Add --cite_url to tool_init.

Allows bootstrapping some of the bibtex boilerplate.

Author: jmchilton

planemo/commands/cmd_tool_init.py

@@ -165,6 +165,14 @@
     help=("Supply a DOI (http://www.doi.org/) easing citation of the tool "
           "for Galxy users (e.g. 10.1101/014043).")
 )
+@click.option(
+    "--cite_url",
+    type=click.STRING,
+    default=None,
+    multiple=True,
+    prompt=False,
+    help=("Supply a URL for citation.")
+)
 @click.option(
     "--test_case",
     is_flag=True,

planemo/tool_builder.py

@@ -104,6 +104,9 @@
         <citations>
 {%- for single_doi in doi %}
             <citation type="doi">{{ single_doi }}</citation>
+{%- endfor %}
+{%- for bibtex_citation in bibtex_citations %}
+            <citation type="bibtex">{{ bibtex_citation }}</citation>
 {%- endfor %}
             <yield />
         </citations>
@@ -126,6 +129,12 @@ def build(**kwds):
 
     _handle_help(kwds)
 
+    # process raw cite urls
+    cite_urls = kwds.get("cite_url", [])
+    del kwds["cite_url"]
+    citations = map(UrlCitation, cite_urls)
+    kwds["bibtex_citations"] = citations
+
     # process raw inputs
     inputs = kwds.get("input", [])
     del kwds["input"]
@@ -274,6 +283,41 @@ def _find_command(kwds):
     return command
 
 
+class UrlCitation(object):
+
+    def __init__(self, url):
+        self.url = url
+
+    def __str__(self):
+        if "github.com" in self.url:
+            return self._github_str()
+        else:
+            return self._url_str()
+
+    def _github_str(self):
+        url = self.url
+        title = url.split("/")[-1]
+        return '''
+@misc{github%s,
+  author = {LastTODO, FirstTODO},
+  year = {TODO},
+  title = {%s},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  url = {%s},
+}''' % (title, title, url)
+
+    def _url_str(self):
+        url = self.url
+        return '''
+@misc{renameTODO,
+  author = {LastTODO, FirstTODO},
+  year = {TODO},
+  title = {TODO},
+  url = {%s},
+}''' % (url)
+
+
 class ToolDescription(object):
 
     def __init__(self, contents, macro_contents, test_files):

tests/test_build_and_lint.py

@@ -52,6 +52,8 @@ def _init_command(test_case=True, help_text=True, doi=True, macros=False):
         command.extend(["--help_text", "The help text."])
     if doi:
         command.extend(["--doi", "10.1101/014043"])
+        command.extend(["--cite_url", "https://github.com/ekg/vcflib"])
+        command.extend(["--cite_url", "http://wiki.hpc.ufl.edu/doc/Seqtk"])
     if macros:
         command.append("--macros")
     return command