diff coast_report.xml @ 0:44bd59ba0858 draft

"planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/coast_report.xml	Thu Jul 15 16:52:36 2021 +0000
@@ -0,0 +1,72 @@
+<tool id="coast_report" name="COAST - Report generator" version="0.1.2">
+    <description>Recreate the report and outputs with different settings</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <requirements>
+        <expand macro="requirements"/>
+    </requirements>
+    <command><![CDATA[
+        coast_report
+        @QUERY@
+        "$result_file"
+        @AAI_FILTER@
+        @HYPO_FILTER@
+        @OUTPUT@
+        @QUERY_KEYWORDS@
+        @OUTPUT_FORMAT@
+    ]]></command>
+    <inputs>
+<!--Select the kind of input to be used-->
+        <expand macro="input_query" />
+        <param name="result_file" type="data" format="tabular" label="Load previous COAST generated alignment file"/>
+<!--Outputs selection-->
+        <expand macro="output_format"/>
+<!--AAI filtering score-->
+        <expand macro="aai_filter"/>
+        <expand macro="hypothetical_filter"/>
+    </inputs>
+    <outputs>
+        <expand macro="results_report"/>
+    </outputs>
+    <tests>
+        <test>
+          <param name="query_file" value="protein.faa" />
+          <param name="result_file" value="blast_results.tab" />
+          <param name="aai" value="10" />
+          <param name="min_cov" value="50" />
+          <param name="min_id" value="40" />
+          <output name="coast_report" file="report/coast_report.html"  lines_diff="4"/>
+          <output name="bh_results" file="report/bh_results.tab" />
+          <output name="coast_results" file="report/coast_results.tab" />
+        </test>
+        <test>
+          <param name="query_file" value="protein.faa" />
+          <param name="result_file" value="blast_results.tab" />
+          <param name="aai" value="20" />
+          <param name="min_cov" value="30" />
+          <param name="min_id" value="30" />
+          <param name="hypothetical" value="true" />
+          <output name="coast_report" file="report_h/coast_report.html"  lines_diff="4"/>
+          <output name="bh_results" file="report_h/bh_results.tab" />
+          <output name="coast_results" file="report_h/coast_results.tab" />
+        </test>
+    </tests>
+    <help>
+
+@HYPO_FILTER_WARNING@
+
+COAST Report
+============
+
+Generate COAST reports and outputs based in different parameters, using the tabular alignment output produced by COAST Search jobs.
+
+@GENERAL_DESC@
+@AAI_DESC@
+@OUT_DESC@
+
+    </help>
+    <citations>
+        <expand macro="citations_coast"/>
+    </citations>
+</tool>
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