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changeset 1:d90f4809ccc6 draft

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Uploaded
author hammock
date Fri, 28 Aug 2015 07:38:12 -0400
parents b1ac138f0287
children 4db310b7e37c
files Hammock/dist/Hammock.jar Hammock/settings/misc/blosum62.freq_rownorm Hammock/settings/settings-hhalign.txt Hammock/settings/settings.prop hammock.xml
diffstat 5 files changed, 54 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
Binary file Hammock/dist/Hammock.jar has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Hammock/settings/misc/blosum62.freq_rownorm	Fri Aug 28 07:38:12 2015 -0400
@@ -0,0 +1,25 @@
+# BLOSUM Clustered Target Frequencies=qij
+# Blocks Database = /data/blocks_5.0/blocks.dat
+# Cluster Percentage: >= 62
+# Normalized frequencies (by row) from file: blosum62.qij
+A	R	N	D	C	Q	E	G	H	I	L	K	M	F	P	S	T	W	Y	V
+0.2901	0.0310	0.0256	0.0297	0.0216	0.0256	0.0405	0.0783	0.0148	0.0432	0.0594	0.0445	0.0175	0.0216	0.0297	0.0850	0.0499	0.0054	0.0175	0.0688
+0.0446	0.3450	0.0388	0.0310	0.0078	0.0484	0.0523	0.0329	0.0233	0.0233	0.0465	0.1202	0.0155	0.0174	0.0194	0.0446	0.0349	0.0058	0.0174	0.0310
+0.0427	0.0449	0.3169	0.0831	0.0090	0.0337	0.0494	0.0652	0.0315	0.0225	0.0315	0.0539	0.0112	0.0180	0.0202	0.0697	0.0494	0.0045	0.0157	0.0270
+0.0410	0.0299	0.0690	0.3974	0.0075	0.0299	0.0914	0.0466	0.0187	0.0224	0.0280	0.0448	0.0093	0.0149	0.0224	0.0522	0.0354	0.0037	0.0112	0.0243
+0.0650	0.0163	0.0163	0.0163	0.4837	0.0122	0.0163	0.0325	0.0081	0.0447	0.0650	0.0203	0.0163	0.0203	0.0163	0.0407	0.0366	0.0041	0.0122	0.0569
+0.0559	0.0735	0.0441	0.0471	0.0088	0.2147	0.1029	0.0412	0.0294	0.0265	0.0471	0.0912	0.0206	0.0147	0.0235	0.0559	0.0412	0.0059	0.0206	0.0353
+0.0552	0.0497	0.0405	0.0902	0.0074	0.0645	0.2965	0.0350	0.0258	0.0221	0.0368	0.0755	0.0129	0.0166	0.0258	0.0552	0.0368	0.0055	0.0166	0.0313
+0.0783	0.0229	0.0391	0.0337	0.0108	0.0189	0.0256	0.5101	0.0135	0.0189	0.0283	0.0337	0.0094	0.0162	0.0189	0.0513	0.0297	0.0054	0.0108	0.0243
+0.0420	0.0458	0.0534	0.0382	0.0076	0.0382	0.0534	0.0382	0.3550	0.0229	0.0382	0.0458	0.0153	0.0305	0.0191	0.0420	0.0267	0.0076	0.0573	0.0229
+0.0471	0.0177	0.0147	0.0177	0.0162	0.0133	0.0177	0.0206	0.0088	0.2710	0.1679	0.0236	0.0368	0.0442	0.0147	0.0250	0.0398	0.0059	0.0206	0.1767
+0.0445	0.0243	0.0142	0.0152	0.0162	0.0162	0.0202	0.0213	0.0101	0.1154	0.3755	0.0253	0.0496	0.0547	0.0142	0.0243	0.0334	0.0071	0.0223	0.0962
+0.0570	0.1071	0.0415	0.0415	0.0086	0.0535	0.0708	0.0432	0.0207	0.0276	0.0432	0.2781	0.0155	0.0155	0.0276	0.0535	0.0397	0.0052	0.0173	0.0328
+0.0522	0.0321	0.0201	0.0201	0.0161	0.0281	0.0281	0.0281	0.0161	0.1004	0.1968	0.0361	0.1606	0.0482	0.0161	0.0361	0.0402	0.0080	0.0241	0.0924
+0.0338	0.0190	0.0169	0.0169	0.0106	0.0106	0.0190	0.0254	0.0169	0.0634	0.1142	0.0190	0.0254	0.3869	0.0106	0.0254	0.0254	0.0169	0.0888	0.0550
+0.0568	0.0258	0.0233	0.0310	0.0103	0.0207	0.0362	0.0362	0.0129	0.0258	0.0362	0.0413	0.0103	0.0129	0.4935	0.0439	0.0362	0.0026	0.0129	0.0310
+0.1099	0.0401	0.0541	0.0489	0.0175	0.0332	0.0524	0.0663	0.0192	0.0297	0.0419	0.0541	0.0157	0.0209	0.0297	0.2199	0.0820	0.0052	0.0175	0.0419
+0.0730	0.0355	0.0434	0.0375	0.0178	0.0276	0.0394	0.0434	0.0138	0.0533	0.0651	0.0454	0.0197	0.0237	0.0276	0.0927	0.2465	0.0059	0.0178	0.0710
+0.0303	0.0227	0.0152	0.0152	0.0076	0.0152	0.0227	0.0303	0.0152	0.0303	0.0530	0.0227	0.0152	0.0606	0.0076	0.0227	0.0227	0.4924	0.0682	0.0303
+0.0405	0.0280	0.0218	0.0187	0.0093	0.0218	0.0280	0.0249	0.0467	0.0436	0.0685	0.0312	0.0187	0.1308	0.0156	0.0312	0.0280	0.0280	0.3178	0.0467
+0.0700	0.0219	0.0165	0.0178	0.0192	0.0165	0.0233	0.0247	0.0082	0.1646	0.1303	0.0261	0.0316	0.0357	0.0165	0.0329	0.0494	0.0055	0.0206	0.2689
--- a/Hammock/settings/settings-hhalign.txt	Mon Jan 26 06:24:21 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-hhalignParameters=-realign -id 100 -diff inf -alt 1 -corr 0 -shift 0 -ssm 0 -nocontxt -pcm 2 -tags -nocons -nopred -nodssp -M a2m -alt 1 -sc 0 -v 0 -z 2 -Z 500000 -local -mact 0.0 -p 0
--- a/Hammock/settings/settings.prop	Mon Jan 26 06:24:21 2015 -0500
+++ b/Hammock/settings/settings.prop	Fri Aug 28 07:38:12 2015 -0400
@@ -14,13 +14,12 @@
 #hmmDirectory=
 #hhDirectory=
 #hmmsearchOutDirectory=
-#hhalignOutDirectory=
 #hhsearchOutDirectory=
 #fastaDatabaseFile=
 #Tool parameters. Generally, it is not recommended to change this section.
 clustalOmegaParameters=
-hmmbuildParameters=--enone --fragthresh 1.0 --hand --wnone --amino
-hmmsearchParameters=--nobias --F1 0.5 --F2 0.05 --F3 1e-2 --nonull2
-hmmalignParameters=--outformat selex --amino
+hmmbuildParameters=--enone --fragthresh 1.0 --hand --wnone --amino --seed 42
+hmmsearchParameters=--nobias --F1 0.5 --F2 0.05 --F3 1e-2 --nonull2 --seed 42
+hmmalignParameters=--outformat selex --amino --seed 42
 hhmakeParameters=-M a2m -id 100 -diff inf -pcm 3 -nocontxt -v 0
-hhsearchParameters=-norealign -alt 1 -corr 0 -shift 0 -ssm 0 -tags -nocons -nopred -nodssp -sc 0 -v 0 -z 2 -Z 500000 -local -p 0.0 -vit -b 100.0 -E 100.0 -e 100.0 -z 100 -BLOSUM65
+hhsearchParameters=-norealign -alt 1 -corr 0 -shift 0 -ssm 0 -tags -nocons -nopred -nodssp -sc 0 -v 0 -z 2 -Z 500000 -local -p 0.0 -vit -b 100.0 -E 100.0 -e 100.0 -z 100
--- a/hammock.xml	Mon Jan 26 06:24:21 2015 -0500
+++ b/hammock.xml	Fri Aug 28 07:38:12 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="hammock_1.0" name="Hammock - cluster peptides">
+<tool id="hammock_1.0" name="Hammock - cluster peptides" version="1.0.2" hidden="false">
 
     <description>Clusters short peptide sequences</description>
 
@@ -15,6 +15,12 @@
 	    #if $advanced_greedy_params.set_greedy_params == "set":
 		-x $advanced_greedy_params.max_shift
 		-p $advanced_greedy_params.shift_penalty
+		-R $advanced_greedy_params.set_order.order
+
+		#if $advanced_greedy_params.set_order.order == "random":
+			-S $advanced_greedy_params.set_order.seed
+		#end if
+	
 		-m \${MATRIX_PATH}${advanced_greedy_params.scoring_matrix}.txt
             	#if $advanced_greedy_params.greedy_params.set_greedy == "set":
                 	-g $advanced_greedy_params.greedy_params.greedy_threshold
@@ -103,6 +109,24 @@
 
          	<param name="shift_penalty" type="integer" value="0" label="Sequence shift penalty" help="Score penalty added to to each alignment score during greedy clustering. This penalty is added for every amino acid aligned towards a (trailing) gap. This value should typically be non-positive (With a positive value, sequences benefit from containing more gaps). See -p, --gap penalty in manual for details."/>
 
+	      <conditional name="set_order">
+
+              		<param name="order" type="select" label="Greedy clustering order" help="Select the order of sequences during the greedy clustering. See -R, --order in manual for details.">
+                  		<option value="size">Size</option>
+                  		<option value="alphabetic">Alphabetic</option>
+                  		<option value="random">Random</option>
+              		</param>
+
+			<when value="size" />
+			<when value="alphabetic" />
+            		<when value="random">
+         			<param name="seed" type="integer" value="42" label="Seed for random number generation" help="Set a seed value for the pseudorandom sequence order. See -S, --seed in manual for details."/>
+			</when>
+
+		</conditional>
+
+		
+
               <param name="scoring_matrix" type="select" label="Substitiution matrix schema." help="Select a substitution matrix to be used to score alignments during glreedy clustering. See -m, --matrix in manual for details.">
                   <option value="blosum62">Blosum 62</option>
                   <option value="blosum30">Blosum 30</option>