Merge bash community scripts and update microgalaxy

bin/filter_microgalaxy_tools.sh → 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"
+        --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'

data/microgalaxy/tools_to_exclude

@@ -139,6 +139,7 @@ inforna
 intarna
 kinwalker
 locarna
+mea
 mqc
 nastiseq
 paralyzer

data/microgalaxy/tools_to_keep

@@ -47,7 +47,6 @@ nucleosome_prediction
 pfamscan
 racon
 infernal
-mea
 rRNA
 reago
 sortmerna

results/microgalaxy/index.html

@@ -1057,26 +1057,6 @@
       <td>bgruening</td>
       <td>https://github.com/bgruening/galaxytools/tree/master/tools/infernal</td>
     </tr>
-    <tr>
-      <td></td>
-      <td>mea</td>
-      <td>0.6.4.1</td>
-      <td>0.6.4</td>
-      <td>mea</td>
-      <td>To update</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>Maximum expected accuracy prediction</td>
-      <td></td>
-      <td>To update</td>
-      <td>http://www.bioinf.uni-leipzig.de/Software/mea</td>
-      <td>RNA</td>
-      <td>mea</td>
-      <td>rnateam</td>
-      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea</td>
-    </tr>
     <tr>
       <td></td>
       <td>rRNA</td>

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