Mercurial > repos > proteore > proteore_tissue_specific_expression_data

changeset 12:0a170577648b draft

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"planemo upload commit 20b2ab253fe8386e248493316760a3fb5ccc309d-dirty"
author proteore
date Mon, 03 Feb 2020 16:58:18 +0000
parents ad853c9b3232
children 8d825dec073b
files Build_tissue-specific_expression_dataset.xml tool_data_table_conf.xml.sample
diffstat 2 files changed, 13 insertions(+), 88 deletions(-) [+]
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line diff
--- a/Build_tissue-specific_expression_dataset.xml	Mon Feb 03 16:28:54 2020 +0000
+++ b/Build_tissue-specific_expression_dataset.xml	Mon Feb 03 16:58:18 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="retrieve_from_hpa" name="Build tissue-specific expression dataset" version="2020.02.03.4">
+<tool id="retrieve_from_hpa" name="Build tissue-specific expression dataset" version="2020.02.03.5">
 <description>[Human Protein Atlas]</description>
 <requirements>
   <requirement type="package" version="3.4.1">R</requirement>
@@ -40,54 +40,9 @@
         </options>
     </param>
     <param name="normal_tissue" type="select" label="Select tissue (by clicking in the box)" multiple="True" optional="False">
-      <option value="adrenal gland" >Adrenal gland</option>
-      <option value="appendix" >Appendix</option>
-      <option value="bone marrow" >Bone marrow</option>
-      <option value="breast" >Breast</option>
-      <option value="bronchus" >Bronchus</option>
-      <option value="caudate" >Caudate</option>
-      <option value="cerebellum" >Cerebellum</option>
-      <option value="cerebral cortex" >Cerebral cortex</option>
-      <option value="cervix" >Cervix</option>
-      <option value="colon" >Colon</option>
-      <option value="duodenum" >Duodenum</option>
-      <option value="endometrium 1" >Endometrium 1</option>
-      <option value="endometrium 2" >Endometrium 2</option>
-      <option value="epididymis" >Epididymis</option>
-      <option value="esophagus" >Esophagus</option>
-      <option value="fallopian tube" >Fallopian tube</option>
-      <option value="gallbladder" >Gallbladder</option>
-      <option value="heart muscle" >Heart muscle</option>
-      <option value="hippocampus" >Hippocampus</option>
-      <option value="kidney" >Kidney</option>
-      <option value="liver" >Liver</option>
-      <option value="lung" >Lung</option>
-      <option value="lymph node" >Lymph node</option>
-      <option value="nasopharynx" >Nasopharynx</option>
-      <option value="oral mucosa" >Oral mucosa</option>
-      <option value="ovary" >Ovary</option>
-      <option value="pancreas" >Pancreas</option>
-      <option value="parathyroid gland" >Parathyroid gland</option>
-      <option value="placenta" >Placenta</option>
-      <option value="prostate" >Prostate</option>
-      <option value="rectum" >Rectum</option>
-      <option value="salivary gland" >Salivary gland</option>
-      <option value="seminal vesicle" >Seminal vesicle</option>
-      <option value="skeletal muscle" >Skeletal muscle</option>
-      <option value="skin 1" >Skin 1</option>
-      <option value="skin 2" >Skin 2</option>
-      <option value="small intestine" >Small intestine</option>
-      <option value="smooth muscle" >Smooth muscle</option>
-      <option value="soft tissue 1" >Soft tissue 1</option>
-      <option value="soft tissue 2" >Soft tissue 2</option>
-      <option value="spleen" >Spleen</option>
-      <option value="stomach 1" >Stomach 1</option>
-      <option value="stomach 2" >Stomach 2</option>
-      <option value="testis" >Testis</option>
-      <option value="thyroid gland" >Thyroid gland</option>
-      <option value="tonsil" >Tonsil</option>
-      <option value="urinary bladder" >Urinary bladder</option>
-      <option value="vagina" >Vagina</option>
+        <options from_data_table="HPA_normal_tissues">
+            <filter type="sort_by" column="1"/>
+        </options>
     </param>
     <param name="level" type="select" label="Expression level" display="checkboxes" multiple="True" optional="False">
       <option value="High" selected="true">High</option>
@@ -110,47 +65,9 @@
         </options>
     </param>
     <param name="sample" type="select" label="Select tissue (by clicking in the box)" multiple="True" optional="False">
-        <options from_data_table="Tissue.loc">
-            <filter type="remove_value" column="3"   value="2018-10-23"/>
+        <options from_data_table="HPA_rna_tissues">
             <filter type="sort_by" column="1"/>
         </options>
-      <option value="adipose tissue">Adipose tissue</option>
-      <option value="adrenal gland">Adrenal gland</option>
-      <option value="appendix">Appendix</option>
-      <option value="bone marrow">Bone marrow</option>
-      <option value="breast">Breast</option>
-      <option value="cerebral cortex">Cerebral cortex</option>
-      <option value="cervix, uterine">Cervix, uterine</option>
-      <option value="colon">Colon</option>
-      <option value="duodenum">Duodenum</option>
-      <option value="endometrium">Endometrium</option>
-      <option value="epididymis">Epididymis</option>
-      <option value="esophagus">Esophagus</option>
-      <option value="fallopian tube">Fallopian tube</option>
-      <option value="gallbladder">Gallbladder</option>
-      <option value="heart muscle">Heart muscle</option>
-      <option value="kidney">Kidney</option>
-      <option value="liver">Liver</option>
-      <option value="lung">Lung</option>
-      <option value="lymph node">Lymph node</option>
-      <option value="ovary">Ovary</option>
-      <option value="pancreas">Pancreas</option>
-      <option value="parathyroid gland">Parathyroid gland</option>
-      <option value="placenta">Placenta</option>
-      <option value="prostate">Prostate</option>
-      <option value="rectum">Rectum</option>
-      <option value="salivary gland">Salivary gland</option>
-      <option value="seminal vesicle">Seminal vesicle</option>
-      <option value="skeletal muscle">Skeletal muscle</option>
-      <option value="skin">Skin</option>
-      <option value="small intestine">Small intestine</option>
-      <option value="smooth muscle">Smooth muscle</option>
-      <option value="spleen">Spleen</option>
-      <option value="stomach">Stomach</option>
-      <option value="testis">Testis</option>
-      <option value="thyroid gland">Thyroid gland</option>
-      <option value="tonsil">Tonsil</option>
-      <option value="urinary bladder">Urinary bladder</option>
     </param>
   </when>
 </conditional>
--- a/tool_data_table_conf.xml.sample	Mon Feb 03 16:28:54 2020 +0000
+++ b/tool_data_table_conf.xml.sample	Mon Feb 03 16:58:18 2020 +0000
@@ -7,4 +7,12 @@
       <columns>id, release, name, tissue, value</columns>
       <file path="tool-data/proteore_protein_atlas_rna_tissue.loc" />
     </table>
+    <table name="HPA_normal_tissues" comment_char="#">
+      <columns>value, name, release</columns>
+      <file path="tool-data/HPA_normal_tissues.loc" />
+    </table>
+    <table name="HPA_rna_tissues" comment_char="#">
+      <columns>value, name, release</columns>
+      <file path="tool-data/HPA_rna_tissues.loc" />
+    </table>
 </tables>
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