Mercurial > repos > fubar > weblogo3

--- a/weblogo3-91fa0a8ce39d/rgweblogo/README	Wed Dec 04 19:58:06 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,38 +0,0 @@
-This is a Galaxy tool wrapper for weblogo3 already available as a web app at the site below but neat as a Galaxy tool
-Last updated by Ross to install iuc ghostscript and numpy dependencies.
-
-Weblogo generates sequence logos from fasta files such as the alignments generated by clustalw
-
-Note that the image for the help must be in static/images for it to show up on the tool form - it's the same image as goes in test-data
-
-**Automated Installation**
-As a Galaxy admin, use the admin menu and select the search ToolShed option. This tool should be on the main toolshed - if not try the test toolshed.
-Select it and choose "preview and install" - the process of downloading and installing weblogo3.3 and this wrapper should take a few minutes at most.
-
-** Manual Installation**
-
-Don't.
-
-If you insist,
-Make sure weblogo3 is installed in your system python and is available on the path for all your nodes
-
-Move the test data files to your galaxy root test-data
-Move the xml file to a subdirectory of your tools folder (eg rgenetics/) and then add a line in your tool_conf.xml to point there.
-Run
-sh run_functional_tests.sh -id weblogo3
-to make sure the tests work
-
-then restart Galaxy and you should be good to go.
-
-
-**Attribution**
-
-Source for the weblogo3 python executable is at http://weblogo.berkeley.edu
-
-Galaxy tool wrapper written by Ross Lazarus for the Rgenetics project
-
-Copyright Ross Lazarus at gmail com 2011
-
-All rights reserved.
-
-Released under the LGPL - see http://www.gnu.org/copyleft/lesser.html
--- a/weblogo3-91fa0a8ce39d/rgweblogo/rgWebLogo3.py	Wed Dec 04 19:58:06 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,157 +0,0 @@
-"""
-# modified june 2 ross lazarus to add units option at Assaf Gordon's suggestion
-# rgWebLogo3.py
-# wrapper to check that all fasta files are same length
-
-"""
-import optparse, os, sys, subprocess, tempfile
-
-WEBLOGO = 'weblogo' # executable name for weblogo3 - confusing isn't it?
-
-class WL3:
-    """
-    simple wrapper class to check fasta sequence lengths are all identical
-    """
-    FASTASTARTSYM = '>'
-    badseq = '## error - sequences in file %s are not all the same length - cannot proceed. Please read the tool documentation carefully'
-
-    def __init__(self,opts=None):
-        assert opts<>None,'WL3 class needs opts passed in - got None'
-        self.opts = opts
-        self.fastaf = file(self.opts.input,'r')
-        self.clparams = {}
-
-    def whereis(self,program):
-        for path in os.environ.get('PATH', '').split(':'):
-            if os.path.exists(os.path.join(path, program)) and not os.path.isdir(os.path.join(path, program)):
-                return os.path.join(path, program)
-        return None
-
-    def runCL(self):
-        """ construct and run a command line
-        """
-        wl = self.whereis(WEBLOGO)
-        if not wl:
-             print >> sys.stderr, '## rgWebLogo3.py error - cannot locate the weblogo binary %s on the current path' % WEBLOGO
-             print >> sys.stderr, '## Please ensure it is installed and working from http://code.google.com/p/weblogo'
-             sys.exit(1)
-        cll = [WEBLOGO,]
-        cll += [' '.join(it) for it in list(self.clparams.items())]
-        cl = ' '.join(cll)
-        assert cl > '', 'runCL needs a command line as clparms'
-        fd,templog = tempfile.mkstemp(suffix='rgtempRun.txt')
-        tlf = open(templog,'w')
-        process = subprocess.Popen(cl, shell=True, stderr=tlf, stdout=tlf)
-        rval = process.wait()
-        tlf.close()
-        tlogs = ''.join(open(templog,'r').readlines())
-        if len(tlogs) > 1:
-            s = '## executing %s returned status %d and log (stdout/stderr) records: \n%s\n' % (cl,rval,tlogs)
-        else:
-            s = '## executing %s returned status %d. Nothing appeared on stderr/stdout\n' % (cl,rval)
-        os.unlink(templog) # always
-        if rval <> 0:
-             print >> sys.stderr, '## rgWebLogo3.py error - executing %s returned error code %d' % (cl,rval)
-             print >> sys.stderr, '## This may be a data problem or a tool dependency (%s) installation problem' % WEBLOGO
-             print >> sys.stderr, '## Please ensure %s is correctly installed and working on the command line -see http://code.google.com/p/weblogo' % WEBLOGO
-             sys.exit(1)
-        return s
-
-
-    def iter_fasta(self):
-        """
-        generator for fasta sequences from a file
-        """
-        aseq = []
-        seqname = None
-        for i,row in enumerate(self.fastaf):
-            if row.startswith(self.FASTASTARTSYM):
-                if seqname <> None: # already in a sequence
-                    s = ''.join(aseq)
-                    l = len(s)
-                    yield (seqname,l)
-                    seqname = row[1:].strip()
-                    aseq = []
-                else:
-                    if i > 0:
-                        print >> sys.stderr,'Invalid fasta file %s - does not start with %s - please read the tool documentation carefully' % (self.opts.input,self.FASTASTARTSYM)
-                        sys.exit(1)
-                    else:
-                        seqname = row[1:].strip()
-            else: # sequence row
-                if seqname == None:
-                    print >> sys.stderr,'Invalid fasta file %s - does not start with %s - please read the tool documentation carefully' % (self.opts.input,self.FASTASTARTSYM)
-                    sys.exit(1)
-                else:
-                    aseq.append(row.strip())
-
-        if seqname <> None: # last one
-            l = len(''.join(aseq))
-            yield (seqname,l)
-
-
-    def fcheck(self):
-        """ are all fasta sequence same length?
-        might be mongo big
-        """
-        flen = None
-        lasti = None
-        f = self.iter_fasta()
-        for i,(seqname,seqlen) in enumerate(f):
-            lasti = i
-            if i == 0:
-                flen = seqlen
-            else:
-                if seqlen <> flen:
-                    print >> sys.stderr,self.badseq % self.opts.input
-                    sys.exit(1)
-        return '# weblogo input %s has %d sequences all of length %d' % (self.opts.input,lasti,flen)
-
-
-    def run(self):
-        check = self.fcheck()
-        self.clparams['-f'] = self.opts.input
-        self.clparams['-o'] = self.opts.output
-        self.clparams['-t'] = '"%s"' % self.opts.logoname # must be wrapped as a string
-        self.clparams['-F'] = self.opts.outformat
-        if self.opts.size <> None:
-            self.clparams['-s'] = self.opts.size
-        if self.opts.lower <> None:
-            self.clparams['-l'] = self.opts.lower
-        if self.opts.upper <> None:
-            self.clparams['-u'] = self.opts.upper
-        if self.opts.colours <> None:
-            self.clparams['-c'] = self.opts.colours
-        if self.opts.units <> None:
-            self.clparams['-U'] = self.opts.units
-        s = self.runCL()
-        return check,s
-
-
-if __name__ == '__main__':
-    '''
-    called as
-<command interpreter="python">
-    rgWebLogo3.py --outformat $outformat -s $size -i $input -o $output -t "$logoname" -c "$colours"
-#if $range.mode == 'part'
--l "$range.seqstart" -u "$range.seqend"
-#end if
-    </command>
-
-    '''
-    op = optparse.OptionParser()
-    op.add_option('-i', '--input', default=None)
-    op.add_option('-F', '--outformat', default='png')
-    op.add_option('-s', '--size', default=None)
-    op.add_option('-o', '--output', default='rgWebLogo3')
-    op.add_option('-t', '--logoname', default='rgWebLogo3')
-    op.add_option('-c', '--colours', default=None)
-    op.add_option('-l', '--lower', default=None)
-    op.add_option('-u', '--upper', default=None)
-    op.add_option('-U', '--units', default=None)
-    opts, args = op.parse_args()
-    assert opts.input <> None,'weblogo3 needs a -i parameter with a fasta input file - cannot open'
-    assert os.path.isfile(opts.input),'weblogo3 needs a valid fasta input file - cannot open %s' % opts.input
-    w = WL3(opts)
-    checks,s = w.run()
-    print >> sys.stdout, checks # for info
--- a/weblogo3-91fa0a8ce39d/rgweblogo/rgWebLogo3.xml	Wed Dec 04 19:58:06 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,145 +0,0 @@
-<tool id="rgweblogo3" name="Sequence Logo" version="0.5">
-  <stdio>
-   <regex match=".*" source="both" level="warning" description="chatter from weblogo:"/>
-  </stdio>
-  <requirements>
-      <requirement type="package" version="3.3">package_weblogo</requirement>
-      <requirement type="package" version="1.7.1">numpy</requirement>
-      <requirement type="package" version="9.07">ghostscript</requirement>
-   </requirements>
-   <description>Generator from fasta</description>
-   <command interpreter="python">
-    rgWebLogo3.py -F $outformat -s $size -i $input -o $output -t "$logoname" -c "$colours" -U "$units"
-#if $range.mode == 'part'
--l "$range.seqstart" -u "$range.seqend"
-#end if
-    </command>
-  <inputs>
-   <page>
-    <param format="fasta" name="input" type="data" label="Fasta File" />
-    <param name="logoname" label="Title for output Sequence Logo" type="text" size="50" value="Galaxy-Rgenetics Sequence Logo" />
-    <param name="outformat" type="select" label="Output format for image (or text report)" >
-      <option value="png" selected="True">PNG screen quality</option>
-      <option value="png_print">High quality printable PNG</option>
-      <option value="pdf">PDF</option>
-      <option value="jpeg">JPG</option>
-      <option value="eps">EPS</option>
-      <option value="txt">Text (shows the detailed calculations for each position - no image)</option>
-    </param>
-    <param name="units" type="select" label="Display Units"
-      help="What the height of each logo element depicts - eg bits of entropy (default)">
-      <option value="bits" selected="True">Entropy (bits)</option>
-      <option value="probability">Probability</option>
-      <option value="nats">Nats</option>
-      <option value="kT">kT</option>
-      <option value="kJ/mol">kJ/mol</option>
-      <option value="kcal/mol">kcal/mol</option>
-    </param>
-    <param name="colours" type="select" label="Colour scheme for output Sequence Logo"
-      help="Note that some of these only make sense for protein sequences!">
-      <option value="auto" selected="True">Default automatic colour selection</option>
-      <option value="base pairing">Base pairing</option>
-      <option value="charge">Charge colours</option>
-      <option value="chemistry">Chemistry colours</option>
-      <option value="classic">Classical colours</option>
-      <option value="hydrophobicity">Hydrophobicity</option>
-      <option value="monochrome">monochrome</option>
-    </param>
-
-
-    <conditional name="range">
-        <param name="mode" type="select" label="Include entire sequence (default) or specify a subsequence range to use">
-          <option value="complete" selected="true">complete sequence</option>
-          <option value="part">Only use a part of the sequence</option>
-        </param>
-        <when value="complete">
-        </when>
-        <when value="part">
-           <param name="seqstart" size="5" type="integer" value="1" help="WARNING: Specifying indexes outside the sequence lengths will cause unpredictable but bad consequences!"
-             label="Index (eg 1=first letter) of the start of the sequence range to include in the logo">
-           </param>
-           <param name="seqend" size="5" type="integer" value="99999" label="Index (eg 75=75th letter) of the end of the sequence range to include in the logo" >
-           </param>
-        </when>
-    </conditional>
-    <param name="size" type="select" label="Output weblogo size" >
-      <option value="large" selected="True">Large</option>
-      <option value="medium">Medium</option>
-      <option value="small">Small</option>
-    </param>
-   </page>
-  </inputs>
-  <outputs>
-    <data format="pdf" name="output"  label="${logoname}.${outformat}">
-       <change_format>
-           <when input="outformat" value="png_print" format="png" />
-           <when input="outformat" value="png" format="png" />
-           <when input="outformat" value="jpeg" format="jpg" />
-           <when input="outformat" value="eps" format="eps" />
-           <when input="outformat" value="txt" format="txt" />
-       </change_format>
-    </data>
-  </outputs>
-  <tests>
-    <test>
-      <param name="input" value="rgClustal_testout.fasta" />
-      <param name = "logoname" value="Galaxy/Rgenetics weblogo" />
-      <param name = "outformat" value="jpeg" />
-      <param name = "mode" value="complete" />
-      <param name = "size" value="medium" />
-      <param name = "colours" value="auto" />
-      <param name = "units" value="bits" />
-      <output name="output" file="rgWebLogo3_test.jpg" ftype="jpg" compare="sim_size" delta="10000" />
-    </test>
-    <test>
-      <param name="input" value="rgClustal_testout.fasta" />
-      <param name = "logoname" value="Galaxy/Rgenetics weblogo" />
-      <param name = "outformat" value="png" />
-      <param name = "mode" value="complete" />
-      <param name = "size" value="medium" />
-      <param name = "colours" value="auto" />
-      <param name = "units" value="probability" />
-      <output name="output" file="rgWebLogo3_test2.png" ftype="png" compare="sim_size" delta="10000" />
-    </test>
-  </tests>
-  <help>
-
-**Note**
-
-This tool uses Weblogo3_ in Galaxy to generate a sequence logo. The input file must be a fasta file in your current history.
-
-It is recommended for (eg) viewing multiple sequence alignments output from the clustalw tool - set the output to fasta and feed
-it in to this tool.
-
-A typical output looks like this
-
-.. image:: $PATH_TO_IMAGES/rgWebLogo3_test.jpg
-
-----
-
-**Warning about input Fasta format files**
-
-The Weblogo3 program used by this tool will fail if your fasta sequences are not all EXACTLY the same length. The tool will provide a warning
-and refuse to call the weblogo3 executable if irregular length sequences are detected.
-
-Fasta alignments from the companion ClustalW Galaxy tool will work but many other fasta files may cause this tool to fail - please do not file
-a Galaxy bug report - this is a feature of the tool and a problem with your source data - not a tool error - please make certain all your fasta
-sequences are exactly the same length!
-
-
-**Attribution**
-
-Weblogo attribution and associated documentation are available at Weblogo3_
-
-This Galaxy wrapper calls their software so depends on it and their license for your legal comfort.
-The wrapper was written by Ross Lazarus for the rgenetics project and the source code is licensed under the LGPL_ like other rgenetics artefacts
-
-.. _Weblogo3: http://weblogo.threeplusone.com/manual.html
-
-.. _LGPL: http://www.gnu.org/copyleft/lesser.html
-
-  </help>
-
-</tool>
-
-
--- a/weblogo3-91fa0a8ce39d/rgweblogo/test-data/rgClustal_testout.fasta	Wed Dec 04 19:58:06 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,48 +0,0 @@
->c_briggsae-chrII_+_
----ATGAGCTTCCACAAAAGCATGAGCTTT
-CTCAGCTTCTGCCACATCAGCATTCAAATG
-ATC
->c_brenneri-Cbre_Contig60_+_
----ATGAGCCTCCACAACAGCATGATTTTT
-CTCGGCTTCCGCCACATCCGCATTCAAATG
-ATC
->c_remanei-Crem_Contig172_-_
----ATGAGCCTCTACAACCGCATGATTCTT
-TTCAGCCTCTGCCACGTCCGCATTCAAATG
-CTC
->c_elegans-II_+_
----ATGAGCCTCTACTACAGCATGATTCTT
-CTCAGCTTCTGCAACGTCAGCATTCAGATG
-ATC
->c_briggsae-chrII_+_bar
----CCGGAGTCGATCCCTGAAT--------
-------------------------------
----
->c_brenneri-Cbre_Contig60fee_+_
----ACGAAGTCGATCCCTGAAA--------
--TCAGATGAGCGGTTGACCA---GAGAACA
-ACC
->c_remanei-Crem_Contig172zot_-_
----ACGAAGTCGGTCCCTATAAGGTATGAT
-TTTATATGA----TGTACCATAAGGAAATA
-GTC
->c_elegans-II_+_meh
----ACGAAGTCGGTCCCTGAAC--AATTAT
-TT----TGA----TATA---GAAAGAAACG
-GTA
->c_briggsae-chrIfooI_+_
-CGCACAAATATGATGCACAAATCCACAACC
-TAAAGCATCTCCGATAACGTTGACCGAAGT
----
->c_brenneri-Cbre_Contig60gak_+_
-CGCACAAATGTAGTGGACAAATCCGCATCC
-CAAAGCGTCTCCGATAACATTTACCGAAGT
----
->c_remanei-Crem_Contig172foo_-_
-AGCACAAATGTAATGAACGAATCCGCATCC
-CAACGCATCGCCAATCACATTCACAGATGT
----
->c_elegans-II_+_more
-TGCACAAATGTGATGAACGAATCCACATCC
-CAATGCATCACCGATCACATTGACAGATGT
----
Binary file weblogo3-91fa0a8ce39d/rgweblogo/test-data/rgWebLogo3_test.jpg has changed
Binary file weblogo3-91fa0a8ce39d/rgweblogo/test-data/rgWebLogo3_test2.png has changed
--- a/weblogo3-91fa0a8ce39d/rgweblogo/tool_dependencies.xml	Wed Dec 04 19:58:06 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,43 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="numpy" version="1.7.1">
-        <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="ghostscript" version="9.07">
-        <repository changeset_revision="c842299349c0" name="package_ghostscript_9_07" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
-    </package>
-
-    <package name="package_weblogo" version="3.3">
-        <install version="1.0">
-            <actions>
-                <!-- populate the environment variables from the dependend repos -->
-                <action type="download_by_url">http://weblogo.googlecode.com/files/weblogo-3.3.tar.gz</action>
-                <action type="shell_command">echo `ls -lt` &amp;&amp; echo `pwd`</action>
-
-                <action type="set_environment_for_install">
-                    <repository changeset_revision="c842299349c0" name="package_ghostscript_9_07" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu/">
-                        <package name="ghostscript" version="9.07" />
-                    </repository>
-                    <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu/">
-                        <package name="numpy" version="1.7.1" />
-                    </repository>
-                </action>
-                <!-- install weblogo -->
-                <action type="make_directory">$INSTALL_DIR/lib/python</action>
-                <action type="shell_command">export PYTHONPATH=$INSTALL_DIR/lib/python:$PYTHONPATH_NUMPY:$PYTHONPATH &amp;&amp;
-                    python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
-                <action type="set_environment">
-                    <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
-                    <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
-                    <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                    <environment_variable action="set_to" name="WEBLOGO_PATH">$INSTALL_DIR/bin/weblogo</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-            weblogo3 is a python version of the old weblogo2.8 or so. Requires numpy and ghostscript so these are installed if not already on your system - if that happens, please be patient
-            while numpy compiles - especially if the ATLAS libraries are being installed - which is not at present.
-        </readme>
-     </package>
-</tool_dependency>