Mercurial > repos > proteore > proteore_expression_levels_by_tissue

changeset 1:da2db27bb32b draft

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planemo upload commit 9a0ade72c1ad81829e7db319f38ab7822fa29f02-dirty
author proteore
date Thu, 06 Dec 2018 09:54:00 -0500
parents 0b0589513632
children db2cd451835f
files sel_ann_hpa.xml tool-data/proteinatlas.loc.sample
diffstat 2 files changed, 8 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- a/sel_ann_hpa.xml	Mon Nov 12 11:23:32 2018 -0500
+++ b/sel_ann_hpa.xml	Thu Dec 06 09:54:00 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="sel_ann_hpa" name="Get human expression data" version="2018.11.07">
+<tool id="sel_ann_hpa" name="Get human expression data" version="2018.12.06">
     <description>by tissue (normal or tumor tissue Human Protein Atlas)
     </description>
     <requirements>
@@ -61,12 +61,13 @@
             </param>
             <when value="normal">
                 <param name="proteinatlas" type="select" label="Human Protein Atlas" >
-                    <options from_file="proteinatlas.loc" >
+                    <!--options from_file="proteinatlas.loc" >
                         <column name="name" index="1"/>
                         <column name="value" index="2"/>
                         <filter type="remove_value" key="name" value="Full Human Protein Atlas (23/10/18)"/>
                         <filter type="remove_value" key="name" value="HPA Tumor Tissue (23/10/18)"/>
-	                </options>
+	                </options-->
+                    <option value="tool-data/HPA_normal_tissue_23-10-2018.tsv">HPA Normal Tissue (23/10/18)</option>
 	            </param>
                 <param name="normal_tissue" type="select" label="Select tissue(s)" multiple="True" display="checkboxes" optional="False">
                     <option value="adrenal gland" >Adrenal gland</option>
@@ -133,12 +134,13 @@
             </when>
             <when value="tumor">
                 <param name="proteinatlas" type="select" label="Human Protein Atlas" >
-                    <options from_file="proteinatlas.loc" >
+                    <!--options from_file="proteinatlas.loc" >
 		                <column name="name" index="1" />
 		                <column name="value" index="2" />
 		                <filter type="remove_value" meta_ref="proteinatlas" key="name" value="Full Human Protein Atlas (23/10/18)" />
                         <filter type="remove_value" meta_ref="proteinatlas" key="name" value="HPA Normal Tissue (23/10/18)" />
-	                </options>
+	                </options-->
+                    <option value="tool-data/HPA_pathology_23-10-2018.tsv">HPA Tumor Tissue (23/10/18)</option>
 	            </param>
                 <param name="cancer_tissue" type="select" label="Keep and annotate genes present in the following tissue(s)" multiple="True" display="checkboxes" optional="False">
                     <option value="breast cancer" >Breast cancer</option>
--- a/tool-data/proteinatlas.loc.sample	Mon Nov 12 11:23:32 2018 -0500
+++ b/tool-data/proteinatlas.loc.sample	Thu Dec 06 09:54:00 2018 -0500
@@ -1,5 +1,5 @@
 #This file lists the locations and dbkeys of Human Protein Atlas files.
 #<name>	<display_name (value)>          <file_path>
-full	Full Human Protein Atlas (23/10/18)	tool-data/HPA_full_atlas_23-10-2018.tsv
+#full	Full Human Protein Atlas (23/10/18)	tool-data/HPA_full_atlas_23-10-2018.tsv
 normal_tissue	HPA Normal Tissue (23/10/18)	tool-data/HPA_normal_tissue_23-10-2018.tsv
 pathology	HPA Tumor Tissue (23/10/18)	tool-data/HPA_pathology_23-10-2018.tsv