\n- <assert_stdout>\n <has_text_matching expression=\'attr="maxthreads" val0="\\d+"\'/>\n- </assert_stdout>\n- <assert_stdout>\n <has_text_matching expression=\'attr="insertThreads" val0="\\d+"\'/>\n- </assert_stdout>\n- <assert_stdout>\n <has_text_matching expression=\'attr="maxvirtmem" val0="\\d+"\'/>\n- </assert_stdout>\n- <assert_stdout>\n <has_text text="hybridScaffold"/>\n </assert_stdout>\n </test>\n@@ -509,11 +501,6 @@\n <has_line line=">Super-Scaffold_1"/>\n </assert_contents>\n </output>\n- <output name="ngs_contigs_not_scaffolded" ftype="fasta">\n- <assert_contents>\n- <has_size value="0" />\n- </assert_contents>\n- </output>\n'..b'/assert_stdout>\n- <assert_stdout>\n <has_text_matching expression=\'attr="insertThreads" val0="\\d+"\'/>\n- </assert_stdout>\n- <assert_stdout>\n <has_text_matching expression=\'attr="maxvirtmem" val0="\\d+"\'/>\n- </assert_stdout>\n- <assert_stdout>\n <has_text text="hybridScaffold"/>\n </assert_stdout>\n </test>\n@@ -673,9 +627,43 @@\n <has_line line=">Super-Scaffold_1"/>\n </assert_contents>\n </output>\n- <output name="ngs_contigs_not_scaffolded_trimmed" ftype="fasta">\n+ <output name="conflicts" ftype="txt">\n+ <assert_contents>\n+ <has_text text="alignmentOrientation" />\n+ </assert_contents>\n+ </output> \n+ <output name="report" file="test_05_report.txt" ftype="txt"/>\n+ <output name="ngs_contigs_scaffold_agp" ftype="agp">\n <assert_contents>\n- <has_size value="0" />\n+ <has_size value="311" delta="20" />\n+ <has_text text="##agp-version"/>\n+ <has_n_lines n="9"/>\n+ </assert_contents>\n+ </output>\n+ <assert_stdout>\n+ <has_text_matching expression=\'attr="maxmem" val0="\\d+"\'/>\n+ <has_text_matching expression=\'attr="maxthreads" val0="\\d+"\'/>\n+ <has_text_matching expression=\'attr="insertThreads" val0="\\d+"\'/>\n+ <has_text_matching expression=\'attr="maxvirtmem" val0="\\d+"\'/>\n+ <has_text text="hybridScaffold"/>\n+ </assert_stdout>\n+ </test>\n+ <test expect_num_outputs="6">\n+ <param name="ngs_fasta" value="assembly.fasta.gz"/>\n+ <param name="bionano_cmap" value="colormap_assembly.cmap"/>\n+ <param name="conflict_filter_genome" value="3"/>\n+ <param name="conflict_filter_sequence" value="3"/>\n+ <param name="all_files" value="true"/>\n+ <conditional name="configuration_options">\n+ <param name="configuration" value="file"/>\n+ <param name="configuration_file" value="configuration.xml"/>\n+ </conditional>\n+ <param name="trim_cut_sites" value="true"/>\n+ <output name="ngs_contigs_scaffold_trimmed" ftype="fasta">\n+ <assert_contents>\n+ <has_size value="4832591" delta="100" />\n+ <has_n_lines n="79224"/>\n+ <has_line line=">Super-Scaffold_1"/>\n </assert_contents>\n </output>\n <output name="conflicts" ftype="txt">\n@@ -691,19 +679,19 @@\n <has_n_lines n="9"/>\n </assert_contents>\n </output>\n+ <output_collection name="allfiles" type="list" count="21">\n+ <element name="BSPQI_bionano_bppAdjust_cmap_ngs_fasta_BNGcontigs_NGScontigs_q">\n+ <assert_contents>\n+ <has_text text="Number of Consensus Maps"/>\n+ <has_n_lines n="534" delta="50"/>\n+ </assert_contents>\n+ </element>\n+ </output_collection>\n <assert_stdout>\n <has_text_matching expression=\'attr="maxmem" val0="\\d+"\'/>\n- </assert_stdout>\n- <assert_stdout>\n <has_text_matching expression=\'attr="maxthreads" val0="\\d+"\'/>\n- </assert_stdout>\n- <assert_stdout>\n <has_text_matching expression=\'attr="insertThreads" val0="\\d+"\'/>\n- </assert_stdout>\n- <assert_stdout>\n <has_text_matching expression=\'attr="maxvirtmem" val0="\\d+"\'/>\n- </assert_stdout>\n- <assert_stdout>\n <has_text text="hybridScaffold"/>\n </assert_stdout>\n </test>\n' |
| b |
| diff -r 5258e18bbe23 -r faee8629b460 macros.xml --- a/macros.xml Sat Feb 05 18:15:29 2022 +0000 +++ b/macros.xml Tue Dec 13 09:26:04 2022 +0000 |
| b |
| @@ -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. |