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changeset 2:4db310b7e37c draft

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Uploaded
author hammock
date Mon, 25 Jan 2016 07:58:32 -0500
parents d90f4809ccc6
children 7950e4c52972
files Hammock/dist/Hammock.jar hammock.xml tool_dependencies.xml
diffstat 3 files changed, 19 insertions(+), 11 deletions(-) [+]
line wrap: on
line diff
Binary file Hammock/dist/Hammock.jar has changed
--- a/hammock.xml	Fri Aug 28 07:38:12 2015 -0400
+++ b/hammock.xml	Mon Jan 25 07:58:32 2016 -0500
@@ -1,9 +1,9 @@
-<tool id="hammock_1.0" name="Hammock - cluster peptides" version="1.0.2" hidden="false">
+<tool id="hammock_1.0" name="Hammock - cluster peptides" version="1.0.4" hidden="false">
 
     <description>Clusters short peptide sequences</description>
 
     <command interpreter="bash">
-wrapper.sh \$HAMMOCK_JAR full --galaxy -t \${GALAXY_SLOTS:-4} -i $input --goc $output_clusters --gos $output_sequences
+wrapper.sh \$HAMMOCK_JAR full --galaxy -t \${GALAXY_SLOTS:-4} -i $input --goc $output_clusters --gos $output_sequences --goo $output_sequences_ordered
 
 	   #if $label_params.set_labels == "set":
                 #for $s in $label_params.round_labels:
@@ -242,8 +242,9 @@
 </inputs>
 
    <outputs>  
-       <data format="csv" name="output_clusters" />
-	<data format="csv" name="output_sequences" />
+       <data format="tsv" name="output_clusters" />
+	<data format="tsv" name="output_sequences" />
+	<data format="tsv" name="output_sequences_ordered" />
    </outputs>
 
   <requirements>
@@ -252,7 +253,7 @@
 		<requirement type="set_environment">MATRIX_PATH</requirement>
 		<requirement type="package" version="1.6.0">java</requirement>
 		<requirement type="package" version="1.2.0">clustalomega</requirement>
-		<requirement type="package" version="3.1b1">hmmer</requirement>
+		<requirement type="package" version="3.1b2">hmmer</requirement>
 		<requirement type="package" version="2.0.16">hhsuite</requirement>
   </requirements>
 
@@ -278,6 +279,8 @@
 <help>
 
 
+**HAMMOCK version 1.0.4**
+
 **Hammock overview**
 
 Hammock performs peptide sequence clustering. It is able to identify clusters of sequences sharing a sequence motif within big datasets. For news, documentation and other available versions, see http://www.recamo.cz/en/software/hammock-cluster-peptides/
@@ -289,7 +292,7 @@
 **Citation**
 Please cite: 
 
-Krejci A, et al. *in preparation* 
+Krejci, Adam, et al. "Hammock: a hidden Markov model-based peptide clustering algorithm to identify protein-interaction consensus motifs in large datasets." Bioinformatics 32.1 (2016): 9-16.
 
 ------
 
@@ -312,7 +315,7 @@
 
 **Outputs**
 
-Hammock returns two files, both are semicolon-separated tables.
+Hammock returns three files, all of them are tab-separated tables.
 
 The first is the cluster overview file. It contains one line for each resulting cluster plus header. Columns are: 
 
@@ -324,7 +327,9 @@
   | label1, label2 etc. Counts of sequences with particular labels
 
 
-The second file provides more detailed information. It contains one line for each clustered sequence plus header. Columns are: 
+The second file provides more detailed information. It contains one line for each clustered (unique) sequence plus header. The sequences are ordered according to their presence in clusters, from the largest cluster and within a cluster, from the most abundant sequence.
+
+Columns are: 
 
 cluster_id sequence alignment sum label1 label2 label3 ...
 
@@ -334,10 +339,13 @@
   | sum: Total count of copies of this sequence (sum over all labels)
   | label1, label2 etc. Counts of copies with particular labels
 
+
+The third file is the same as the second file, with two differences: it also contains sequences not belonging to any cluster (these have "NA" in the cluster_id column) and the order of the sequences in this file is the same as their order in the input fasta file.
+
 ------
 
 **Parameters**
-Default and auto-detected parameters have been carefully tuned and tested to work well with several datasets, they are especially suited for short peptides from Phage display experiments. Neverheless, there is no such thing as universal rules suitable for every dataset - parameter understanding and tuning may be needed. For more detailed description of parameters, see the documentation_.
+Default and auto-detected parameters have been carefully tuned and tested to work well with several datasets, they are especially suited for short peptides from phage display experiments. Neverheless, there is no such thing as universal rules suitable for every dataset - parameter understanding and tuning may be needed. For more detailed description of parameters, see the documentation_.
 
 .. _documentation: http://www.recamo.cz/userfiles/file/Software/Hammock/Hammock-manual.pdf
 
--- a/tool_dependencies.xml	Fri Aug 28 07:38:12 2015 -0400
+++ b/tool_dependencies.xml	Mon Jan 25 07:58:32 2016 -0500
@@ -25,11 +25,11 @@
 			</install>
 		</package>
 
-        <package name="hmmer" version="3.1b1">
+        <package name="hmmer" version="3.1b2">
             <install version="1.0">
 				<actions_group>
                     <actions architecture="x86_64" os="linux">
-                        <action type="download_by_url">http://selab.janelia.org/software/hmmer3/3.1b1/hmmer-3.1b1-linux-intel-x86_64.tar.gz</action>
+                        <action type="download_by_url">http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2-linux-intel-x86_64.tar.gz</action>
 						<action type="move_file">
                     		<source>binaries/hmmbuild</source>
                     		<destination>$INSTALL_DIR</destination>