File sample-files.patch of Package xtandem

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File sample-files.patch of Package xtandem (Revision 6e11502273c36655b9fe496485bcefcd)

Currently displaying revision 6e11502273c36655b9fe496485bcefcd , Show latest

diff -ur tandem-linux-13-02-01-1.orig/bin/default_input.xml tandem-linux-13-02-01-1/bin/default_input.xml
--- tandem-linux-13-02-01-1.orig/bin/default_input.xml	2009-05-07 02:44:10.000000000 -0500
+++ tandem-linux-13-02-01-1/bin/default_input.xml	2013-02-08 16:11:44.000000000 -0600
@@ -1,11 +1,11 @@
 <?xml version="1.0"?>
-<?xml-stylesheet type="text/xsl" href="tandem-input-style.xsl"?>
+<?xml-stylesheet type="text/xsl" href="xsl/tandem-input-style.xsl"?>
 <bioml>
 <note>list path parameters</note>
 	<note type="input" label="list path, default parameters">default_input.xml</note>
 		<note>This value is ignored when it is present in the default parameter
 		list path.</note>
-	<note type="input" label="list path, taxonomy information">taxonomy.xml</note>
+	<note type="input" label="list path, taxonomy information">/usr/share/xtandem/taxonomy.xml</note>
 
 <note>spectrum parameters</note>
 	<note type="input" label="spectrum, fragment monoisotopic mass error">0.4</note>
@@ -61,7 +61,7 @@
 		</note>
 
 <note>protein parameters</note>
-	<note type="input" label="protein, taxon">other mammals</note>
+	<note type="input" label="protein, taxon">human</note>
 		<note>This value is interpreted using the information in taxonomy.xml.</note>
 	<note type="input" label="protein, cleavage site">[RK]|{P}</note>
 		<note>this setting corresponds to the enzyme trypsin. The first characters
@@ -131,7 +131,7 @@
 		<note>values = protein|spectrum (spectrum is the default)</note>
 	<note type="input" label="output, path hashing">yes</note>
 		<note>values = yes|no</note>
-	<note type="input" label="output, xsl path">tandem-style.xsl</note>
+	<note type="input" label="output, xsl path">file:///usr/share/xtandem/xsl/tandem-style.xsl</note>
 	<note type="input" label="output, parameters">yes</note>
 		<note>values = yes|no</note>
 	<note type="input" label="output, performance">yes</note>
diff -ur tandem-linux-13-02-01-1.orig/bin/input.xml tandem-linux-13-02-01-1/bin/input.xml
--- tandem-linux-13-02-01-1.orig/bin/input.xml	2009-05-07 02:44:10.000000000 -0500
+++ tandem-linux-13-02-01-1/bin/input.xml	2013-02-08 16:06:27.000000000 -0600
@@ -10,8 +10,8 @@
 	files are linked to a taxon name.
 	</note>
 
-	<note type="input" label="list path, default parameters">default_input.xml</note>
-	<note type="input" label="list path, taxonomy information">taxonomy.xml</note>
+	<note type="input" label="list path, default parameters">/usr/share/xtandem/default_input.xml</note>
+	<note type="input" label="list path, taxonomy information">/usr/share/xtandem/taxonomy.xml</note>
 
 	<note type="input" label="protein, taxon">yeast</note>
 	
diff -ur tandem-linux-13-02-01-1.orig/bin/taxonomy.xml tandem-linux-13-02-01-1/bin/taxonomy.xml
--- tandem-linux-13-02-01-1.orig/bin/taxonomy.xml	2009-05-07 02:44:12.000000000 -0500
+++ tandem-linux-13-02-01-1/bin/taxonomy.xml	2013-02-11 15:17:11.000000000 -0600
@@ -1,8 +1,17 @@
 <?xml version="1.0"?>
 <bioml label="x! taxon-to-file matching list">
+	<taxon label="human">
+		<file format="peptide" URL="/usr/share/xtandem/fasta/uniprot_misc/human_uprot.fasta.pro"/>
+	</taxon>
+	<taxon label="mouse">
+		<file format="peptide" URL="/usr/share/xtandem/fasta/uniprot_misc/mouse_uprot.fasta.pro"/>
+	</taxon>
+	<taxon label="rat">
+		<file format="peptide" URL="/usr/share/xtandem/fasta/uniprot_misc/rat_uprot.fasta.pro"/>
+	</taxon>
 	<taxon label="yeast">
-		<file format="peptide" URL="../fasta/scd.fasta.pro" />
-		<file format="peptide" URL="../fasta/scd_1.fasta.pro" />
-		<file format="peptide" URL="../fasta/crap.fasta.pro" />
+		<file format="peptide" URL="/usr/share/xtandem/fasta/scd.fasta.pro"/>
+		<file format="peptide" URL="/usr/share/xtandem/fasta/scd_1.fasta.pro"/>
+		<file format="peptide" URL="/usr/share/xtandem/fasta/crap.fasta.pro"/>
 	</taxon>
 </bioml>

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File sample-files.patch of Package xtandem (Revision 6e11502273c36655b9fe496485bcefcd)

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