Mercurial > repos > public-health-bioinformatics > screen_abricate_report

diff screen_abricate_report.xml @ 0:b2d56a44a872 draft

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"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
author public-health-bioinformatics
date Thu, 31 Oct 2019 15:43:15 -0400
parents
children 4f963b583186
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/screen_abricate_report.xml	Thu Oct 31 15:43:15 2019 -0400
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+<tool id="screen_abricate_report" name="Screen Abricate Report" version="0.1.0">
+    <description>Screens an abricate report for genes of interest</description>
+    <requirements>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        '${__tool_directory__}/screen_abricate_report.py'
+             '${abricate_report}'
+             --screening_file '${screening_file.fields.path}'
+             --screened_report '${screened_report}'
+             --gene_detection_status '${gene_detection_status}'
+    ]]></command>
+    <inputs>
+        <param name="abricate_report" type="data" format="tabular" />
+        <param name="screening_file" type="select" format="tabular">
+	    <options from_data_table="abricate_report_screening_files">
+	        <validator type="no_options" message="No abricate report screening files are available" />
+            </options>
+	</param>
+    </inputs>
+    <outputs>
+        <data name="screened_report" type="data" format="tabular" label="Screened Abricate Report" />
+        <data name="gene_detection_status" type="data" format="tabular" label="Gene Detection Status" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="screening_file" value="test_entry"/>
+            <param name="abricate_report" value="SAMN13042171_abricate_report.tsv"/>
+	    <output name="screened_report" file="SAMN13042171_abricate_report_screened.tsv" ftype="tabular"/>
+	    <output name="gene_detection_status" file="SAMN13042171_gene_detection_status.tsv" ftype="tabular"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+    ]]></help>
+    <citations>
+    </citations>
+</tool>