diff tooldistillator_summarize.xml @ 0:05c1bcba20c9 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tooldistillator_summarize.xml	Tue Apr 30 08:41:54 2024 +0000
@@ -0,0 +1,50 @@
+<tool id="tooldistillator_summarize" name="ToolDistillator Summarize" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>
+        Aggregate several JSON reports from ToolDistillator
+    </description>
+    <macros>
+        <import>macro.xml</import>
+    </macros>
+    <expand macro="biotools"/>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="aggressive"><![CDATA[
+tooldistillator --version &&
+mkdir -p input_files &&
+#for $file in $summarize_data
+cp '$file' ./input_files/ &&
+#end for
+tooldistillator 
+    summarize
+    input_files/*
+    -o summary.json
+]]>
+    </command>
+    <inputs>
+        <param name="summarize_data" type="data" multiple="true" format="json" label="Results in Json format" help="Summarize results from tooldistillator in json format"/>
+    </inputs>
+    <outputs>
+        <data name="summary_json" format="json" from_work_dir="summary.json" label="${tool.name} on ${on_string}"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1"> <!-- TEST_1 sumarize json results -->
+            <param name="summarize_data" ftype="json" value="summarize/abricate_output.json,summarize/bracken_full_output.json,summarize/plasmidfinder_output.json"/>
+            <output name="summary_json" ftype="json" value="summarize/summarize.json" compare="sim_size">
+                <assert_contents>
+                    <has_text_matching expression="Enterococcus.*faecalis" />
+                    <has_json_property_with_text property="name" text="plasmid_hit" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools.
+
+
+
+This tool here summarize JSON output file from ToolDistillator to only one JSON file
+    ]]></help>
+    <expand macro="citations"/>
+</tool>