# HG changeset patch
# User pieter.lukasse@wur.nl
# Date 1422249855 -3600
# Node ID d31c6978d9d0737c198a4e74ddec4619f7cb27c8
# Parent  ad911e9aaf336e276feee0965818377c3a1cc6da
fixes for NapQ

diff -r ad911e9aaf33 -r d31c6978d9d0 Csv2Apml.jar
Binary file Csv2Apml.jar has changed
diff -r ad911e9aaf33 -r d31c6978d9d0 MsFilt.jar
Binary file MsFilt.jar has changed
diff -r ad911e9aaf33 -r d31c6978d9d0 NapQ.jar
Binary file NapQ.jar has changed
diff -r ad911e9aaf33 -r d31c6978d9d0 PRIMS.jar
Binary file PRIMS.jar has changed
diff -r ad911e9aaf33 -r d31c6978d9d0 ProgenesisConv.jar
Binary file ProgenesisConv.jar has changed
diff -r ad911e9aaf33 -r d31c6978d9d0 Quantifere.jar
Binary file Quantifere.jar has changed
diff -r ad911e9aaf33 -r d31c6978d9d0 Quantiline.jar
Binary file Quantiline.jar has changed
diff -r ad911e9aaf33 -r d31c6978d9d0 SedMat_cli.jar
Binary file SedMat_cli.jar has changed
diff -r ad911e9aaf33 -r d31c6978d9d0 napq.xml
--- a/napq.xml	Fri Aug 01 17:22:37 2014 +0200
+++ b/napq.xml	Mon Jan 26 06:24:15 2015 +0100
@@ -27,8 +27,25 @@
 		<param name="namingConventionCodesForSamples" type="text" size="100" value="" 
 		label="Part of run/file name that identifies the sample" 
 		help="Add the CSV list of codes that occur in the file names 
-			and that stand for a sample code. E.g. '_S1,_S2,_S3,etc.' "/> <!-- could do regular expressions as well but this would be hard for biologists, e.g. _F\d\b -->
-
+			and that stand for a sample code. E.g. '_S1,_S2,_S3,etc.' "> <!-- could do regular expressions as well but this would be hard for biologists, e.g. _F\d\b -->
+			<sanitizer>
+				<!-- adding more characters to the set of "valid" ones: -->
+				<valid>
+					<add preset="string.printable"/>
+					<add value="#"/>
+					<add value="@"/>
+					<add value="$"/>
+					<add value="%"/>
+					<add value="&"/>
+					<add value="*"/>
+					<add value="["/>
+					<add value="]"/>
+					<add value="|"/>
+					<add value="{"/>
+					<add value="}"/>
+				</valid>
+			</sanitizer>
+		</param>
    		
    		<conditional name="is2D_LC_MS">
      		<param name="fractions" type="boolean" truevalue="Yes" falsevalue="No" checked="false" 
@@ -39,7 +56,26 @@
      			label="Part of run/file name that identifies the 2D LC-MS fraction" 
      			help="Add the CSV list of codes that occur in the file names 
      				and that stand for a fraction code. E.g. '_F1,_F2,_F3,etc.' Use this to avoid
-     				that each (fraction) file is seen as a separate run."/> <!-- could do regular expressions as well but this would be hard for biologists, e.g. _F\d\b -->
+     				that each (fraction) file is seen as a separate run."> <!-- could do regular expressions as well but this would be hard for biologists, e.g. _F\d\b -->
+     					<sanitizer>
+							<!-- adding more characters to the set of "valid" ones: -->
+							<valid>
+								<add preset="string.printable"/>
+								<add value="#"/>
+								<add value="@"/>
+								<add value="$"/>
+								<add value="%"/>
+								<add value="&"/>
+								<add value="*"/>
+								<add value="["/>
+								<add value="]"/>
+								<add value="|"/>
+								<add value="{"/>
+								<add value="}"/>
+							</valid>
+						</sanitizer>
+					</param>
+     		
      		</when>
      		<when value="No">
      		</when>
diff -r ad911e9aaf33 -r d31c6978d9d0 quantifere.xml
--- a/quantifere.xml	Fri Aug 01 17:22:37 2014 +0200
+++ b/quantifere.xml	Mon Jan 26 06:24:15 2015 +0100
@@ -56,6 +56,8 @@
      				way different peptide identifications from the same sample but measured 
      				in different fractions can be merged together. Otherwise each (fraction) file
      				is seen as a separate sample."/> <!-- could do regular expressions as well but this would be hard for biologists, e.g. _F\d\b -->
+     				<!-- on help above: the given codes are removed from source name...separate features are clustered, not peptides, peptides
+     				     are quantified based on summing features (raw), or summing patterns : TODO document the quantification columns present in the output CSV -->
      		</when>
      		<when value="No">
      		</when>
@@ -89,15 +91,17 @@
 		sample intensity values correlation. Set here the minimum correlation expected between grouped members. This is used to guide the clustering algorithm."/>
 
 		<!--  simple extra heuristics to remove some "noise" protein hits  -->
-		<param name="minProtCoverage" type="float" size="10" value="5.0" label="Minimum protein coverage (%)" help="This will remove proteins that have a too small 
-		portion of their sequence covered by peptide matches."/>
+		<param name="minProtCoverage" type="float" size="10" value="0.0" label="Minimum protein coverage (%)" help="Set this to e.g. 5.0 if you have protein coverage 
+		information in your data. This will remove proteins that have a too small portion of their sequence covered by peptide matches."/>
+		<!-- TODO : ADD warning to report if this is left 0 and no coverage is found ...or maybe validate the other way around-->
 		
 		<param name="minAboveAverageHits" type="integer" size="10" value="1" label="Minimum number of different peptide matches with a score above average" 
 		help="This will remove proteins that do not have enough reasonable peptides hits."/>
 
 		<param name="minNrIdsForInferencePeptide" type="integer" size="10" value="1" label="Minimum number of peptide identifications for inference peptides" 
 		help="Minimum number of peptide identifications a peptide needs to be used as inference peptide for secondary proteins."/>
-
+		<!--  currently, when one feature clusters with foreign peptide, then it is not inference peptide anymore...quite strict, could be less strict
+		      by letting user indicate for example: 90% of features should be inference features...then it is an inference pep. See QuantifereTool.inferSecondaryProteins() -->
 
      	<param name="functionalAnnotationCSV" type="data" format="csv,txt,tsv" optional="true" 
      	label="(Functional)annotation mapping file (csv or tsv format)" 
@@ -207,6 +211,20 @@
 .. _Cytoscape chartplugin: http://apps.cytoscape.org/apps/chartplugin
 
 
+**References**
+
+If you use this Galaxy tool in work leading to a scientific publication please
+cite the following papers:
+
+Pieter N. J. Lukasse and Antoine H. P. America (2014).
+Protein Inference Using Peptide Quantification Patterns.
+http://dx.doi.org/10.1021/pr401072g
+
 
   </help>
+  <citations>
+        <citation type="doi">10.1021/pr401072g</citation> <!-- example 
+        see also https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set
+        -->
+   </citations>
 </tool>
diff -r ad911e9aaf33 -r d31c6978d9d0 static/images/napq_overview.png
Binary file static/images/napq_overview.png has changed