Mercurial > repos > proteore > proteore_ms_observation_pepatlas

changeset 4:299eb4a62e0c draft

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planemo upload commit 23c8d2008471f194131da1c7705c8bb0b6388236-dirty
author proteore
date Fri, 01 Feb 2019 11:48:49 -0500
parents e446b013c048
children 034cfb96a482
files Get_ms-ms_observations.xml peptide_atlas.loc.sample tool-data/Human_Adrenal_gland_2014-08.tsv tool-data/Human_Brain_2015-01.tsv tool-data/Human_Breast_2014-08.tsv tool-data/Human_CSF_2014-09.tsv tool-data/Human_Colon_cancer_2013-02.tsv tool-data/Human_Digestive_system_2014-08.tsv tool-data/Human_Female_reproductive_system_2014-08.tsv tool-data/Human_Heart_2014-08.tsv tool-data/Human_Kidney_2014-08.tsv tool-data/Human_Liver_2014-08.tsv tool-data/Human_Lung_2014-08.tsv tool-data/Human_Male_reproductive_system_2014-08.tsv tool-data/Human_Pancreas_2014-08.tsv tool-data/Human_Plasma_non_glyco_2017-04.tsv tool-data/Human_Spleen_2014-08.tsv tool-data/Human_Testis_2017-01.tsv tool-data/Human_Urinary_bladder_2014-08.tsv tool-data/Human_Urine_2014-08.tsv tool_data_table_conf.xml.sample
diffstat 21 files changed, 121169 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/Get_ms-ms_observations.xml	Fri Feb 01 11:34:12 2019 -0500
+++ b/Get_ms-ms_observations.xml	Fri Feb 01 11:48:49 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="retr_pepatlas1" name="Get MS/MS observations in tissue/fluid" version="2019.02.01">
+<tool id="retr_pepatlas1" name="Get MS/MS observations in tissue/fluid" version="2019.02.01.1">
     <description>[Peptide Atlas]</description>
     <requirements>
         <requirement type="package" version="3.4.1">R</requirement>
--- a/peptide_atlas.loc.sample	Fri Feb 01 11:34:12 2019 -0500
+++ b/peptide_atlas.loc.sample	Fri Feb 01 11:48:49 2019 -0500
@@ -1,4 +1,4 @@
-#<id>   <name>  <value> <path>
+#<id>   <name>  <tissue> <value>
 Human_Adrenal_gland_2014-08 Human Adrenal gland 2014/08	Human_Adrenal_gland	tool-data/peptide_atlas/Human_Adrenal_gland_2014-08.tsv
 Human_Brain_2015-01 Human Brain 2015/01	Human_Brain	tool-data/peptide_atlas/Human_Brain_2015-01.tsv
 Human_Breast_2014-08    Human Breast 2014/08	Human_Breast	tool-data/peptide_atlas/Human_Breast_2014-08.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/Human_Adrenal_gland_2014-08.tsv	Fri Feb 01 11:48:49 2019 -0500
@@ -0,0 +1,6299 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/Human_Brain_2015-01.tsv	Fri Feb 01 11:48:49 2019 -0500
@@ -0,0 +1,8885 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/Human_Breast_2014-08.tsv	Fri Feb 01 11:48:49 2019 -0500
@@ -0,0 +1,13363 @@
+Uniprot_AC	nb_obs
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/Human_CSF_2014-09.tsv	Fri Feb 01 11:48:49 2019 -0500
@@ -0,0 +1,3302 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/Human_Colon_cancer_2013-02.tsv	Fri Feb 01 11:48:49 2019 -0500
@@ -0,0 +1,670 @@
+Uniprot_AC	nb_obs
+Q9NSC7	5
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/Human_Digestive_system_2014-08.tsv	Fri Feb 01 11:48:49 2019 -0500
@@ -0,0 +1,8883 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/Human_Female_reproductive_system_2014-08.tsv	Fri Feb 01 11:48:49 2019 -0500
@@ -0,0 +1,10606 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/Human_Heart_2014-08.tsv	Fri Feb 01 11:48:49 2019 -0500
@@ -0,0 +1,6645 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/Human_Kidney_2014-08.tsv	Fri Feb 01 11:48:49 2019 -0500
@@ -0,0 +1,5279 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/Human_Liver_2014-08.tsv	Fri Feb 01 11:48:49 2019 -0500
@@ -0,0 +1,7071 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/Human_Lung_2014-08.tsv	Fri Feb 01 11:48:49 2019 -0500
@@ -0,0 +1,5677 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/Human_Male_reproductive_system_2014-08.tsv	Fri Feb 01 11:48:49 2019 -0500
@@ -0,0 +1,9839 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/Human_Pancreas_2014-08.tsv	Fri Feb 01 11:48:49 2019 -0500
@@ -0,0 +1,7489 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/Human_Plasma_non_glyco_2017-04.tsv	Fri Feb 01 11:48:49 2019 -0500
@@ -0,0 +1,3634 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/Human_Spleen_2014-08.tsv	Fri Feb 01 11:48:49 2019 -0500
@@ -0,0 +1,5700 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/Human_Testis_2017-01.tsv	Fri Feb 01 11:48:49 2019 -0500
@@ -0,0 +1,10339 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/Human_Urinary_bladder_2014-08.tsv	Fri Feb 01 11:48:49 2019 -0500
@@ -0,0 +1,5058 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/Human_Urine_2014-08.tsv	Fri Feb 01 11:48:49 2019 -0500
@@ -0,0 +1,2427 @@
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--- a/tool_data_table_conf.xml.sample	Fri Feb 01 11:34:12 2019 -0500
+++ b/tool_data_table_conf.xml.sample	Fri Feb 01 11:48:49 2019 -0500
@@ -2,7 +2,7 @@
 <tables>
     <!-- Location of peptide reference files for proteore_ms_observation -->
     <table name='peptide_atlas' comment_char="#">
-        <columns>tissue,name,value</columns>
+        <columns>id,name,tissue,value</columns>
         <file path="tool-data/peptide_atlas.loc" />
     </table>
 </tables> 
\ No newline at end of file