Mercurial > repos > jjohnson > contig_annotation_tool

diff cat_add_names.xml @ 0:ad7507073c3f draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
author jjohnson
date Sun, 24 Nov 2019 21:56:00 -0500
parents
children 226949352e31
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cat_add_names.xml	Sun Nov 24 21:56:00 2019 -0500
@@ -0,0 +1,41 @@
+<tool id="cat_add_names" name="CAT add_names" version="@VERSION@.0">
+    <description>annotate with taxonomic classification</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <command detect_errors="exit_code"><![CDATA[
+    CAT add_names -i '$input'
+    @CAT_TAXONOMY@
+    @ADD_NAMES_OPTIONS@
+    -o output_names.txt
+    && @TXT2TSV@ -i output_names.txt -o $output
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="tabular,txt" label="classification.txt or ORF2LCA.txt"/>
+        <expand macro="cat_db" />
+        <expand macro="add_names_options" />
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" ftype="tabular" value="test_contig.contig2classification.txt"/>
+            <expand macro="test_catdb"/>
+            <output name="output">
+                <assert_contents>
+                    <has_text text="Firmicutes" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+**CAT/BAT add_names** 
+Add names for the NCBI taxomy IDs.
+
+@COMMON_HELP@
+    ]]></help>
+    <expand macro="citations" />
+</tool>