diff abromics_galaxy_json_extractor_summarize.xml @ 0:35704a6837a7 draft

planemo upload commit bb69b191fe3ce756655bf90af4d69e4472f94ba9-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/abromics_galaxy_json_extractor_summarize.xml	Sun Jun 04 17:15:36 2023 +0000
@@ -0,0 +1,35 @@
+<tool id="abromics_extractor_summarize" name="abromics_extractor_summarize" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>
+        Summarize results from abromicsextractor
+    </description>
+    <macros>
+        <import>macro.xml</import>
+    </macros>
+    <expand macro='edam'/>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="aggressive"><![CDATA[     
+        mkdir -p input_files &&
+        #for $file in $summarize_data
+            cp $file input_files &&
+        #end for
+        abromics_extract summarize input_files/* -o abromics_summary.json
+        ]]>
+    </command>
+    <inputs>
+        <param name="summarize_data" type="data" multiple="true" format="json" label="Results in Json format" help="Summarize results from abromicsextractor in json format"/>
+    </inputs>
+    <outputs>
+        <data name="summary_json" format="json" from_work_dir="abromics_summary.json" label="${tool.name} on ${on_string}: Summarized file"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1"> <!-- TEST_1 sumarize json results -->
+            <param name="summarize_data" ftype="json" value="abricate/abricate_output.json,bracken/bracken_full_output.json,plasmidfinder/plasmidfinder_output.json"/>
+            <output name="summary_json" ftype="json" value="summarize/summarize.json" compare="sim_size"/>
+        </test>
+    </tests>
+    <help><![CDATA[**What it does**
+        Summarize Json output file from abromics_galaxy_json_extractor to only one json file
+    ]]></help>
+    <expand macro="citations"/>
+</tool>