Mercurial > repos > bimib > marea

changeset 4:cf3d3d8f4ef5 draft

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Modifica a xml
author bimib
date Tue, 13 Nov 2018 07:34:43 -0500
parents 02577e65dcca
children 146cb8e171b8
files Marea/marea.xml Marea/marea_cluster.xml Marea/marea_macros.xml
diffstat 2 files changed, 23 insertions(+), 9 deletions(-) [+]
line wrap: on
line diff
--- a/Marea/marea.xml	Tue Nov 13 05:12:32 2018 -0500
+++ b/Marea/marea.xml	Tue Nov 13 07:34:43 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="MaREA" name="Metabolic Enrichment Analysis">
+<tool id="MaREA" name="Metabolic Enrichment Analysis" version="1.0.0">
     <description>for Galaxy</description>
     <macros>
         <import>marea_macros.xml</import>
@@ -73,10 +73,10 @@
                 <option value="dataset_class">RNAseq of all samples + sample group specification</option>
             </param>
             <when value="datasets">
-                <repeat name="input_Datasets" title="RNAseq" type="data" min="2">
+                <repeat name="input_Datasets" title="RNAseq" min="2">
                     <param name="input" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" />	
                     <param name="input_name" argument="--names" type="text" label="Dataset's name:" value="Dataset" help="Defalut: Dataset" />
-	        </repeat>
+                </repeat>
             </when>
             <when value="dataset_class">
                 <param name="input_data" argument="--input_data" type="data" format="tabular, csv, tsv" label="RNAseq of all samples" />
@@ -102,9 +102,12 @@
             <discover_datasets pattern="__name_and_ext__" directory="table_out" />
         </collection>
     </outputs>
-
-    
-
+    <tests>
+        <test>
+            <param name="pValue" value="0.56"/>
+            <output name="log" file="log.txt"/>
+        </test>
+    </tests>
     <help>
 <![CDATA[
 
--- a/Marea/marea_cluster.xml	Tue Nov 13 05:12:32 2018 -0500
+++ b/Marea/marea_cluster.xml	Tue Nov 13 07:34:43 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="MaREA_cluester" name="MaREA cluster analysis">
+<tool id="MaREA_cluester" name="MaREA cluster analysis" version="1.0.0">
     <description>of Reaction Activity Scores</description>
     <macros>
         <import>marea_macros.xml</import>
@@ -11,7 +11,7 @@
         <requirement type="package">scikit-learn</requirement>
         <requirement type="package">matplotlib</requirement>
     </requirements>
-    <command>
+    <command detect_errors="exit_code">
         <![CDATA[
       	python $__tool_directory__/marea_cluster.py
         --rules_selector $cond_rule.rules_selector
@@ -39,6 +39,10 @@
             <when value="Custom">
                 <param name="Custom_rules" type="data" format="tabular, csv, tsv, xml" label="Custom rules" />
             </when>
+            <when value="HMRcore">
+            </when>
+            <when value="Recon">
+            </when>
         </conditional>
         <param name="input" argument="--data" type="data" format="tabular, csv, tsv" label="RNAseq of all samples" />
         <param name="name" argument="--name" type="text" label="Output name prefix" value="dataset" />
@@ -57,6 +61,8 @@
                     <option value="average">Average: average distance between all observations of two sets</option>
                 </param>
             </when>
+            <when value="no">
+            </when>
         </conditional>
     </inputs>
 
@@ -70,7 +76,12 @@
             <discover_datasets pattern="__name_and_ext__" directory="cluster_out" />
         </collection>
     </outputs>
-
+    <tests>
+        <test>
+            <param name="k_min" value="4"/>
+            <output name="log" file="log.txt"/>
+        </test>
+    </tests>
     <help>
 <![CDATA[