--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phage_coast_search.xml	Thu Jul 15 16:51:26 2021 +0000
@@ -0,0 +1,62 @@
+<tool id="phage_coast_search" name="PhageCOAST - Search" version="0.1.2">
+    <description>Run a new job, and identify the closest proteomes</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <requirements>
+        <expand macro="requirements"/>
+    </requirements>
+    <command><![CDATA[
+        coast
+        @QUERY@
+        "$db"
+        --engine blast
+        --inplace_workspace
+        @AAI_FILTER@
+        @OUTPUT@
+        @QUERY_KEYWORDS@
+        @OUTPUT_FORMAT@
+        @BLAST_TAX_FILTER@
+        @BLAST_ALN_OPTIONS@
+        @GENERIC_ALN_OPTIONS@
+        -w 'http://rosalind.di.uminho.pt:6082/'
+        --email phage@coast.um
+    ]]></command>
+    <inputs>
+        <expand macro="input_query" />
+        <expand macro="merlin_db_selection"/>
+        <expand macro="blast_taxon_filter"/>
+        <expand macro="output_format"/>
+        <expand macro="aai_filter"/>
+        <section name="aln_adv" title="Advanced Alignment Settings" >
+            <expand macro="blast_aln_options"/>
+            <expand macro="generic_aln_options"/>
+        </section>
+    </inputs>
+    <outputs>
+        <expand macro="results_alignment"/>
+        <expand macro="results_report"/>
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+
+@TIME_WARNING@
+
+PhageCOAST
+==========
+
+@GENERAL_DESC@
+
+PhageCOAST is COAST adapted for the Phage Toolkit. The current build uses BLASTp as the search backend tool.
+
+@AAI_DESC@
+@TAX_FILTER_WARNING@
+@OUT_DESC@
+
+    </help>
+    <citations>
+        <expand macro="citations_coast"/>
+        <expand macro="citations_blast"/>
+    </citations>
+</tool>
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