diff data_manager/resource_building.xml @ 0:55efb19f0b34 draft

planemo upload commit e5e768b479ddc6b36270a1b5b0443a4c80d693bc-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/resource_building.xml	Tue Oct 23 04:59:28 2018 -0400
@@ -0,0 +1,91 @@
+<tool id="data_manager_proteore_test" name="Get source files for proteore tools" version="2018.10.23" tool_type="manage_data">
+<description>
+to create or update reference files for proteore tools
+</description>
+<requirements>
+</requirements>
+<stdio>
+  <exit_code range="1:" />
+</stdio>
+<command><![CDATA[
+
+    python $__tool_directory__/resource_building.py
+    #if $database.database == "human_protein_atlas"
+        --hpa "$database.tissues"
+    #else if $database.database == "peptide_atlas"
+        --peptideatlas "$database.tissues"
+    #else if $database.database == "id_mapping"
+        --id_mapping="$database.species"
+    #end if
+    --output "$output"
+    
+]]></command>
+
+<inputs>
+    <conditional name="database">
+        <param name="database" type="select">
+            <option value="human_protein_atlas">Human Protein Atlas</option>
+            <option value="peptide_atlas">Peptide Atlas</option>
+            <option value="id_mapping">ID mapping</option>
+        </param>
+        <when value="human_protein_atlas">
+            <param name="tissues" type="select" multiple="false" label="Please select tissue">
+                <option value="HPA_normal_tissue">Normal tissue</option>
+                <option value="HPA_pathology">Pathology</option>
+                <option value="HPA_full_atlas">Full Atlas</option>
+            </param>
+        </when>
+        <when value="peptide_atlas">
+            <param name="tissues" type="select" multiple="false" label="Please select the tissue">
+                <option value="1-Human_Liver">Human liver</option>
+                <option value="2-Human_Brain">Human brain</option>
+                <option value="4-Human_Heart">Human heart</option>
+                <option value="5-Human_Kidney">Human kidney</option>
+                <option value="10-Human_Plasma">Human blood plasma</option>
+                <option value="13-Human_Urine">Human urine</option>
+                <option value="24-Human_CSF">Human cerebrospinal fluid</option>
+            </param>
+        </when>
+        <when value="id_mapping">
+            <param name="species" type="select" multiple="false" label="Please select the species">
+                <option value="human">Human (Homo sapiens)</option>
+                <option value="mouse">Mouse (Mus musculus)</option>
+                <option value="rat">Rat (Rattus norvegicus)</option>
+            </param>
+        </when>
+    </conditional>
+</inputs>
+
+<outputs>
+    <!--data format="tabular" name="output">
+        <discover_datasets pattern="(?P&lt;designation&gt;.+).tsv" ext="tabular" visible="true" assign_primary_output="true" />
+    </data-->
+    <data name="output" format="data_manager_json"/>
+</outputs>
+
+<tests>
+</tests>
+
+<help><![CDATA[
+
+TODO
+
+-----
+
+.. class:: infomark
+
+**Authors**
+
+Lisa Peru, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
+
+Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform
+
+This work has been partially funded through the French National Agency for Research (ANR) IFB project.
+
+Contact [e-mail] for any questions or concerns about the Galaxy implementation of this tool.
+ 
+    ]]></help>
+    <citations>
+    </citations>
+
+</tool>