| Previous changeset 0:fec6a0b53189 (2021-05-17) Next changeset 2:c612f2d2881c (2021-05-17) |
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Commit message:
"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 70c17a8d4b839becfda3e41fccc6bb6a8d3a6eb0-dirty" |
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modified:
macros.xml |
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added:
bionano_scaffold.xml bionano_scaffold_edited_test_report.html test-data/foo.zip test-data/foo2.zip |
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removed:
bionano_scaffold_edited.xml |
| b |
| diff -r fec6a0b53189 -r 9bd94d9a1b2e bionano_scaffold.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bionano_scaffold.xml Mon May 17 21:13:20 2021 +0000 |
| [ |
| b'@@ -0,0 +1,622 @@\n+<tool id="bionano_scaffold" name="Bionano Hybrid Scaffold" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@" profile="20.01">\n+ <description>automates the scaffolding process</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="edam_ontology"/>\n+ <expand macro="requirements"/>\n+ <version_command>perl /HybridScaffold/hybridScaffold.pl --version</version_command>\n+ <command detect_errors="exit_code"><![CDATA[\n+ #set RefAligner = \'/usr/local/bin/RefAligner\'\n+ ## softlinks do not work\n+ cp \'${ngs_fasta}\' ./ngs.fasta\n+ && cp \'${bionano_cmap}\' ./bionano.cmap\n+ #if $configuration_options.configuration == \'vgp\'\n+ && cp \'${vgp_mode}\' ./config.xml\n+ #else\n+ #import os\n+ #set cores = os.environ.get(\'GALAXY_SLOTS\', 2)\n+ #set memory = os.environ.get(\'GALAXY_MEMORY_MB\', 4000) / 1000\n+ && cp \'${configuration_file}\' ./config.xml\n+ && sed -i \'s|attr="maxmem" val0=.* display|attr="maxmem" val0="$memory" display|\' ./config.xml\n+ && sed -i \'s|attr="maxthreads" val0=.* display|attr="maxthreads" val0="$cores" display|\' ./config.xml\n+ && sed -i \'s|attr="maxvirtmem" val0=.*/>|attr="maxvirtmem" val0="$cores"/>|\' ./config.xml\n+ && sed -i \'s|attr="insertThreads" val0=.*/>|attr="insertThreads" val0="$cores"/>|\' ./config.xml\n+ #end if\n+ ## output the configuration file on stdout\n+ && cat ./config.xml\n+ && perl \'/HybridScaffold/hybridScaffold.pl\'\n+ -n ./ngs.fasta\n+ -b ./bionano.cmap\n+ -c ./config.xml\n+ -r $RefAligner\n+ #if $conflict_resolution\n+ -M \'${conflict_resolution}\'\n+ #end if\n+ #if not $conflict_resolution\n+ -B $conflict_filter_genome\n+ -N $conflict_filter_sequence\n+ #end if\n+ ##$align_molecules_options.align_molecules\n+ ###if $align_molecules_options.align_molecules\n+ ## -m $align_molecules_options.bionano_molecules\n+ ## -q \'${align_molecules_options.optarguments_xml}\'\n+ ## -p ##/home/bionano/tools/pipeline/1.0/Pipeline/1.0/ \n+ ###end if\n+ ##$quimeric_quality_options.quimeric_quality\n+ ###if $quimeric_quality_options.quimeric_quality\n+ ## -m $align_molecules_options.bionano_molecules\n+ ## #if $quimeric_quality_conditional.noise_parameter\n+ ## -e \'${quimeric_quality_conditional.noise_parameter}\'\n+ ## #end if\n+ ###end if\n+ -f\n+ $zip_file\n+ -o ./\n+ ##;\n+ ##sleep 1000000\n+\n+ ]]> </command>\n+ <configfiles>\n+ <configfile name="vgp_mode"><![CDATA[\n+ #if $configuration_options.configuration == \'vgp\'\n+ #import os\n+ #set cores = os.environ.get(\'GALAXY_SLOTS\', 2)\n+ #set memory = os.environ.get(\'GALAXY_MEMORY_MB\', 4000) / 1000\n+ <hybridScaffold>\n+ <version>\n+ <flag attr="version" val0="\\$Id: hybridScaffold_DLE1_config.xml 7702 2018-06-25 20:53:51Z apang \\$"/>\n+ </version>\n+ <global>\n+ <flag attr="maxmem" val0="$memory" display="Maximum memory (GB)" group="Global options" description="Define the maximum amount of RAM in gigabytes to be used by each process."/>\n+ <flag attr="maxthreads" val0="$cores" display="Max threads" group="Global options" description="Define maximum number of threads to be used by each process."/>\n+ <flag attr="maxvirtmem" val0="$memory"/>\n+ <flag attr="RAmem" val0="3" val1="1"/>\n+ </global>\n+ <fasta2cmap>\n+ <flag attr="enzyme" val0="$configuration_options.enzyme" display="Enzyme" group="FASTA to CMAP digestion" description="Define single enzyme for '..b' <has_text text=\'attr="maxvirtmem" val0="4.0"\'/>\n+ </assert_stdout>\n+ <assert_stdout>\n+ <has_text text="hybridScaffold"/>\n+ </assert_stdout>\n+ </test>\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+ <param name="conflict_filter_sequence" value="3"/>\n+ <conditional name="configuration_options">\n+ <param name="configuration" value="vgp"/>\n+ <param name="enzyme" value="BspQI"/>\n+ </conditional>\n+ <param name="zip_file" value="true"/>\n+ <output name="ngs_contigs_scaffold_fasta" 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_scaffold_agp" file="test_04.agp" ftype="txt"/>\n+ <output name="ngs_contigs_scaffold_gap" file="test_04.gap" ftype="txt"/>\n+ <output name="report" file="test_04_report.txt" ftype="txt"/>\n+ <output name="results" ftype="zip">\n+ <assert_contents>\n+ <has_archive_member path=".*/status.txt"/>\n+ </assert_contents>\n+ </output>\n+ <assert_stdout>\n+ <has_text text=\'attr="maxmem" val0="4.0"\'/>\n+ </assert_stdout>\n+ <assert_stdout>\n+ <has_text text=\'attr="maxthreads" val0="2"\'/>\n+ </assert_stdout>\n+ <assert_stdout>\n+ <has_text text=\'attr="insertThreads" val0="2"\'/>\n+ </assert_stdout>\n+ <assert_stdout>\n+ <has_text text=\'attr="maxvirtmem" val0="4.0"\'/>\n+ </assert_stdout>\n+ <assert_stdout>\n+ <has_text text="hybridScaffold"/>\n+ </assert_stdout>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+.. class:: infomark\n+\n+**Purpose**\n+\n+The Hybrid Scaffold pipeline automates the comprehensive scaffolding process and is consisted of five major steps: 1) generate in silico maps for sequence assembly; 2) align in silico sequence maps against Bionano genome maps to identify and resolve potential conflicts in either data set; 3) merge the non-conflicting maps into hybrid scaffolds; 4) align sequence maps to the hybrid scaffolds; and 5) generate AGP and FASTA files for the scaffolds. \n+\n+----\n+\n+.. class:: infomark\n+\n+**Coverage**\n+\n+For Hybrid Scaffold, we recommend using as input a minimum of 80X effective molecule coverage in order to build an accurate and contiguous consensus genome map assembly for each enzyme. When using nickases, using more coverage does not significantly improve map contiguity. When using a DLS enzyme such as DLE-1, effective coverage up to and beyond 100X has shown improved map contiguities for some plants and animals.\n+\n+----\n+\n+.. class:: infomark\n+\n+**Input Bionano assembly**\n+\n+When running the de novo assembly pipeline for hybrid scaffolding applications, users are recommended to use assembly parameters for non-haplotype-aware assembly. The current Hybrid Scaffold pipeline does not explicitly handle haplotype information and assumes there is only one genome map or NGS sequence contig covering a given genomic region. If multiple haplotypes are present, the pipeline may make false positive conflict cuts and incorrectly mix haplotypes in the final scaffolds. We understand that haplotype information is important in many applications, and a fully haplotype-aware Hybrid Scaffold pipeline is in our roadmap for a future release.\n+\n+----\n+\n+.. class:: infomark\n+\n+@BIONANO_SUPPORT_TEXT@\n+\n+ ]]> </help>\n+ <expand macro="citations"/>\n+</tool>\n' |
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| diff -r fec6a0b53189 -r 9bd94d9a1b2e bionano_scaffold_edited.xml --- a/bionano_scaffold_edited.xml Mon May 17 15:07:05 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,617 +0,0 @@\n-<tool id="bionano_scaffold" name="Bionano Hybrid Scaffold" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@" profile="20.01">\n- <description>automates the scaffolding process</description>\n- <macros>\n- <import>macros.xml</import>\n- </macros>\n- <expand macro="edam_ontology"/>\n- <expand macro="requirements"/>\n- <version_command>perl /HybridScaffold/hybridScaffold.pl --version</version_command>\n- <command detect_errors="exit_code"><![CDATA[\n- #set RefAligner = \'/usr/local/bin/RefAligner\'\n- ## softlinks do not work\n- cp \'${ngs_fasta}\' ./ngs.fasta\n- && cp \'${bionano_cmap}\' ./bionano.cmap\n- #if $configuration_options.configuration == \'vgp\'\n- && cp \'${vgp_mode}\' ./config.xml\n- #else\n- #import os\n- #set cores = os.environ.get(\'GALAXY_SLOTS\', 2)\n- #set memory = os.environ.get(\'GALAXY_MEMORY_MB\', 4000) / 1000\n- && cp \'${configuration_file}\' ./config.xml\n- && sed -i \'s|attr="maxmem" val0=.* display|attr="maxmem" val0="$memory" display|\' ./config.xml\n- && sed -i \'s|attr="maxthreads" val0=.* display|attr="maxthreads" val0="$cores" display|\' ./config.xml\n- && sed -i \'s|attr="maxvirtmem" val0=.*/>|attr="maxvirtmem" val0="$cores"/>|\' ./config.xml\n- && sed -i \'s|attr="insertThreads" val0=.*/>|attr="insertThreads" val0="$cores"/>|\' ./config.xml\n- #end if\n- ## output the configuration file on stdout\n- && cat ./config.xml\n- && perl \'/HybridScaffold/hybridScaffold.pl\'\n- -n ./ngs.fasta\n- -b ./bionano.cmap\n- -c ./config.xml\n- -r $RefAligner\n- #if $conflict_resolution\n- -M \'${conflict_resolution}\'\n- #end if\n- #if not $conflict_resolution\n- -B $conflict_filter_genome\n- -N $conflict_filter_sequence\n- #end if\n- ##$align_molecules_options.align_molecules\n- ###if $align_molecules_options.align_molecules\n- ## -m $align_molecules_options.bionano_molecules\n- ## -q \'${align_molecules_options.optarguments_xml}\'\n- ## -p ##/home/bionano/tools/pipeline/1.0/Pipeline/1.0/ \n- ###end if\n- ##$quimeric_quality_options.quimeric_quality\n- ###if $quimeric_quality_options.quimeric_quality\n- ## -m $align_molecules_options.bionano_molecules\n- ## #if $quimeric_quality_conditional.noise_parameter\n- ## -e \'${quimeric_quality_conditional.noise_parameter}\'\n- ## #end if\n- ###end if\n- -f\n- $zip_file\n- -o ./\n- ##;\n- ##sleep 1000000\n-\n- ]]> </command>\n- <configfiles>\n- <configfile name="vgp_mode"><![CDATA[\n- #if $configuration_options.configuration == \'vgp\'\n- #import os\n- #set cores = os.environ.get(\'GALAXY_SLOTS\', 2)\n- #set memory = os.environ.get(\'GALAXY_MEMORY_MB\', 4000) / 1000\n- <hybridScaffold>\n- <version>\n- <flag attr="version" val0="\\$Id: hybridScaffold_DLE1_config.xml 7702 2018-06-25 20:53:51Z apang \\$"/>\n- </version>\n- <global>\n- <flag attr="maxmem" val0="$memory" display="Maximum memory (GB)" group="Global options" description="Define the maximum amount of RAM in gigabytes to be used by each process."/>\n- <flag attr="maxthreads" val0="$cores" display="Max threads" group="Global options" description="Define maximum number of threads to be used by each process."/>\n- <flag attr="maxvirtmem" val0="$memory"/>\n- <flag attr="RAmem" val0="3" val1="1"/>\n- </global>\n- <fasta2cmap>\n- <flag attr="enzyme" val0="$configuration_options.enzyme" display="Enzyme" group="FASTA to CMAP digestion" description="Define single enzyme for '..b' </assert_stdout>\n- <assert_stdout>\n- <has_text text="hybridScaffold"/>\n- </assert_stdout>\n- </test>\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- <param name="conflict_filter_sequence" value="3"/>\n- <conditional name="configuration_options">\n- <param name="configuration" value="vgp"/>\n- <param name="enzyme" value="BspQI"/>\n- </conditional>\n- <param name="zip_file" value="true"/>\n- <output name="ngs_contigs_scaffold_fasta" 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_scaffold_agp" file="test_04.agp" ftype="txt"/>\n- <output name="ngs_contigs_scaffold_gap" file="test_04.gap" ftype="txt"/>\n- <output name="report" file="test_04_report.txt" ftype="txt"/>\n- <output name="results" ftype="zip">\n- <assert_contents>\n- <has_archive_member path=".*/status.txt"/>\n- </assert_contents>\n- </output>\n- <assert_stdout>\n- <has_text text=\'attr="maxmem" val0="4.0"\'/>\n- </assert_stdout>\n- <assert_stdout>\n- <has_text text=\'attr="maxthreads" val0="2"\'/>\n- </assert_stdout>\n- <assert_stdout>\n- <has_text text=\'attr="insertThreads" val0="2"\'/>\n- </assert_stdout>\n- <assert_stdout>\n- <has_text text=\'attr="maxvirtmem" val0="4.0"\'/>\n- </assert_stdout>\n- <assert_stdout>\n- <has_text text="hybridScaffold"/>\n- </assert_stdout>\n- </test>\n- </tests>\n- <help><![CDATA[\n-.. class:: infomark\n-\n-**Purpose**\n-\n-The Hybrid Scaffold pipeline automates the comprehensive scaffolding process and is consisted of five major steps: 1) generate in silico maps for sequence assembly; 2) align in silico sequence maps against Bionano genome maps to identify and resolve potential conflicts in either data set; 3) merge the non-conflicting maps into hybrid scaffolds; 4) align sequence maps to the hybrid scaffolds; and 5) generate AGP and FASTA files for the scaffolds. \n-\n-----\n- \n-.. class:: infomark\n- \n-**Coverage**\n-\n-For Hybrid Scaffold, we recommend using as input a minimum of 80X effective molecule coverage in order to build an accurate and contiguous consensus genome map assembly for each enzyme. When using nickases, using more coverage does not significantly improve map contiguity. When using a DLS enzyme such as DLE-1, effective coverage up to and beyond 100X has shown improved map contiguities for some plants and animals.\n-\n-----\n- \n-.. class:: infomark\n- \n-**Input Bionano assembly**\n-\n-When running the de novo assembly pipeline for hybrid scaffolding applications, users are recommended to use assembly parameters for non-haplotype-aware assembly. The current Hybrid Scaffold pipeline does not explicitly handle haplotype information and assumes there is only one genome map or NGS sequence contig covering a given genomic region. If multiple haplotypes are present, the pipeline may make false positive conflict cuts and incorrectly mix haplotypes in the final scaffolds. We understand that haplotype information is important in many applications, and a fully haplotype-aware Hybrid Scaffold pipeline is in our roadmap for a future release.\n-\n-\n- ]]> </help>\n- <expand macro="citations"/>\n-</tool>\n' |
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| diff -r fec6a0b53189 -r 9bd94d9a1b2e bionano_scaffold_edited_test_report.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bionano_scaffold_edited_test_report.html Mon May 17 21:13:20 2021 +0000 |
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| b'@@ -0,0 +1,287 @@\n+<!DOCTYPE html>\n+<html lang="en">\n+ <head>\n+ <meta charset="utf-8">\n+ <meta http-equiv="X-UA-Compatible" content="IE=edge">\n+ <meta name="viewport" content="width=device-width, initial-scale=1">\n+ <title>Test Results (powered by Planemo)</title>\n+\n+ <!-- Bootstrap -->\n+ <style>/*!\n+ * Bootstrap v3.3.1 (http://getbootstrap.com)\n+ * Copyright 2011-2014 Twitter, Inc.\n+ * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)\n+ *//*! normalize.css v3.0.2 | MIT License | git.io/normalize */html{font-family:sans-serif;-webkit-text-size-adjust:100%;-ms-text-size-adjust:100%}body{margin:0}article,aside,details,figcaption,figure,footer,header,hgroup,main,menu,nav,section,summary{display:block}audio,canvas,progress,video{display:inline-block;vertical-align:baseline}audio:not([controls]){display:none;height:0}[hidden],template{display:none}a{background-color:transparent}a:active,a:hover{outline:0}abbr[title]{border-bottom:1px dotted}b,strong{font-weight:700}dfn{font-style:italic}h1{margin:.67em 0;font-size:2em}mark{color:#000;background:#ff0}small{font-size:80%}sub,sup{position:relative;font-size:75%;line-height:0;vertical-align:baseline}sup{top:-.5em}sub{bottom:-.25em}img{border:0}svg:not(:root){overflow:hidden}figure{margin:1em 40px}hr{height:0;-webkit-box-sizing:content-box;-moz-box-sizing:content-box;box-sizing:content-box}pre{overflow:auto}code,kbd,pre,samp{font-family:monospace,monospace;font-size:1em}button,input,optgroup,select,textarea{margin:0;font:inherit;color:inherit}button{overflow:visible}button,select{text-transform:none}button,html input[type=button],input[type=reset],input[type=submit]{-webkit-appearance:button;cursor:pointer}button[disabled],html input[disabled]{cursor:default}button::-moz-focus-inner,input::-moz-focus-inner{padding:0;border:0}input{line-height:normal}input[type=checkbox],input[type=radio]{-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box;padding:0}input[type=number]::-webkit-inner-spin-button,input[type=number]::-webkit-outer-spin-button{height:auto}input[type=search]{-webkit-box-sizing:content-box;-moz-box-sizing:content-box;box-sizing:content-box;-webkit-appearance:textfield}input[type=search]::-webkit-search-cancel-button,input[type=search]::-webkit-search-decoration{-webkit-appearance:none}fieldset{padding:.35em .625em .75em;margin:0 2px;border:1px solid silver}legend{padding:0;border:0}textarea{overflow:auto}optgroup{font-weight:700}table{border-spacing:0;border-collapse:collapse}td,th{padding:0}/*! 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</script>\n+ </body>\n+</html>\n\\ No newline at end of file\n" |
| b |
| diff -r fec6a0b53189 -r 9bd94d9a1b2e macros.xml --- a/macros.xml Mon May 17 15:07:05 2021 +0000 +++ b/macros.xml Mon May 17 21:13:20 2021 +0000 |
| b |
| @@ -1,8 +1,20 @@ <macros> <token name="@TOOL_VERSION@">3.6.1</token> <token name="@GALAXY_TOOL_VERSION@">galaxy0</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. +Bionanno Solve as shipped in this container may not be the latest and +may not run efficiently on non-validated hardware. Hence, it is not +supported by Bionano Genomics. Any questions concerning this version +should be passed to the VGP (https://github.com/VGP/vgp-assembly/issues) +or Galaxy community (https://help.galaxyproject.org). +For the latest supported Bionano software, visit Bionano Support +https://bionanogenomics.com/support/ + </token> + <xml name="edam_ontology"> - <edam_topics> + <edam_topics> <edam_topic>topic_0196</edam_topic> </edam_topics> <edam_operations> |
| b |
| diff -r fec6a0b53189 -r 9bd94d9a1b2e test-data/foo.zip |
| b |
| Binary file test-data/foo.zip has changed |
| b |
| diff -r fec6a0b53189 -r 9bd94d9a1b2e test-data/foo2.zip |
| b |
| Binary file test-data/foo2.zip has changed |