changeset 1:0d0cbb69a03f draft

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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/COPYING	Fri Sep 26 15:10:34 2014 -0400
@@ -0,0 +1,121 @@
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--- a/LICENSE	Thu Jun 20 11:07:47 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,11 +0,0 @@
---2012-09-19 08:46:18--  http://www.apache.org/licenses/LICENSE-2.0.txt
-Resolving www.apache.org... 140.211.11.131, 192.87.106.229, 2001:610:1:80bc:192:87:106:229
-Connecting to www.apache.org|140.211.11.131|:80... connected.
-HTTP request sent, awaiting response... 200 OK
-Length: 11358 (11K) [text/plain]
-Saving to: “LICENSE-2.0.txt”
-
-     0K .......... .                                          100%  200K=0.06s
-
-2012-09-19 08:46:18 (200 KB/s) - “LICENSE-2.0.txt” saved [11358/11358]
-

--- a/README.md	Thu Jun 20 11:07:47 2013 -0400
+++ b/README.md	Fri Sep 26 15:10:34 2014 -0400
@@ -1,23 +1,52 @@
-Tool wrapper for the commercial proteomics application Scaffold.
-# Obtaining Tools
+GalaxyP - Scaffold
+==================
+
+* Home: <https://bitbucket.org/galaxyp/scaffold>
+* Galaxy Tool Shed: <http://toolshed.g2.bx.psu.edu/view/galaxyp/scaffold>
+* Tool ID: `scaffold`
+* Tool Type: `default`
+
+
+Description
+-----------
 
-Repositories for all Galaxy-P tools can be found at
-https:/bitbucket.org/galaxyp/.
+Export data out of Scaffold's binary data format (sf3) into tabular reports or XML.
+
+See:
+
+* <http://www.proteomesoftware.com/products/scaffold/>
+
 
-# Contact
+GalaxyP Community
+-----------------
 
-Please send suggestions for improvements and bug reports to
[e-mail].
+Current governing community policies for [GalaxyP](https://bitbucket.org/galaxyp/) and other information can be found at:
+
+<https://bitbucket.org/galaxyp/galaxyp>
 
-# License
+
+License
+-------
+
+Copyright (c) 2014 Regents of the University of Minnesota and Authors listed below.
 
-All Galaxy-P tools are licensed under the Apache License Version 2.0
-unless otherwise documented.
+To the extent possible under law, the author(s) have dedicated all copyright and related and neighboring rights to this software to the public domain worldwide. This software is distributed without any warranty.
+
+You should have received a copy of the CC0 Public Domain Dedication along with this software. If not, see <https://creativecommons.org/publicdomain/zero/1.0/>.
+
+You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission.
+
 
-# Tool Versioning
+Contributing
+------------
+
+Contributions to this repository are reviewed through pull requests. If you would like your work acknowledged, please also add yourself to the Authors section. If your pull request is accepted, you will also be acknowledged in <https://bitbucket.org/galaxyp/galaxyp/CONTRIBUTORS.md> unless you opt-out.
+
 
-Galaxy-P tools will have versions of the form X.Y.Z. Versions
-differing only after the second decimal should be completely
-compatible with each other. Breaking changes should result in an
-increment of the number before and/or after the first decimal. All
-tools of version less than 1.0.0 should be considered beta.
+Authors
+-------
+
+Authors and contributors:
+
+* John Chilton <[e-mail]>
+* Minnesota Supercomputing Institute, Univeristy of Minnesota

--- a/README_GALAXYP.md	Thu Jun 20 11:07:47 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,22 +0,0 @@
-# Obtaining Tools
-
-Repositories for all Galaxy-P tools can be found at
-https:/bitbucket.org/galaxyp/.
-
-# Contact
-
-Please send suggestions for improvements and bug reports to
[e-mail].
-
-# License
-
-All Galaxy-P tools are licensed under the Apache License Version 2.0
-unless otherwise documented.
-
-# Tool Versioning
-
-Galaxy-P tools will have versions of the form X.Y.Z. Versions
-differing only after the second decimal should be completely
-compatible with each other. Breaking changes should result in an
-increment of the number before and/or after the first decimal. All
-tools of version less than 1.0.0 should be considered beta.

--- a/README_REPO.md	Thu Jun 20 11:07:47 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-Tool wrapper for the commercial proteomics application Scaffold.

--- a/macros.xml	Thu Jun 20 11:07:47 2013 -0400
+++ b/macros.xml	Fri Sep 26 15:10:34 2014 -0400
@@ -27,4 +27,4 @@
     <param name="minimum_peptide_count" label="Minimum Peptide Count" type="integer" help="" value="2" />
     <param name="peptide_probability" label="Peptide Probability" type="float" help="" value="0.95" />
   </macro>
-</macros>
\ No newline at end of file
+</macros>

--- a/scaffold.xml	Thu Jun 20 11:07:47 2013 -0400
+++ b/scaffold.xml	Fri Sep 26 15:10:34 2014 -0400
@@ -7,10 +7,10 @@
 #if $sample_mode.mode == "full"
 #set $samples = $sample_mode.samples
 #for $sample in $samples:
-#if $sample.category.specify 
+#if $sample.category.specify
 #set $category = $sample.category.name
 #else
-#set $category = $sample.sample_name 
+#set $category = $sample.sample_name
 #end if
 sample:$sample.sample_name
 mudpit:$sample.mudpit
@@ -47,7 +47,7 @@
     #end if
     #if $advanced.specify
     #if $advanced.output_driver
-    --output_driver $output_drirver \
+    --output_driver $output_driver \
     #end if
     #end if
   </command>
@@ -87,7 +87,7 @@
               <param name="name" type="text" label="Category Name" help="" />
             </when>
           </conditional>
-        </repeat>        
+        </repeat>
       </when>
       <when value="sample_per_file">
         <param format="t.xml,omx" name="sample_inputs" type="data" multiple="true" label="Input Files" />
@@ -114,7 +114,7 @@
     </conditional>
   </inputs>
   <outputs>
-    <data format="xml" name="output_drirver" label="Scaffold Driver for ${on_string}">
+    <data format="xml" name="output_driver" label="Scaffold Driver for ${on_string}">
       <filter>(advanced['specify'] and advanced["output_driver"])</filter>
     </data>
     <data format="sf3" name="output" />
@@ -134,6 +134,6 @@
 
 For the underlying tool, please cite `TODO`
 
-If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-scaffold
+If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/scaffold
   </help>
-</tool>
\ No newline at end of file
+</tool>

--- a/scaffold_export.xml	Thu Jun 20 11:07:47 2013 -0400
+++ b/scaffold_export.xml	Fri Sep 26 15:10:34 2014 -0400
@@ -70,6 +70,6 @@
 
 For the underlying tool, please cite `TODO`
 
-If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-scaffold
+If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/scaffold
   </help>
-</tool>
\ No newline at end of file
+</tool>

--- a/scaffold_wrapper.py	Thu Jun 20 11:07:47 2013 -0400
+++ b/scaffold_wrapper.py	Fri Sep 26 15:10:34 2014 -0400
@@ -47,8 +47,8 @@
                 if returncode != 0:
                     raise Exception("Program returned with non-zero exit code %d. stderr: %s" % (returncode, read_stderr()))
     finally:
-        print open(tmp_stderr_name, "r").read(64000)
-        print open(tmp_stdout_name, "r").read(64000)
+        print((open(tmp_stderr_name, "r").read(64000)))
+        print((open(tmp_stdout_name, "r").read(64000)))
 
 
 def delete_file(path):
@@ -152,7 +152,7 @@
 def build_samples(samples_file):
     group_data = parse_groups(samples_file, group_parts=["sample", "mudpit", "category"], input_parts=["name", "path", "ext"])
     samples_description = ""
-    for sample_name, sample_data in group_data.iteritems():
+    for sample_name, sample_data in list(group_data.items()):
         files = sample_data["inputs"]
         mudpit = sample_data["group_data"]["mudpit"]
         category = sample_data["group_data"]["category"]
@@ -307,7 +307,7 @@
 
     # Prepare and create driver file
     driver_contents = Template(template).substitute(template_parameters)
-    print driver_contents
+    print(driver_contents)
     driver_path = os.path.abspath("driver.xml")
     open(driver_path, "w").write(driver_contents)
 

--- a/update.sh	Thu Jun 20 11:07:47 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,35 +0,0 @@
-#!/bin/bash
-
-LICENSE_FILE=LICENSE
-# Ensure repository contains license file.
-if [ ! -e "$LICENSE_FILE" ];
-then
-    wget http://www.apache.org/licenses/LICENSE-2.0.txt -O "$LICENSE_FILE"
-fi
-
-# Run repository specific update actions.
-if [ -f update_repo.sh ];
-then
-    ./update_repo.sh
-fi
-
-wget https://raw.github.com/gist/3749747/README_GALAXYP.md -O README_GALAXYP.md
-
-# Create repository README
-if [ ! -e README_REPO.md ];
-then
-    echo "TODO: Document this tool repository." > README_REPO.md
-fi
-cat README_REPO.md README_GALAXYP.md > README.md
-
-
-# If version file exists, update all tools to this version
-VERSION_FILE=version
-if [ -e "$VERSION_FILE" ];
-then
-    VERSION=`cat $VERSION_FILE`
-    
-    # Replace tool version in each tool XML file   `
-    find -iname "*xml" -exec sed -i'' -e '0,/version="\(.\+\)"/s/version="\(.\+\)"/version="'$VERSION'"/1g' {} \;
-
-fi