| Previous changeset 0:8ea9b4e5a389 (2011-06-22) |
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Commit message:
added fixes from Brad Langhorst; https://bitbucket.org/account/notifications/read/3443176/patch-for-proportional-venn-tool-in-galaxy; added tool_dependencies for Mako template untested |
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modified:
README.md prop_venn.xml venner.py |
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added:
tool_dependencies.xml |
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| diff -r 8ea9b4e5a389 -r cc6707a1e044 README.md --- a/README.md Wed Jun 22 03:28:25 2011 -0400 +++ b/README.md Mon Sep 24 16:46:21 2012 +0200 |
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| @@ -11,7 +11,8 @@ contains an integration test for the cli interface (vennerTest.py), no galaxy unit tests. - +CLI example: +python venner.py --files testFiles/fileA.tab,testFiles/fileB.tab --columns 1,1 --outname out.html --asNames As,Bs Proportional Venn Diagram: -------------------------- @@ -26,6 +27,6 @@ Outputs: -------- -- Html page with the proportional Venn diagram and a table for the counts in each section. +- Html page with the proportional Venn diagram and a table for the counts in each set. |
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| diff -r 8ea9b4e5a389 -r cc6707a1e044 prop_venn.xml --- a/prop_venn.xml Wed Jun 22 03:28:25 2011 -0400 +++ b/prop_venn.xml Mon Sep 24 16:46:21 2012 +0200 |
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| @@ -1,14 +1,14 @@ -<tool id="prop_venn" name="proportional venn" version="0.4"> +<tool id="prop_venn" name="proportional venn" version="0.5"> <description> from 2-3 sets</description> <command interpreter="python">venner.py #if str( $twoThree['tt']) == 'three': --files $inputFile1,$inputFile2,$twoThree.inputFile3 --columns $column1,$column2,$twoThree.column3 - --asNames $asName1,$asName2,$twoThree.asName3 + --asNames "$asName1","$asName2","$twoThree.asName3" #else: --file $inputFile1,$inputFile2 --columns $column1,$column2 - --asNames $asName1,$asName2 + --asNames "$asName1","$asName2" #end if --title '$title' --size $size @@ -16,7 +16,6 @@ </command> <inputs> <param name="title" label="title" type="text" help="title of plot" optional="true" value=""/> - <param name="name" label="name" type="text" help="name of output file" value="venn of NA"/> <param name="size" label="size" type="integer" help="size of plot ( < 540)" optional="true" value="300"/> <param format="tabular" name="inputFile1" label="input file 1" type="data" help="tabular input file" optional="false"/> @@ -43,7 +42,7 @@ </inputs> <outputs> - <data name="outPath" format="html" label="${name}"/> + <data name="outPath" format="html" label="${title}"/> </outputs> <help> |
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| diff -r 8ea9b4e5a389 -r cc6707a1e044 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Sep 24 16:46:21 2012 +0200 |
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| @@ -0,0 +1,19 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="Mako" version="0.7.2"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://pypi.python.org/packages/source/M/Mako/Mako-0.7.2.tar.gz</action> + <action type="make_directory">$INSTALL_DIR/lib/python</action> + <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action> + <action type="set_environment"> + <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme> + prop_venn uses a templating engine called mako + </readme> + </package> +</tool_dependency> |
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| diff -r 8ea9b4e5a389 -r cc6707a1e044 venner.py --- a/venner.py Wed Jun 22 03:28:25 2011 -0400 +++ b/venner.py Mon Sep 24 16:46:21 2012 +0200 |
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| @@ -27,6 +27,7 @@ cleanname = re.sub("/","",name) self.name = urllib.quote(cleanname, safe="%/:=&?~#+!$,;'@()*[]") self.dict = {} + def read(self): dict = {} lineNr = 0 @@ -88,13 +89,12 @@ <title>Venn diagram ${title}</title> </head> <body> - <h3>${ title }</h3> <div> <img src="${ url }"/> </div> <div> <table> - <tr><th>Segment</th><th>Count</th></tr> + <tr><th>Set</th><th>Count</th></tr> <tr><td>${ one }</td><td>${ n.one_keys }</td></tr> <tr><td>${ two }</td><td>${ n.two_keys }</td></tr> <tr><td>${ one } \ ${ two }</td><td>${ n.one_only }</td></tr> @@ -104,7 +104,7 @@ </div> </body> </html>""" - result = Template(template).render(one=self.one.name, two=self.two.name, n=numbers, title=self.title, url=self.toUrl()) + result = Template(template).render(one=urllib.unquote(self.one.name), two=urllib.unquote(self.two.name), n=numbers, title=self.title, url=self.toUrl()) return(result) @@ -158,13 +158,12 @@ <title>Venn diagram ${title}</title> </head> <body> - <h3>${ title }</h3> <div> <img src="${ url }"/> </div> <div> <table> - <tr><th>Segment</th><th>Count</th></tr> + <tr><th>Set</th><th>Count</th></tr> <tr><td>${ one }</td><td>${ n.one_keys }</td></tr> <tr><td>${ two }</td><td>${ n.two_keys }</td></tr> <tr><td>${ three }</td><td>${ n.three_keys }</td></tr> @@ -179,7 +178,7 @@ </div> </body> </html>""" - result = Template(template).render(one=self.one.name, two=self.two.name, three=self.three.name, n=numbers, title=self.title, url=self.toUrl()) + result = Template(template).render(one=urllib.unquote(self.one.name), two=urllib.unquote(self.two.name), three=urllib.unquote(self.three.name), n=numbers, title=self.title, url=self.toUrl()) return(result) |