diff --git a/bin/create_interactive_table.sh b/bin/create_interactive_table.sh deleted file mode 100644 index 59869e58..00000000 --- a/bin/create_interactive_table.sh +++ /dev/null @@ -1,8 +0,0 @@ -#!/usr/bin/env bash - -mkdir -p 'results/microgalaxy' - -python bin/create_interactive_table.py \ - --table 'results/microgalaxy/tools.tsv' \ - --template 'data/microgalaxy/datatable_template.html' \ - --output 'results/microgalaxy/index.html' diff --git a/bin/filter_microgalaxy_tools.sh b/bin/get_microgalaxy_tools.sh similarity index 74% rename from bin/filter_microgalaxy_tools.sh rename to bin/get_microgalaxy_tools.sh index b3613fd6..b8684d5b 100644 --- a/bin/filter_microgalaxy_tools.sh +++ b/bin/get_microgalaxy_tools.sh @@ -18,4 +18,9 @@ python bin/extract_galaxy_tools.py \ --filtered_tools 'results/microgalaxy/tools.tsv' \ --categories "data/microgalaxy/categories" \ --exclude "data/microgalaxy/tools_to_exclude" \ - --keep "data/microgalaxy/tools_to_keep" \ No newline at end of file + --keep "data/microgalaxy/tools_to_keep" + +python bin/create_interactive_table.py \ + --table 'results/microgalaxy/tools.tsv' \ + --template 'data/interactive_table_template.html' \ + --output 'results/microgalaxy/index.html' diff --git a/data/microgalaxy/tools_to_exclude b/data/microgalaxy/tools_to_exclude index d451b4a0..6f30553a 100644 --- a/data/microgalaxy/tools_to_exclude +++ b/data/microgalaxy/tools_to_exclude @@ -139,6 +139,7 @@ inforna intarna kinwalker locarna +mea mqc nastiseq paralyzer diff --git a/data/microgalaxy/tools_to_keep b/data/microgalaxy/tools_to_keep index 96cfbdfe..0e2d8278 100644 --- a/data/microgalaxy/tools_to_keep +++ b/data/microgalaxy/tools_to_keep @@ -47,7 +47,6 @@ nucleosome_prediction pfamscan racon infernal -mea rRNA reago sortmerna diff --git a/results/microgalaxy/index.html b/results/microgalaxy/index.html index b5fe6647..ae0ad294 100644 --- a/results/microgalaxy/index.html +++ b/results/microgalaxy/index.html @@ -1057,26 +1057,6 @@ bgruening https://github.com/bgruening/galaxytools/tree/master/tools/infernal - - - mea - 0.6.4.1 - 0.6.4 - mea - To update - - - - - Maximum expected accuracy prediction - - To update - http://www.bioinf.uni-leipzig.de/Software/mea - RNA - mea - rnateam - https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea - rRNA diff --git a/results/microgalaxy/tools.tsv b/results/microgalaxy/tools.tsv index e2919ba7..1195fd8b 100644 --- a/results/microgalaxy/tools.tsv +++ b/results/microgalaxy/tools.tsv @@ -189,7 +189,7 @@ inforna INFO-RNA is a service for the design of RNA sequences that fold into a intarna intarna Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites. Up-to-date https://github.com/BackofenLab/IntaRNA RNA intarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna 3.3.2 intarna 3.3.2 True False kinwalker Kinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event. To update http://www.bioinf.uni-leipzig.de/Software/Kinwalker/ RNA kinwalker rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker True False locarna locarna_exparnap, locarna_multiple, locarna_pairwise, locarna_pairwise_p, locarna_reliability_profile LocARNA - A suite for multiple alignment and folding of RNAs To update http://www.bioinf.uni-freiburg.de/Software/LocARNA/ RNA locarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna 1.9.2.3 locarna 2.0.0 True False -mea mea Maximum expected accuracy prediction To update http://www.bioinf.uni-leipzig.de/Software/mea RNA mea rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea 0.6.4.1 mea 0.6.4 True True +mea mea Maximum expected accuracy prediction To update http://www.bioinf.uni-leipzig.de/Software/mea RNA mea rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea 0.6.4.1 mea 0.6.4 True False mqc mqc Ribosome profiling mapping quality control tool To update https://github.com/Biobix/mQC Sequence Analysis mqc rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc/ 1.9 mqc 1.10 True False nastiseq nastiseq A method to identify cis-NATs using ssRNA-seq Up-to-date https://ohlerlab.mdc-berlin.de/software/NASTIseq_104/ RNA nastiseq rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq 1.0 r-nastiseq 1.0 True False paralyzer paralyzer A method to generate a high resolution map of interaction sites between RNA-binding proteins and their targets. Up-to-date https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/ RNA paralyzer rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer 1.5 paralyzer 1.5 True False