| Previous changeset 4:8cc3862f8b8e (2021-05-25) Next changeset 6:5d7c5ae1b69b (2021-10-21) |
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Commit message:
"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 01f4a0a13563b0ae33565ddb26a8fc3a23726e03" |
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modified:
bionano_scaffold.xml macros.xml |
| b |
| diff -r 8cc3862f8b8e -r 96cacb31d571 bionano_scaffold.xml --- a/bionano_scaffold.xml Tue May 25 20:12:52 2021 +0000 +++ b/bionano_scaffold.xml Sat May 29 15:58:03 2021 +0000 |
| b |
| b'@@ -55,9 +55,9 @@\n -f\n $zip_file\n -o ./\n- && cat $output_file_NCBI $output_file_not_scaffolded > total_contigs_raw.fasta\n #if $trim_cut_sites\n- && python \'$__tool_directory__/remove_fake_cut_sites.py\' \'total_contigs_raw.fasta\' \'total_contigs_trimmed.fasta\' \'output.log\'\n+ && python \'$__tool_directory__/remove_fake_cut_sites.py\' $output_file_NCBI \'SCAFFOLD_NCBI_trimmed.fasta\' \'output.log\'\n+ && python \'$__tool_directory__/remove_fake_cut_sites.py\' $output_file_not_scaffolded \'NOT_SCAFFOLDED_trimmed.fasta\' \'output.log\'\n #end if \n ]]> </command>\n <configfiles>\n@@ -420,22 +420,26 @@\n -->\n </inputs>\n <outputs>\n- <data name="ngs_contigs" format="fasta" from_work_dir="total_contigs_raw.fasta" label="${tool.name} on ${on_string}: NGScontigs">\n+ <data name="ngs_contigs_scaffold" format="fasta" from_work_dir="hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD_NCBI.fasta" label="${tool.name} on ${on_string}: NGScontigs scaffold NCBI">\n <filter>trim_cut_sites == False</filter>\n </data>\n- <data name="ngs_contigs_trimmed" format="fasta" from_work_dir="total_contigs_trimmed.fasta" label="${tool.name} on ${on_string}: NGScontigs trimmed">\n+ <data name="ngs_contigs_not_scaffolded" format="fasta" from_work_dir="hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD_NOT_SCAFFOLDED.fasta" label="${tool.name} on ${on_string}: NGScontigs not scaffolded">\n+ <filter>trim_cut_sites == False</filter>\n+ </data>\n+ <data name="ngs_contigs_scaffold_trimmed" format="fasta" from_work_dir="SCAFFOLD_NCBI_trimmed.fasta" label="${tool.name} on ${on_string}: NGScontigs scaffold NCBI trimmed">\n <filter>trim_cut_sites</filter>\n </data>\n- <data name="ngs_contigs_trimmed_report" format="txt" from_work_dir="output.log" label="${tool.name} on ${on_string}: NGScontigs trimmed log">\n+ <data name="ngs_contigs_not_scaffolded_trimmed" format="fasta" from_work_dir="NOT_SCAFFOLDED_trimmed.fasta" label="${tool.name} on ${on_string}: NGScontigs not scaffolded trimmed">\n <filter>trim_cut_sites</filter>\n </data>\n <data name="report" format="txt" from_work_dir="hybrid_scaffolds/hybrid_scaffold_informatics_report.txt" label="${tool.name} on ${on_string}: hybrid scaffold report"/>\n+ <data name="conflicts" format="txt" from_work_dir="hybrid_scaffolds/conflicts.txt" label="${tool.name} on ${on_string}: conflicts"/>\n <data name="results" format="zip" from_work_dir="results.zip" label="${tool.name} on ${on_string}: results">\n <filter>zip_file</filter>\n </data>\n </outputs>\n <tests>\n- <test expect_num_outputs="3">\n+ <test expect_num_outputs="5">\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@@ -446,12 +450,24 @@\n </conditional>\n <param name="zip_file" value="true"/>\n <param name="trim_cut_sites" value="false"/>\n- <output name="ngs_contigs" ftype="fasta">\n+ <output name="ngs_contigs_scaffold" ftype="fasta">\n <assert_contents>\n- <has_size value="4753369" delta="300" />\n+ <has_size value="4753369" delta="100" />\n+ <has_n_lines n="2"/>\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="conflicts" ft'..b'-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_03_report.txt" ftype="txt"/>\n+ <output name="conflicts" ftype="txt">\n+ <assert_contents>\n+ <has_text text="alignmentOrientation" />\n+ </assert_contents>\n+ </output> \n <output name="results" ftype="zip">\n <assert_contents>\n <!--<has_size value="4231908" delta="300" />-->\n@@ -550,7 +585,7 @@\n <has_text text="hybridScaffold"/>\n </assert_stdout>\n </test>\n- <test expect_num_outputs="3">\n+ <test expect_num_outputs="5">\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="2"/>\n@@ -561,14 +596,24 @@\n </conditional>\n <param name="zip_file" value="true"/>\n <param name="trim_cut_sites" value="false"/>\n- <output name="ngs_contigs" ftype="fasta">\n+ <output name="ngs_contigs_scaffold" ftype="fasta">\n <assert_contents>\n <has_size value="4753369" delta="100" />\n <has_n_lines n="2"/>\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_04_report.txt" ftype="txt"/>\n+ <output name="conflicts" ftype="txt">\n+ <assert_contents>\n+ <has_text text="alignmentOrientation" />\n+ </assert_contents>\n+ </output>\n <output name="results" ftype="zip">\n <assert_contents>\n <has_archive_member path=".*/status.txt"/>\n@@ -590,7 +635,7 @@\n <has_text text="hybridScaffold"/>\n </assert_stdout>\n </test>\n- <test expect_num_outputs="3">\n+ <test expect_num_outputs="4">\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@@ -600,16 +645,23 @@\n <param name="configuration_file" value="configuration.xml"/>\n </conditional>\n <param name="trim_cut_sites" value="true"/>\n- <output name="ngs_contigs_trimmed" ftype="fasta">\n+ <output name="ngs_contigs_scaffold_trimmed" ftype="fasta">\n <assert_contents>\n- <has_size value="4832591" delta="300" />\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="ngs_contigs_trimmed_report" ftype="txt">\n+ <output name="ngs_contigs_not_scaffolded_trimmed" ftype="fasta">\n <assert_contents>\n <has_size value="0" />\n </assert_contents>\n </output>\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 <assert_stdout>\n <has_text text=\'attr="maxmem" val0="8"\'/>\n' |
| b |
| diff -r 8cc3862f8b8e -r 96cacb31d571 macros.xml --- a/macros.xml Tue May 25 20:12:52 2021 +0000 +++ b/macros.xml Sat May 29 15:58:03 2021 +0000 |
| b |
| @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">3.6.1</token> - <token name="@GALAXY_TOOL_VERSION@">galaxy1</token> + <token name="@GALAXY_TOOL_VERSION@">galaxy2</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. |