--- a/toolfactory/.github/workflows/commit.yml	Sun Aug 16 08:51:14 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,68 +0,0 @@
-name: Galaxy Tool Linting and Tests for PR
-# run planemo on a git repository containing a single tool
-# as a github action. Does NOT run flake8. So, bite me.
-# ross lazarus august 2020
-on: [pull_request,push]
-env:
-  GALAXY_REPO: https://github.com/galaxyproject/galaxy
-  GALAXY_RELEASE: release_20.05
-jobs:
-  setup:
-    name: setup environment and python
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: [3.7]
-    steps:
-    - name: Print github context properties
-      run: |
-        echo 'event: ${{ github.event_name }}'
-        echo 'sha: ${{ github.sha }}'
-        echo 'ref: ${{ github.ref }}'
-        echo 'head_ref: ${{ github.head_ref }}'
-        echo 'base_ref: ${{ github.base_ref }}'
-        echo 'event.before: ${{ github.event.before }}'
-        echo 'event.after: ${{ github.event.after }}'
-    - uses: actions/setup-python@v1
-      with:
-        python-version: ${{ matrix.python-version }}
-    - uses: actions/checkout@v2
-      with:
-    # planemo does not seem to want to install the requirement galaxyxml 
-    # into the venv it manages at tool testing so do it the old skool way
-        repository: 'galaxyproject/galaxy'
-        path: 'galaxy'
-    - name: make venv ready for this galaxy and planemo 
-      run:  |
-        python3 -m venv $GITHUB_WORKSPACE/galaxy/.venv
-        . $GITHUB_WORKSPACE/galaxy/.venv/bin/activate
-        pip install --upgrade pip
-        pip install wheel
-        pip install -r $GITHUB_WORKSPACE/galaxy/requirements.txt
-        # pip install galaxyxml # currently includes a patched working version awaiting PR merge
-    - name: Upgrade pip
-      run: pip install --upgrade pip
-    # Install the `wheel` package so that when installing other packages which
-    # are not available as wheels, pip will build a wheel for them, which can be cached.
-    - name: Install wheel
-      run: pip install wheel
-    - name: Install Planemo and flake8
-      run: pip install planemo flake8 flake8-import-order
-    # galaxyxml temporarily removed until PR accepted
-    - uses: actions/checkout@v2
-      with:
-        fetch-depth: 1
-    - name: flake8
-      run: flake8 --ignore=E2,E3,E4,E5,W3,W505
-    - name: Planemo lint
-      run: planemo lint .
-    - name: Planemo test tool
-      run: planemo test --galaxy_root $GITHUB_WORKSPACE/galaxy --test_output tool_test_output.html --skip_venv --test_output_json tool_test_output.json --galaxy_python_version ${{ matrix.python-version }}  .
-    - name: Copy artifacts into place
-      run: |
-        mkdir upload
-        mv tool_test_output.json tool_test_output.html upload/
-    - uses: actions/upload-artifact@v2.0.1
-      with:
-        name: 'All tool test results'
-        path: upload

--- a/toolfactory/.gitignore	Sun Aug 16 08:51:14 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,129 +0,0 @@
-# Byte-compiled / optimized / DLL files
-__pycache__/
-*.py[cod]
-*$py.class
-
-# C extensions
-*.so
-
-# Distribution / packaging
-.Python
-build/
-develop-eggs/
-dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-wheels/
-pip-wheel-metadata/
-share/python-wheels/
-*.egg-info/
-.installed.cfg
-*.egg
-MANIFEST
-
-# PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
-*.spec
-
-# Installer logs
-pip-log.txt
-pip-delete-this-directory.txt
-
-# Unit test / coverage reports
-htmlcov/
-.tox/
-.nox/
-.coverage
-.coverage.*
-.cache
-nosetests.xml
-coverage.xml
-*.cover
-*.py,cover
-.hypothesis/
-.pytest_cache/
-
-# Translations
-*.mo
-*.pot
-
-# Django stuff:
-*.log
-local_settings.py
-db.sqlite3
-db.sqlite3-journal
-
-# Flask stuff:
-instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
-
-# Sphinx documentation
-docs/_build/
-
-# PyBuilder
-target/
-
-# Jupyter Notebook
-.ipynb_checkpoints
-
-# IPython
-profile_default/
-ipython_config.py
-
-# pyenv
-.python-version
-
-# pipenv
-#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
-#   However, in case of collaboration, if having platform-specific dependencies or dependencies
-#   having no cross-platform support, pipenv may install dependencies that don't work, or not
-#   install all needed dependencies.
-#Pipfile.lock
-
-# PEP 582; used by e.g. github.com/David-OConnor/pyflow
-__pypackages__/
-
-# Celery stuff
-celerybeat-schedule
-celerybeat.pid
-
-# SageMath parsed files
-*.sage.py
-
-# Environments
-.env
-.venv
-env/
-venv/
-ENV/
-env.bak/
-venv.bak/
-
-# Spyder project settings
-.spyderproject
-.spyproject
-
-# Rope project settings
-.ropeproject
-
-# mkdocs documentation
-/site
-
-# mypy
-.mypy_cache/
-.dmypy.json
-dmypy.json
-
-# Pyre type checker
-.pyre/

--- a/toolfactory/.shed.yml	Sun Aug 16 08:51:14 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,13 +0,0 @@
-name: toolfactory
-owner: fubar
-description: ToolFactory - tool to make Galaxy tools ready for the toolshed
-homepage_url: https://github.com/fubar2/toolfactory
-long_description: |
-    ToolFactory - turn executable packages and R/python/perl/bash scripts into ordinary Galaxy tools
-
-    Creating re-usable tools from scripts: The Galaxy Tool Factory Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team 
-    Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573
-remote_repository_url: https://github.com/fubar2/toolfactory
-type: tool_dependency_definition
-categories:
-- Tool Generators

--- a/toolfactory/html_dir.py	Sun Aug 16 08:51:14 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,180 +0,0 @@
-
-class tooloutHTMLifyer(self):
-
-    def compressPDF(self,inpdf=None,thumbformat='png'):
-        """need absolute path to pdf
-           note that GS gets confoozled if no $TMP or $TEMP
-           so we set it
-        """
-        assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf,self.myName)
-        hlog = os.path.join(self.opts.output_dir,"compress_%s.txt" % os.path.basename(inpdf))
-        sto = open(hlog,'a')
-        our_env = os.environ.copy()
-        our_tmp = our_env.get('TMP',None)
-        if not our_tmp:
-            our_tmp = our_env.get('TEMP',None)
-        if not (our_tmp and os.path.exists(our_tmp)):
-            newtmp = os.path.join(self.opts.output_dir,'tmp')
-            try:
-                os.mkdir(newtmp)
-            except:
-                sto.write('## WARNING - cannot make %s - it may exist or permissions need fixing\n' % newtmp)
-            our_env['TEMP'] = newtmp
-            if not self.temp_warned:
-               sto.write('## WARNING - no $TMP or $TEMP!!! Please fix - using %s temporarily\n' % newtmp)
-               self.temp_warned = True          
-        outpdf = '%s_compressed' % inpdf
-        cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dUseCIEColor", "-dBATCH","-dPDFSETTINGS=/printer", "-sOutputFile=%s" % outpdf,inpdf]
-        x = subprocess.Popen(cl,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env)
-        retval1 = x.wait()
-        sto.close()
-        if retval1 == 0:
-            os.unlink(inpdf)
-            shutil.move(outpdf,inpdf)
-            os.unlink(hlog)
-        hlog = os.path.join(self.opts.output_dir,"thumbnail_%s.txt" % os.path.basename(inpdf))
-        sto = open(hlog,'w')
-        outpng = '%s.%s' % (os.path.splitext(inpdf)[0],thumbformat)
-        if self.useGM:        
-            cl2 = ['gm', 'convert', inpdf, outpng]
-        else: # assume imagemagick
-            cl2 = ['convert', inpdf, outpng]
-        x = subprocess.Popen(cl2,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env)
-        retval2 = x.wait()
-        sto.close()
-        if retval2 == 0:
-             os.unlink(hlog)
-        retval = retval1 or retval2
-        return retval
-
-
-    def getfSize(self,fpath,outpath):
-        """
-        format a nice file size string
-        """
-        size = ''
-        fp = os.path.join(outpath,fpath)
-        if os.path.isfile(fp):
-            size = '0 B'
-            n = float(os.path.getsize(fp))
-            if n > 2**20:
-                size = '%1.1f MB' % (n/2**20)
-            elif n > 2**10:
-                size = '%1.1f KB' % (n/2**10)
-            elif n > 0:
-                size = '%d B' % (int(n))
-        return size
-
-    def makeHtml(self):
-        """ Create an HTML file content to list all the artifacts found in the output_dir
-        """
-
-        galhtmlprefix = """<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> 
-        <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> 
-        <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> 
-        <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" /> 
-        <title></title> 
-        <link rel="stylesheet" href="/static/style/base.css" type="text/css" /> 
-        </head> 
-        <body> 
-        <div class="toolFormBody"> 
-        """ 
-        galhtmlattr = """<hr/><div class="infomessage">This tool (%s) was generated by the <a href="https://bitbucket.org/fubar/galaxytoolfactory/overview">Galaxy Tool Factory</a></div><br/>""" 
-        galhtmlpostfix = """</div></body></html>\n"""
-
-        flist = os.listdir(self.opts.output_dir)
-        flist = [x for x in flist if x != 'Rplots.pdf']
-        flist.sort()
-        html = []
-        html.append(galhtmlprefix % progname)
-        html.append('<div class="infomessage">Galaxy Tool "%s" run at %s</div><br/>' % (self.toolname,timenow()))
-        fhtml = []
-        if len(flist) > 0:
-            logfiles = [x for x in flist if x.lower().endswith('.log')] # log file names determine sections
-            logfiles.sort()
-            logfiles = [x for x in logfiles if os.path.abspath(x) != os.path.abspath(self.tlog)]
-            logfiles.append(os.path.abspath(self.tlog)) # make it the last one
-            pdflist = []
-            npdf = len([x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf'])
-            for rownum,fname in enumerate(flist):
-                dname,e = os.path.splitext(fname)
-                sfsize = self.getfSize(fname,self.opts.output_dir)
-                if e.lower() == '.pdf' : # compress and make a thumbnail
-                    thumb = '%s.%s' % (dname,self.thumbformat)
-                    pdff = os.path.join(self.opts.output_dir,fname)
-                    retval = self.compressPDF(inpdf=pdff,thumbformat=self.thumbformat)
-                    if retval == 0:
-                        pdflist.append((fname,thumb))
-                    else:
-                        pdflist.append((fname,fname))
-                if (rownum+1) % 2 == 0:
-                    fhtml.append('<tr class="odd_row"><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))
-                else:
-                    fhtml.append('<tr><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))
-            for logfname in logfiles: # expect at least tlog - if more
-                if os.path.abspath(logfname) == os.path.abspath(self.tlog): # handled later
-                    sectionname = 'All tool run'
-                    if (len(logfiles) > 1):
-                        sectionname = 'Other'
-                    ourpdfs = pdflist
-                else:
-                    realname = os.path.basename(logfname)
-                    sectionname = os.path.splitext(realname)[0].split('_')[0] # break in case _ added to log
-                    ourpdfs = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] == sectionname]
-                    pdflist = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] != sectionname] # remove
-                nacross = 1
-                npdf = len(ourpdfs)
-
-                if npdf > 0:
-                    nacross = math.sqrt(npdf) ## int(round(math.log(npdf,2)))
-                    if int(nacross)**2 != npdf:
-                        nacross += 1
-                    nacross = int(nacross)
-                    width = min(400,int(1200/nacross))
-                    html.append('<div class="toolFormTitle">%s images and outputs</div>' % sectionname)
-                    html.append('(Click on a thumbnail image to download the corresponding original PDF image)<br/>')
-                    ntogo = nacross # counter for table row padding with empty cells
-                    html.append('<div><table class="simple" cellpadding="2" cellspacing="2">\n<tr>')
-                    for i,paths in enumerate(ourpdfs): 
-                        fname,thumb = paths
-                        s= """<td><a href="%s"><img src="%s" title="Click to download a PDF of %s" hspace="5" width="%d" 
-                           alt="Image called %s"/></a></td>\n""" % (fname,thumb,fname,width,fname)
-                        if ((i+1) % nacross == 0):
-                            s += '</tr>\n'
-                            ntogo = 0
-                            if i < (npdf - 1): # more to come
-                               s += '<tr>'
-                               ntogo = nacross
-                        else:
-                            ntogo -= 1
-                        html.append(s)
-                    if html[-1].strip().endswith('</tr>'):
-                        html.append('</table></div>\n')
-                    else:
-                        if ntogo > 0: # pad
-                           html.append('<td>&nbsp;</td>'*ntogo)
-                        html.append('</tr></table></div>\n')
-                logt = open(logfname,'r').readlines()
-                logtext = [x for x in logt if x.strip() > '']
-                html.append('<div class="toolFormTitle">%s log output</div>' % sectionname)
-                if len(logtext) > 1:
-                    html.append('\n<pre>\n')
-                    html += logtext
-                    html.append('\n</pre>\n')
-                else:
-                    html.append('%s is empty<br/>' % logfname)
-        if len(fhtml) > 0:
-           fhtml.insert(0,'<div><table class="colored" cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr>\n')
-           fhtml.append('</table></div><br/>')
-           html.append('<div class="toolFormTitle">All output files available for downloading</div>\n')
-           html += fhtml # add all non-pdf files to the end of the display
-        else:
-            html.append('<div class="warningmessagelarge">### Error - %s returned no files - please confirm that parameters are sane</div>' % self.opts.interpreter)
-        html.append(galhtmlpostfix)
-        htmlf = file(self.opts.output_html,'w')
-        htmlf.write('\n'.join(html))
-        htmlf.write('\n')
-        htmlf.close()
-        self.html = html
-
-

--- a/toolfactory/testtf.sh	Sun Aug 16 08:51:14 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-planemo test --no_cleanup --no_dependency_resolution --skip_venv --galaxy_root ~/galaxy ~/galaxy/tools/tool_makers/toolfactory &>foo
-