Merge branch 'topic/image_upload'
[sgn.git] / mason / secretom / secretary.mas
blobe21f0cc93a2ed8e4ce852d3d47bbe0573f287fba
1 <& /page/page_title.mas, title => '<span class="secretary">SecreTary</span>: Computational prediction of secreted proteins' &>
3 <& /secretom/secretary/nav.mas, curr_page => 'tool' &>
5 <&| /page/info_section.mas, title => 'Submit Sequences' &>
6   <form id="secretary_input" method="post" action="/secretom/secretary/run" name="secretary" enctype="multipart/form-data">
7     <div class="examples">
8       <input type="submit" onclick="set_secretary_example_inputs(); return false;" value="Show Input Example" />
9       <input class="reset" type="reset" name="reset" value="Clear form" />
10     </div>
12     <label for="sequence_input_text">Paste one or more protein sequences in FASTA format</label>
13     <textarea id="sequence_input_text" name="sequence" rows="10" cols="100"></textarea>
15     <table><tr>
16       <td>
17        <label for="sequence_input_file">And/or upload a FASTA file of protein sequences</label><br />
18        <input style="margin: 0.8em 1em"   id="sequence_input_file" type="file" name="sequence_file" />
19       </td>
21       <td>
22        <input type="checkbox" value="Sort by score" name="sort" id="sort_by_score">
23          <label for="sort_by_score">Sort by score</label>
24        <br />
25        <input type="checkbox" value="show_only_sp" name="show_only_sp" id="show_only_sp">
26          <label for="show_only_sp">Show predicted signal peptides only</label>
27       </td>
29       <td>
30        <input class="submit" type="submit" name="submit" onclick="return validate_form()" value="Submit" />
31       </td>
33     </tr></table>
34   </form>
35 </&>
37 <&| /page/info_section.mas, title => 'Other tools' &>
38   <ul>
39   <li><a href="http://www.cbs.dtu.dk/services/SignalP">SignalP</a></li>
40   <li><a href="http://www.predisi.de">PrediSi</a></li>
41   <li><a href="http://rpsp.bioinfo.pl/">Rapid Prediction of Signal Peptides (RPSP)</a></li>
42   <li><a href="http://phobius.sbc.su.se/">Phobius</a></li>
43   <li><a href="http://urgi.versailles.inra.fr/predotar/predotar.html">Predotar</a></li>
44   </ul>
45 </&>
47 <script language="javascript">
49 var seq_input = document.getElementById('sequence_input_text');
50 var seq_file_input = document.getElementById('sequence_input_file');
51 function set_secretary_example_inputs() {
52         seq_input.value = ">AT1G73440.1  \nMARGESEGESSGSERESSSSSSGNESEPTKGTISKYEKQRLSRIAENKARLDALGISKAAKALLSPSPVSKKRRVKRNSGEEDDDYTPVIADGDGDEDDDEVEEIDEDEEFLCKRKNKSSASKRKVSSRKILNTSVSLGEDDDDLDKAIALSLQGSVAGSDKEAATMKKKRPELMSKTQMTQDELVMYFCQFDEGGKGFITLRDVAKMATVHDFTWTEEELQDMIRCFDMDKDGKLSLDEFRKIVSRCRMLKGS* \n>AT1G75120.1 AI22=119.545 Gravy22=0.5864 nR=2 nS=0 nT=0 nDRQPEN=6 Nitrogen=31 Oxygen=27 \nMAVRKEKVQPFRECGIAIAVLVGIFIGCVCTILIPNDFVNFRSSKVASASCESPERVKMFKAEFAIISEKNGELRKQVSDLTEKVRLAEQKEVIKAGPFGTVTGLQTNPTVAPDESANPRLAKLLEKVAVNKEIIVVLANNNVKPMLEVQIASVKRVGIQNYLVVPLDDSLESFCKSNEVAYYKRDPDNAIDVVGKSRRSSDVSGLKFRVLREFLQLGYGVLLSDVDIVFLQNPFGHLYRDSDVESMSDGHDNNTAYGFNDVFDDPTMTRSRTVYTNRIWVFNSGFFYLRPTLPSIELLDRVTDTLSKSGGWDQAVFNQHLFYPSHPGYTGLYASKRVMDVYEFMNSRVLFKTVRKDEEMKKLKPVIIHMNYHSDKLERMQAAVEFYVNGKQDALDRFRDGS* \n>AT1G17600.1 AI22=61.818 Gravy22=-0.2273 nR=2 nS=5 nT=0 nDRQPEN=6 Nitrogen=29 Oxygen=34 \nMVSSSAPRVSKYDVFLSFRGEDTRKTIVSHLYAALDSRGIVTFKDDQRLEIGDHISDELHRALGSSSFAVVVLSENYATSRWCLLELQLIMELMKEGRLEVFPIFYGVDPSVVRHQLGSFSLVKYQGLEMVDKVLRWREALNLIANLSGVVSSHCVDEAIMVGEIARDISRRVTLMHKIDSGNIVGMKAHMEGLNHLLDQESNEVLLVGIWGMGGIGKTSIVKCLYDQLSPKFPAHCFIENIKSVSKDNGHDLKHLQKELLSSILCDDIRLWSVEAGCQEIKKRLGNQKVFLVLDGVDKVAQVHALAKEKNWFGPGSRIIITTRDMGLLNTCGVEVVYEVKCLDDKDALQMFKQIAFEGGLPPCEGFDQLSIRASKLAHGLPSAIQAYALFLRGRTASPEEWEEALGALESSLDENIMEILKISYEGLPKPHQNVFLHVVCLFNGDTLQRITSLLHGPIPQSSLWIRVLAEKSLIKISTNGSVIMHKLVEQMGREIIRDDMSLARKFLRDPMEIRVALAFRDGGEQTECMCLHTCDMTCVLSMEASVVGRMHNLKFLKVYKHVDYRESNLQLIPDQPFLPRSLRLFHWDAFPLRALPSGSDPCFLVELNLRHSDLETLWSGTPSNGVKTENPCEKHNSNYFHVLLYLAQMLKSLKRLDVTGSKHLKQLPDLSSITSLEELLLEQCTRLEGIPECIGKRSTLKKLKLSYRGGRRSALRFFLRKSTRQQHIGLEFPDAKVKMDALINISIGGDITFEFRSKFRGYAEYVSFNSEQQIPIISAMSLQQAPWVISECNRFNSLRIMRFSHKENGESFSFDVFPDFPDLKELKLVNLNIRKIPSGICHLDLLEKLDLSGNDFENLPEAMSSLSRLKTLWLQNCFKLQELPKLTQVQTLTLTNCRNLRSLAKLSNTSQDEGRYCLLELCLENCKSVESLSDQLSHFTKLTCLDLSNHDFETLPSSIRDLTSLVTLCLNNCKKLKSVEKLPLSLQFLDAHGCDSLEAGSAEHFEDIPNKEVNTWLLIRLYYD* \n";
55 function validate_form() {
56   if( seq_input.value || seq_file_input.value )
57         return true;
59   alert('No sequence entered, please paste or upload sequence data to run SecreTary.');
60   return false;
63 </script>