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xtandem
sample-files.patch
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File sample-files.patch of Package xtandem
diff --git a/bin/default_input.xml b/bin/default_input.xml index a761db0..816d881 100644 --- a/bin/default_input.xml +++ b/bin/default_input.xml @@ -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 --git a/bin/input.xml b/bin/input.xml index e8e365f..022a646 100644 --- a/bin/input.xml +++ b/bin/input.xml @@ -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 --git a/bin/taxonomy.xml b/bin/taxonomy.xml index 8fd0c67..1bf1071 100644 --- a/bin/taxonomy.xml +++ b/bin/taxonomy.xml @@ -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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