Archie Cobbs
992971e53f
One package less failing in science. OBS-URL: https://build.opensuse.org/request/show/726471 OBS-URL: https://build.opensuse.org/package/show/science/xtandem?expand=0&rev=18
77 lines
3.3 KiB
Diff
77 lines
3.3 KiB
Diff
diff --git a/bin/default_input.xml b/bin/default_input.xml
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index a761db0..816d881 100644
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--- a/bin/default_input.xml
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+++ b/bin/default_input.xml
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@@ -1,11 +1,11 @@
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<?xml version="1.0"?>
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-<?xml-stylesheet type="text/xsl" href="tandem-input-style.xsl"?>
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+<?xml-stylesheet type="text/xsl" href="xsl/tandem-input-style.xsl"?>
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<bioml>
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<note>list path parameters</note>
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<note type="input" label="list path, default parameters">default_input.xml</note>
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<note>This value is ignored when it is present in the default parameter
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list path.</note>
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- <note type="input" label="list path, taxonomy information">taxonomy.xml</note>
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+ <note type="input" label="list path, taxonomy information">/usr/share/xtandem/taxonomy.xml</note>
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<note>spectrum parameters</note>
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<note type="input" label="spectrum, fragment monoisotopic mass error">0.4</note>
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@@ -61,7 +61,7 @@
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</note>
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<note>protein parameters</note>
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- <note type="input" label="protein, taxon">other mammals</note>
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+ <note type="input" label="protein, taxon">human</note>
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<note>This value is interpreted using the information in taxonomy.xml.</note>
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<note type="input" label="protein, cleavage site">[RK]|{P}</note>
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<note>this setting corresponds to the enzyme trypsin. The first characters
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@@ -131,7 +131,7 @@
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<note>values = protein|spectrum (spectrum is the default)</note>
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<note type="input" label="output, path hashing">yes</note>
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<note>values = yes|no</note>
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- <note type="input" label="output, xsl path">tandem-style.xsl</note>
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+ <note type="input" label="output, xsl path">file:///usr/share/xtandem/xsl/tandem-style.xsl</note>
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<note type="input" label="output, parameters">yes</note>
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<note>values = yes|no</note>
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<note type="input" label="output, performance">yes</note>
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diff --git a/bin/input.xml b/bin/input.xml
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index e8e365f..022a646 100644
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--- a/bin/input.xml
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+++ b/bin/input.xml
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@@ -10,8 +10,8 @@
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files are linked to a taxon name.
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</note>
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- <note type="input" label="list path, default parameters">default_input.xml</note>
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- <note type="input" label="list path, taxonomy information">taxonomy.xml</note>
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+ <note type="input" label="list path, default parameters">/usr/share/xtandem/default_input.xml</note>
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+ <note type="input" label="list path, taxonomy information">/usr/share/xtandem/taxonomy.xml</note>
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<note type="input" label="protein, taxon">yeast</note>
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diff --git a/bin/taxonomy.xml b/bin/taxonomy.xml
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index 8fd0c67..1bf1071 100644
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--- a/bin/taxonomy.xml
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+++ b/bin/taxonomy.xml
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@@ -1,8 +1,17 @@
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<?xml version="1.0"?>
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<bioml label="x! taxon-to-file matching list">
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+ <taxon label="human">
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+ <file format="peptide" URL="/usr/share/xtandem/fasta/uniprot_misc/human_uprot.fasta.pro"/>
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+ </taxon>
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+ <taxon label="mouse">
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+ <file format="peptide" URL="/usr/share/xtandem/fasta/uniprot_misc/mouse_uprot.fasta.pro"/>
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+ </taxon>
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+ <taxon label="rat">
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+ <file format="peptide" URL="/usr/share/xtandem/fasta/uniprot_misc/rat_uprot.fasta.pro"/>
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+ </taxon>
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<taxon label="yeast">
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- <file format="peptide" URL="../fasta/scd.fasta.pro" />
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- <file format="peptide" URL="../fasta/scd_1.fasta.pro" />
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- <file format="peptide" URL="../fasta/crap.fasta.pro" />
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+ <file format="peptide" URL="/usr/share/xtandem/fasta/scd.fasta.pro"/>
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+ <file format="peptide" URL="/usr/share/xtandem/fasta/scd_1.fasta.pro"/>
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+ <file format="peptide" URL="/usr/share/xtandem/fasta/crap.fasta.pro"/>
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</taxon>
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</bioml>
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