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Changeset 4:299eb4a62e0c (2019-02-01)

Previous changeset 3:e446b013c048 (2019-02-01) Next changeset 5:034cfb96a482 (2019-03-13)

Commit message:
planemo upload commit 23c8d2008471f194131da1c7705c8bb0b6388236-dirty

modified:
Get_ms-ms_observations.xml
peptide_atlas.loc.sample
tool_data_table_conf.xml.sample

diff -r e446b013c048 -r 299eb4a62e0c Get_ms-ms_observations.xml
--- 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>

diff -r e446b013c048 -r 299eb4a62e0c peptide_atlas.loc.sample
--- 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

diff -r e446b013c048 -r 299eb4a62e0c tool-data/Human_Adrenal_gland_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

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diff -r e446b013c048 -r 299eb4a62e0c tool-data/Human_Brain_2015-01.tsv
--- /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

b'@@ -0,0 +1,8885 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diff -r e446b013c048 -r 299eb4a62e0c tool-data/Human_Breast_2014-08.tsv
--- /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

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diff -r e446b013c048 -r 299eb4a62e0c tool-data/Human_CSF_2014-09.tsv
--- /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

b'@@ -0,0 +1,3302 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2\r\n+Q16666\t3\r\n+P39023\t2\r\n'

diff -r e446b013c048 -r 299eb4a62e0c tool-data/Human_Colon_cancer_2013-02.tsv
--- /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
+P08575 75
+P05534 15
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diff -r e446b013c048 -r 299eb4a62e0c tool-data/Human_Digestive_system_2014-08.tsv
--- /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

b'@@ -0,0 +1,8883 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diff -r e446b013c048 -r 299eb4a62e0c tool-data/Human_Female_reproductive_system_2014-08.tsv
--- /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

b'@@ -0,0 +1,10606 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diff -r e446b013c048 -r 299eb4a62e0c tool-data/Human_Heart_2014-08.tsv
--- /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

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t2\r\n+Q7Z739\t23\r\n'

diff -r e446b013c048 -r 299eb4a62e0c tool-data/Human_Kidney_2014-08.tsv
--- /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

b'@@ -0,0 +1,5279 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diff -r e446b013c048 -r 299eb4a62e0c tool-data/Human_Liver_2014-08.tsv
--- /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

b'@@ -0,0 +1,7071 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'

diff -r e446b013c048 -r 299eb4a62e0c tool-data/Human_Lung_2014-08.tsv
--- /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

b'@@ -0,0 +1,5677 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diff -r e446b013c048 -r 299eb4a62e0c tool-data/Human_Male_reproductive_system_2014-08.tsv
--- /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

b'@@ -0,0 +1,9839 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diff -r e446b013c048 -r 299eb4a62e0c tool-data/Human_Pancreas_2014-08.tsv
--- /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

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6\t1\r\n+O75323\t36\r\n+Q8WXA3\t3\r\n+Q7Z739\t10\r\n'

diff -r e446b013c048 -r 299eb4a62e0c tool-data/Human_Plasma_non_glyco_2017-04.tsv
--- /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

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diff -r e446b013c048 -r 299eb4a62e0c tool-data/Human_Spleen_2014-08.tsv
--- /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

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r\n+Q9P0S9\t6\r\n+O75323\t24\r\n+Q7Z739\t19\r\n'

diff -r e446b013c048 -r 299eb4a62e0c tool-data/Human_Testis_2017-01.tsv
--- /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

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diff -r e446b013c048 -r 299eb4a62e0c tool-data/Human_Urinary_bladder_2014-08.tsv
--- /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

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diff -r e446b013c048 -r 299eb4a62e0c tool-data/Human_Urine_2014-08.tsv
--- /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

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\t3\r\n+Q9H6S3\t68\r\n+Q16661\t12\r\n'

diff -r e446b013c048 -r 299eb4a62e0c tool_data_table_conf.xml.sample
--- 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>
     
     <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