| Previous changeset 5:96cacb31d571 (2021-05-29) Next changeset 7:a7f16f24e9a1 (2022-01-17) |
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Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit f69dd59785c9674ebd58506d5d8b31289d7e9532" |
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modified:
bionano_scaffold.xml macros.xml |
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removed:
test-data/test_02.agp test-data/test_03.agp test-data/test_04.agp |
| b |
| diff -r 96cacb31d571 -r 5d7c5ae1b69b bionano_scaffold.xml --- a/bionano_scaffold.xml Sat May 29 15:58:03 2021 +0000 +++ b/bionano_scaffold.xml Thu Oct 21 13:47:41 2021 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="bionano_scaffold" name="Bionano Hybrid Scaffold" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@" profile="20.01"> +<tool id="bionano_scaffold" name="Bionano Hybrid Scaffold" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> <description>automates the scaffolding process</description> <macros> <import>macros.xml</import> @@ -58,7 +58,7 @@ #if $trim_cut_sites && python '$__tool_directory__/remove_fake_cut_sites.py' $output_file_NCBI 'SCAFFOLD_NCBI_trimmed.fasta' 'output.log' && python '$__tool_directory__/remove_fake_cut_sites.py' $output_file_not_scaffolded 'NOT_SCAFFOLDED_trimmed.fasta' 'output.log' - #end if + #end if ]]> </command> <configfiles> <configfile name="vgp_mode"><![CDATA[ @@ -437,9 +437,10 @@ <data name="results" format="zip" from_work_dir="results.zip" label="${tool.name} on ${on_string}: results"> <filter>zip_file</filter> </data> + <data name="ngs_contigs_scaffold_agp" format="agp" from_work_dir="hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD.agp" label="${tool.name} on ${on_string}: AGP file"/> </outputs> <tests> - <test expect_num_outputs="5"> + <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"/> @@ -463,6 +464,7 @@ </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"> <assert_contents> <has_text text="alignmentOrientation" /> @@ -490,7 +492,7 @@ <has_text text="hybridScaffold"/> </assert_stdout> </test> - <test expect_num_outputs="4"> + <test expect_num_outputs="5"> <param name="ngs_fasta" value="assembly.fasta.gz"/> <param name="bionano_cmap" value="colormap_assembly.cmap"/> <param name="conflict_filter_genome" value="2"/> @@ -513,6 +515,13 @@ </assert_contents> </output> <output name="report" file="test_02_report.txt" ftype="txt"/> + <output name="ngs_contigs_scaffold_agp" ftype="agp"> + <assert_contents> + <has_size value="311" delta="20" /> + <has_text text="##agp-version"/> + <has_n_lines n="9"/> + </assert_contents> + </output> <output name="conflicts" ftype="txt"> <assert_contents> <has_text text="alignmentOrientation" /> @@ -534,7 +543,7 @@ <!--attribute_is path="hybridScaffold/global/flag[@attr='maxthreads']" attribute="val0" text="2"/--> </assert_stdout> </test> - <test expect_num_outputs="5"> + <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="2"/> @@ -558,6 +567,13 @@ </assert_contents> </output> <output name="report" file="test_03_report.txt" ftype="txt"/> + <output name="ngs_contigs_scaffold_agp" ftype="agp"> + <assert_contents> + <has_size value="311" delta="20" /> + <has_text text="##agp-version"/> + <has_n_lines n="9"/> + </assert_contents> + </output> <output name="conflicts" ftype="txt"> <assert_contents> <has_text text="alignmentOrientation" /> @@ -585,7 +601,7 @@ <has_text text="hybridScaffold"/> </assert_stdout> </test> - <test expect_num_outputs="5"> + <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="2"/> @@ -609,6 +625,13 @@ </assert_contents> </output> <output name="report" file="test_04_report.txt" ftype="txt"/> + <output name="ngs_contigs_scaffold_agp" ftype="agp"> + <assert_contents> + <has_size value="311" delta="20" /> + <has_text text="##agp-version"/> + <has_n_lines n="9"/> + </assert_contents> + </output> <output name="conflicts" ftype="txt"> <assert_contents> <has_text text="alignmentOrientation" /> @@ -635,7 +658,7 @@ <has_text text="hybridScaffold"/> </assert_stdout> </test> - <test expect_num_outputs="4"> + <test expect_num_outputs="5"> <param name="ngs_fasta" value="assembly.fasta.gz"/> <param name="bionano_cmap" value="colormap_assembly.cmap"/> <param name="conflict_filter_genome" value="3"/> @@ -663,6 +686,13 @@ </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="311" delta="20" /> + <has_text text="##agp-version"/> + <has_n_lines n="9"/> + </assert_contents> + </output> <assert_stdout> <has_text text='attr="maxmem" val0="8"'/> </assert_stdout> |
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| diff -r 96cacb31d571 -r 5d7c5ae1b69b macros.xml --- a/macros.xml Sat May 29 15:58:03 2021 +0000 +++ b/macros.xml Thu Oct 21 13:47:41 2021 +0000 |
| b |
| @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">3.6.1</token> - <token name="@GALAXY_TOOL_VERSION@">galaxy2</token> + <token name="@VERSION_SUFFIX@">3</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. |
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| diff -r 96cacb31d571 -r 5d7c5ae1b69b test-data/test_02.agp --- a/test-data/test_02.agp Sat May 29 15:58:03 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,9 +0,0 @@ -##agp-version 2.0 -# Organism: -# Platform: -# Model: -# Enzyme(s): -# BioSample: -# BioProject: -# Obj_Name Obj_Start Obj_End PartNum Compnt_Type CompntId_GapLength CompntStart_GapType CompntEnd_Linkage Orientation_LinkageEvidence -Super-Scaffold_1 1 4753350 1 W Super_scaffold_3 1 4753350 + |
| b |
| diff -r 96cacb31d571 -r 5d7c5ae1b69b test-data/test_03.agp --- a/test-data/test_03.agp Sat May 29 15:58:03 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,9 +0,0 @@ -##agp-version 2.0 -# Organism: -# Platform: -# Model: -# Enzyme(s): -# BioSample: -# BioProject: -# Obj_Name Obj_Start Obj_End PartNum Compnt_Type CompntId_GapLength CompntStart_GapType CompntEnd_Linkage Orientation_LinkageEvidence -Super-Scaffold_1 1 4753350 1 W Super_scaffold_3 1 4753350 + |
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| diff -r 96cacb31d571 -r 5d7c5ae1b69b test-data/test_04.agp --- a/test-data/test_04.agp Sat May 29 15:58:03 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,9 +0,0 @@ -##agp-version 2.0 -# Organism: -# Platform: -# Model: -# Enzyme(s): -# BioSample: -# BioProject: -# Obj_Name Obj_Start Obj_End PartNum Compnt_Type CompntId_GapLength CompntStart_GapType CompntEnd_Linkage Orientation_LinkageEvidence -Super-Scaffold_1 1 4753350 1 W Super_scaffold_3 1 4753350 + |