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changeset 5:dc25a5169a91 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/weblogo3 commit d0f167e74e705788adcd9c846db011aee490074b
author iuc
date Fri, 17 Nov 2017 10:19:39 -0500
parents c1a9e644d580
children
files rgWebLogo3.py rgWebLogo3.xml tool_dependencies.xml
diffstat 3 files changed, 165 insertions(+), 187 deletions(-) [+]
line wrap: on
line diff
--- a/rgWebLogo3.py	Thu Dec 03 15:55:38 2015 -0500
+++ b/rgWebLogo3.py	Fri Nov 17 10:19:39 2017 -0500
@@ -1,12 +1,17 @@
-"""
 # 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
+from __future__ import print_function
 
-WEBLOGO = 'weblogo' # executable name for weblogo3 - confusing isn't it?
+import optparse
+import os
+import subprocess
+import sys
+import tempfile
+
+WEBLOGO = 'weblogo'  # executable name for weblogo3 - confusing isn't it?
+
 
 class WL3:
     """
@@ -15,13 +20,13 @@
     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'
+    def __init__(self, opts=None):
+        assert opts is not None, 'WL3 class needs opts passed in - got None'
         self.opts = opts
-        self.fastaf = file(self.opts.input,'r')
+        self.fastaf = open(self.opts.input, 'r')
         self.clparams = {}
 
-    def whereis(self,program):
+    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)
@@ -32,64 +37,62 @@
         """
         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'
+            print('## rgWebLogo3.py error - cannot locate the weblogo binary %s on the current path' % (WEBLOGO), file=sys.stderr)
+            print('## Please ensure it is installed and working from https://github.com/weblogo/weblogo', file=sys.stderr)
             sys.exit(1)
-        cll = [WEBLOGO,]
+        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')
+        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())
+        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)
+            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
+            s = '## executing %s returned status %d. Nothing appeared on stderr/stdout\n' % (cl, rval)
+        os.unlink(templog)  # always
+        if rval != 0:
+            print('## rgWebLogo3.py error - executing %s returned error code %d' % (cl, rval), file=sys.stderr)
+            print('## This may be a data problem or a tool dependency (%s) installation problem' % WEBLOGO, file=sys.stderr)
+            print('## Please ensure %s is correctly installed and working on the command line -see https://github.com/weblogo/weblogo' % WEBLOGO, file=sys.stderr)
             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):
+        for i, row in enumerate(self.fastaf):
             if row.startswith(self.FASTASTARTSYM):
-                if seqname <> None: # already in a sequence
+                if seqname is not None:  # already in a sequence
                     s = ''.join(aseq)
-                    l = len(s)
-                    yield (seqname,l)
+                    ls = len(s)
+                    yield (seqname, ls)
                     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)
+                        print('Invalid fasta file %s - does not start with %s - please read the tool documentation carefully' % (self.opts.input, self.FASTASTARTSYM), file=sys.stderr)
                         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) 
+                        seqname = row[1:].strip()
+            else:  # sequence row
+                if seqname is None:
+                    print('Invalid fasta file %s - does not start with %s - please read the tool documentation carefully' % (self.opts.input, self.FASTASTARTSYM), file=sys.stderr)
+                    sys.exit(1)
                 else:
                     aseq.append(row.strip())
-                
-        if seqname <> None: # last one
-            l = len(''.join(aseq))
-            yield (seqname,l)
-                
-        
+
+        if seqname is not None:  # last one
+            las = len(''.join(aseq))
+            yield (seqname, las)
+
     def fcheck(self):
         """ are all fasta sequence same length?
         might be mongo big
@@ -97,61 +100,50 @@
         flen = None
         lasti = None
         f = self.iter_fasta()
-        for i,(seqname,seqlen) in enumerate(f):
+        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
+                if seqlen != flen:
+                    print(self.badseq % self.opts.input, file=sys.stderr)
                     sys.exit(1)
-        return '# weblogo input %s has %d sequences all of length %d' % (self.opts.input, lasti+1, flen)
-
+        return '# weblogo input %s has %d sequences all of length %d' % (self.opts.input, lasti + 1, 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['-t'] = '"%s"' % self.opts.logoname  # must be wrapped as a string
+        self.clparams['-F'] = self.opts.outformat
+        if self.opts.size is not None:
             self.clparams['-s'] = self.opts.size
-        if self.opts.lower <> None:
+        if self.opts.lower is not None:
             self.clparams['-l'] = self.opts.lower
-        if self.opts.upper <> None:
-            self.clparams['-u'] = self.opts.upper        
-        if self.opts.colours <> None:
+        if self.opts.upper is not None:
+            self.clparams['-u'] = self.opts.upper
+        if self.opts.colours is not None:
             self.clparams['-c'] = self.opts.colours
-        if self.opts.units <> None:
+        if self.opts.units is not None:
             self.clparams['-U'] = self.opts.units
         s = self.runCL()
-        return check,s
+        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('-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)  
+    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
+    assert opts.input is not 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
+    checks, s = w.run()
+    print(checks, file=sys.stdout)  # for info
--- a/rgWebLogo3.xml	Thu Dec 03 15:55:38 2015 -0500
+++ b/rgWebLogo3.xml	Fri Nov 17 10:19:39 2017 -0500
@@ -1,106 +1,104 @@
-<tool id="rgweblogo3" name="Sequence Logo" version="0.4">
-   <description>generator for fasta (eg Clustal alignments)</description>
-   <requirements>
-      <requirement type="package" version="1.7.1">numpy</requirement>
-      <requirement type="package" version="3.3">weblogo</requirement>
-      <requirement type="package" version="9.10">ghostscript</requirement>
-   </requirements>
-   <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" 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="logodata">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>
+<tool id="rgweblogo3" name="Sequence Logo" version="3.5.0">
+    <description>generator for fasta (eg Clustal alignments)</description>
+    <requirements>
+        <requirement type="package" version="3.5.0">weblogo</requirement>
+    </requirements>
+    <command><![CDATA[
+        python '$__tool_directory__/rgWebLogo3.py'
+            -F $outformat
+            -s $size
+            -i '$input'
+            -o '$output'
+            -t '$logoname'
+            -c '$colours'
+            -U '$units'
 
-    
-    <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>
+        #if $range.mode == 'part'
+            -l '$range.seqstart' -u '$range.seqend'
+        #end if
+    ]]></command>
+    <inputs>
+        <param format="fasta" name="input" type="data" label="Fasta File" />
+        <param name="logoname" label="Title for output Sequence Logo" type="text" 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="logodata">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>
-        <when value="complete">
-        </when>
-        <when value="part">    
-           <param name="seqstart" 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" 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}_output.${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="logodata" 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>
 
+        <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 value="part">
+                <param name="seqstart" 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 name="seqend" type="integer" value="99999" label="Index (eg 75=75th letter) of the end of the sequence range to include in the logo" />
+            </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>
+    </inputs>
+    <outputs>
+        <data format="pdf" name="output"  label="${logoname}_output.${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="logodata" 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><![CDATA[
 **Note**
 
 This tool uses Weblogo3_ in Galaxy to generate a sequence logo. The input file must be a fasta file in your current history.
@@ -119,8 +117,8 @@
 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 
+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 the same length!
 
 ----
@@ -135,8 +133,8 @@
 
 .. _LGPL: http://www.gnu.org/copyleft/lesser.html
 
-  </help>
-
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1101/gr.849004</citation>
+    </citations>
 </tool>
-
-
--- a/tool_dependencies.xml	Thu Dec 03 15:55:38 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,12 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-  <package name="ghostscript" version="9.10">
-      <repository changeset_revision="a285e78179bd" name="package_ghostscript_9_10" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="numpy" version="1.7.1">
-        <repository changeset_revision="300877695495" name="package_numpy_1_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="weblogo" version="3.3">
-      <repository changeset_revision="648e4b32f15c" name="package_weblogo_3_3" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>