Mercurial > repos > bgruening > bionano_scaffold
changeset 8:5258e18bbe23 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit 25785fac3064e7def7ebccd45d452dc0b22ec89a"
author | bgruening |
---|---|
date | Sat, 05 Feb 2022 18:15:29 +0000 |
parents | a7f16f24e9a1 |
children | faee8629b460 |
files | bionano_scaffold.xml macros.xml |
diffstat | 2 files changed, 5 insertions(+), 8 deletions(-) [+] |
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--- a/bionano_scaffold.xml Mon Jan 17 08:15:31 2022 +0000 +++ b/bionano_scaffold.xml Sat Feb 05 18:15:29 2022 +0000 @@ -6,7 +6,7 @@ <expand macro="edam_ontology"/> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ - #set RefAligner = '/usr/local/bin/RefAligner' + #set RefAligner = '/RefAligner/RefAligner' #set output_file_NCBI = 'hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD_NCBI.fasta' #set output_file_not_scaffolded = 'hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD_NOT_SCAFFOLDED.fasta' ## softlinks do not work @@ -56,6 +56,7 @@ $zip_file -o ./ #if $trim_cut_sites + && export PATH=/opt/conda/bin/:\$PATH && python '$__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 @@ -472,7 +473,6 @@ </output> <output name="results" ftype="zip"> <assert_contents> - <!--<has_size value="4231746" delta="300" />--> <has_archive_member path=".*/status.txt"/> </assert_contents> </output> @@ -540,7 +540,6 @@ </assert_stdout> <assert_stdout> <has_text text="hybridScaffold"/> - <!--attribute_is path="hybridScaffold/global/flag[@attr='maxthreads']" attribute="val0" text="2"/--> </assert_stdout> </test> <test expect_num_outputs="6"> @@ -581,7 +580,6 @@ </output> <output name="results" ftype="zip"> <assert_contents> - <!--<has_size value="4231908" delta="300" />--> <has_archive_member path=".*/status.txt"/> </assert_contents> </output>
--- a/macros.xml Mon Jan 17 08:15:31 2022 +0000 +++ b/macros.xml Sat Feb 05 18:15:29 2022 +0000 @@ -1,6 +1,6 @@ <macros> - <token name="@TOOL_VERSION@">3.6.1</token> - <token name="@VERSION_SUFFIX@">3</token> + <token name="@TOOL_VERSION@">3.7.0</token> + <token name="@VERSION_SUFFIX@">0</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. @@ -12,7 +12,6 @@ For the latest supported Bionano software, visit Bionano Support https://bionanogenomics.com/support/ </token> - <xml name="edam_ontology"> <edam_topics> <edam_topic>topic_0196</edam_topic> @@ -23,7 +22,7 @@ </xml> <xml name="requirements"> <requirements> - <container type="docker">quay.io/galaxy/bionano-docker-scaffold:1.6.01-bio</container> + <container type="docker">quay.io/galaxy/bionano-docker-scaffold:1.7.0-bio</container> </requirements> </xml> <macro name="sanitize_string" >