| Previous changeset 6:1f484bf888ca (2014-02-07) Next changeset 8:58469754fd82 (2014-06-05) |
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Commit message:
Uploaded |
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modified:
proteomics.py |
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added:
README display_applications/proteomics/ProtGff.xml tool-data/proteogenomics_display_site.txt.sample |
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| diff -r 1f484bf888ca -r b82d4034e0f8 README --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Tue Feb 11 17:51:48 2014 -0500 |
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| @@ -0,0 +1,9 @@ +## What is it? +Galaxy datatype and display-application definitions for Proteomics data + +## Installation +Install into your local galaxy instance from the main galaxy toolshed at http://toolshed.g2.bx.psu.edu/ + +To visualize data you will need to install the protviz visualization web application. This is available at +[https://bitbucket.org/Andrew_Brock/proteomics-visualise](https://bitbucket.org/Andrew_Brock/proteomics-visualise) + |
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| diff -r 1f484bf888ca -r b82d4034e0f8 display_applications/proteomics/ProtGff.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/display_applications/proteomics/ProtGff.xml Tue Feb 11 17:51:48 2014 -0500 |
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| @@ -0,0 +1,18 @@ +<display id="proteomics_gff" version="1.0.0" name="view gff in"> + <dynamic_links from_file="tool-data/proteogenomics_display_site.txt" skip_startswith="#" id="0" name="0"> + <!-- Define parameters by column from file --> + <dynamic_param name="site_id" value="0"/> + <dynamic_param name="site_url" value="1"/> + <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name --> + <url target_frame="galaxy_main">${site_url}/init_local?file=${encoded_filename.qp}&type=protgff</url> + <param type="data" name="prot_file" viewable="False" format="protgff"/> + <param type="data" dataset="prot_file" name="protgff_file" format="protgff" viewable="False" /> + <param type="template" name="encoded_filename" strip="True" > + #import binascii + ${binascii.hexlify( $protgff_file.file_name )} + </param> + <param type="template" name="galaxy_url" strip="True" > + ${BASE_URL.split(":")[1][2:]} + </param> + </dynamic_links> +</display> \ No newline at end of file |
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| diff -r 1f484bf888ca -r b82d4034e0f8 proteomics.py --- a/proteomics.py Fri Feb 07 09:21:34 2014 -0500 +++ b/proteomics.py Tue Feb 11 17:51:48 2014 -0500 |
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| @@ -6,6 +6,7 @@ import binascii from galaxy.datatypes.sniff import * +from galaxy.datatypes import data from galaxy.datatypes.data import Text from galaxy.datatypes.xml import GenericXml from galaxy.datatypes.binary import Binary |
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| diff -r 1f484bf888ca -r b82d4034e0f8 tool-data/proteogenomics_display_site.txt.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/proteogenomics_display_site.txt.sample Tue Feb 11 17:51:48 2014 -0500 |
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| @@ -0,0 +1,3 @@ +#Proteomic Visualization application should be hosted on the same server as galaxy +#Entries in this file are of the format "site_id" site_url +Proteogenomics Browser http://127.0.0.1:8600 |