diff tools/refseq_parser/refseq_parser.xml @ 0:45533fb9d2f4 draft default tip

Primary version

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/refseq_parser/refseq_parser.xml	Tue Sep 04 02:49:49 2018 -0400
@@ -0,0 +1,38 @@
+<tool id="parse_refseq_masher" name="Parse refseq_masher matches collection" version="0.1.0">
+    <description>and output a list of outliers</description>
+    <requirements>
+        <requirement type="package" version="3.1.1">ete3</requirement>
+    </requirements>
+    <command><![CDATA[
+        $__tool_directory__/refseq_parser $db $taxid #for $report in $reports# $report #end for#
+    ]]></command>
+    <inputs>
+        <param name="db" type="data" format="sqlite" label="(ETE3) Taxonomy Database"/>
+        <param name="reports" type="data" format="tabular" label="Refseq_masher report" help="" optional="false" multiple="True" />
+        <param name="taxid" type="integer" value="0" label="Taxonomic ID of target taxonomic rank" optional="false"/>
+    </inputs>
+    <outputs>
+        <data name="output_file" label="Outliers from dataset" format="txt" from_work_dir="outlier_list.txt"/>
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="report" value="test.tsv" ftype="tabular" />
+            <output name="output" value="output.tsv" ftype="tabular" />
+        </test>
+    </tests>
+
+    <help><![CDATA[
+        Parses refseq_masher output and returns a list of outliers based on two criteria:
+
+        1. If the mash match is not the same or a descendant of the target taxonomic ID
+        2. If the distance between the match and the sample is >0.05
+
+        Command line:
+        refseq_parser <ETE3 taxonomy database> <taxid> [input refseq_masher reports ...]
+    ]]></help>
+
+    <citations>
+        Manuscript in preparation
+    </citations>
+</tool>