diff data_manager/interproscan.xml @ 0:e93e32359b67 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/interproscan.xml	Mon Nov 15 17:21:22 2021 +0000
@@ -0,0 +1,69 @@
+<tool id="data_manager_interproscan" name="InterProScan data manager" version="0.0.1" tool_type="manage_data" profile="20.01">
+    <requirements>
+        <requirement type="package" version="5.52-86.0">interproscan</requirement>
+        <requirement type="package" version="2.26.0">requests</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+python '$__tool_directory__/interproscan.py'
+$partial_data
+--version '$version'
+'interproscan'
+'${output_file}'
+    ]]></command>
+    <inputs>
+        <param name="partial_data" type="hidden" value="" help="Used for testing"/>
+        <param name="version" type="text" value="" label="Version to download" help="Leave empty to download the latest version">
+            <validator type="regex" message="Version must be a valid InterProScan version (e.g. 5.52-86.0)">^([0-9]+\.[0-9]+-[0-9]+\.[0-9]+)?$</validator>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output_file" format="data_manager_json"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="partial_data" value="--partial"/>
+            <output name="output_file">
+                <assert_contents>
+                    <has_text text="InterProScan 5."/>
+                    <has_text text='"interproscan_version": "5.'/>
+                </assert_contents>
+            </output>
+            <assert_stdout>
+                <has_text text="Pressed and indexed" />
+                <has_text text="Completed indexing the hmm models" />
+            </assert_stdout>
+        </test>
+        <test>
+            <param name="partial_data" value="--partial"/>
+            <param name="version" value="5.51-85.0"/>
+            <output name="output_file">
+                <assert_contents>
+                    <has_text text="InterProScan 5.51-85.0"/>
+                    <has_text text='"interproscan_version": "5.51-85.0'/>
+                </assert_contents>
+            </output>
+            <assert_stdout>
+                <has_text text="Pressed and indexed" />
+                <has_text text="Completed indexing the hmm models" />
+            </assert_stdout>
+        </test>
+        <test expect_failure="true">
+            <param name="partial_data" value="--partial"/>
+            <param name="version" value="xxxx"/>
+            <assert_stderr>
+                <has_text text="Version must be a valid InterProScan version" />
+            </assert_stderr>
+        </test>
+    </tests>
+    <help><![CDATA[
+        This data managers fetches data from EBI FTP server for the InterProScan
+        annotation tool and updates the InterProScan data table.
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btu031</citation>
+        <citation type="doi">10.7717/peerj.167</citation>
+        <citation type="doi">10.1093/bioinformatics/17.9.847</citation>
+        <citation type="doi">10.1093/nar/gki442</citation>
+        <citation type="doi">10.1093/nar/gkn785</citation>
+    </citations>
+</tool>