add yaml splitting script

taken from: https://github.com/galaxyproject/usegalaxy-tools/blob/71a7a8eadb3bcb735f02d591cc548c561fb3aaed/scripts/split_tool_yml.py

Author: martenson

scripts/split_tool_yml.py

@@ -0,0 +1,117 @@
+#!/usr/bin/env python
+
+import yaml
+from collections import defaultdict
+import re
+import os
+import string
+import sys
+import argparse
+
+def slugify(value):
+    """
+    Normalizes string, converts to lowercase, removes non-alpha characters,
+    and converts spaces to hyphens.
+    """
+    rval = ''
+    for c in value:
+        rval += (c if c in string.ascii_letters + string.digits else '_').lower()
+    return rval
+
+def strip_superflous(cat):
+    """
+    Re-arranges the ephemeris returned yml format for tools to the usegalaxy-tools minimal tool yml format
+
+    i.e. Takes a list like:
+
+    - name: substitution_rates
+      owner: devteam
+      revisions:
+      - d1b35bcdaacc
+      tool_panel_section_label: Regional Variation
+      tool_shed_url: toolshed.g2.bx.psu.edu
+    - name: indels_3way
+      owner: devteam
+      revisions:
+      - 5ad24b81dd10
+      tool_panel_section_label: Regional Variation
+      tool_shed_url: toolshed.g2.bx.psu.edu
+
+      ...
+
+     and returns:
+
+     tool_panel_section_label: Regional Variation
+     - name: substitution_rates
+       owner: devteam
+     - name: indels_3way
+       owner: devteam
+
+       ...
+    """
+
+    out = {'tool_panel_section_label': cat[0]['tool_panel_section_label']}
+
+    for tool in cat:
+        del tool['tool_panel_section_label']
+        del tool['tool_panel_section_id']
+        del tool['revisions']
+        if tool['tool_shed_url'] == 'toolshed.g2.bx.psu.edu':
+            del tool['tool_shed_url']
+
+    out['tools'] = cat
+
+    return out
+
+
+def main():
+
+    VERSION = 0.2
+
+    parser = argparse.ArgumentParser(description="Splits up a Ephemeris `get_tool_list` yml file for a Galaxy server into individual files for each Section Label.")
+    parser.add_argument("-i", "--infile", help="The returned `get_tool_list` yml file to split.")
+    parser.add_argument("-o", "--outdir", help="The output directory to put the split files into. Defaults to infile without the .yml.")
+    parser.add_argument("-l", "--lockfiles", action='store_true', help="Produce lock files instead of plain yml files.")
+    parser.add_argument("--version", action='store_true')
+    parser.add_argument("--verbose", action='store_true')
+
+    args = parser.parse_args()
+
+    if args.version:
+        print("split_tool_yml.py version: %.1f" % VERSION)
+        return
+
+    filename = args.infile
+
+    a = yaml.safe_load(open(filename, 'r'))
+    outdir = re.sub('\.yml','',filename)
+    if args.outdir:
+        outdir = args.outdir
+
+    if args.verbose:
+        print('Outdir: %s' % outdir)
+    if not os.path.isdir(outdir):
+        os.mkdir(outdir)
+
+    tools = a['tools']
+    categories = defaultdict(list)
+
+    for tool in tools:
+        categories[tool['tool_panel_section_label']].append(tool)
+
+    for cat in categories:
+        fname = str(cat)
+        good_fname = outdir + "/" + slugify(fname) + ".yml"
+        if args.lockfiles:
+            good_fname += ".lock"
+            tool_yaml = {'tools': categories[cat]}
+        else:
+            tool_yaml = strip_superflous(categories[cat])
+        if args.verbose:
+            print("Working on: %s" % good_fname)
+        with open(good_fname, 'w') as outfile:
+            yaml.dump(tool_yaml, outfile, default_flow_style=False)
+
+    return
+
+if __name__ == "__main__": main()