diff cat_contigs.xml @ 0:11a61934bfb3 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cat_contigs.xml	Tue Dec 10 16:05:34 2019 -0500
@@ -0,0 +1,92 @@
+<tool id="cat_contigs" name="CAT contigs" 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 contigs 
+    -c '$contigs_fasta'
+    @CAT_DB@
+    @USE_INTERMEDIATES@
+    @CUSTOM_SETTINGS@
+    @DIAMOND_OPTIONS@
+    && @TXT2TSV@ *.ORF2LCA.txt *.contig2classification.txt
+    @ADD_NAMES@
+    @SUMMARISE@
+    ]]></command>
+    <inputs>
+        <param name="contigs_fasta" type="data" format="fasta" label="Contigs fasta"/>
+        <expand macro="cat_db" />
+        <expand macro="use_intermediates" />
+        <expand macro="custom_settings" />
+        <expand macro="diamond_options" />
+        <expand macro="add_names" />
+        <expand macro="summarise" />
+        <expand macro="select_cat_outputs" />
+    </inputs>
+    <outputs>
+        <expand macro="outputs" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="contigs_fasta" ftype="fasta" value="contigs.fasta"/>
+            <expand macro="test_catdb"/>
+            <param name="select_outputs" value="contig2classification"/>
+            <output name="contig2classification">
+                <assert_contents>
+                    <has_text text="contig_38063" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="contigs_fasta" ftype="fasta" value="contigs.fasta"/>
+            <expand macro="test_catdb"/>
+            <param name="select_outputs" value="predicted_proteins_faa"/>
+            <conditional name="names">
+                <param name="add_names" value="both"/>
+            </conditional>
+            <param name="summarise" value="classification"/>
+            <output name="predicted_proteins_faa">
+                <assert_contents>
+                    <has_text text=">contig_9952" />
+                </assert_contents>
+            </output>
+            <output name="orf2lca_names">
+                <assert_contents>
+                    <has_text text="Listeria" />
+                </assert_contents>
+            </output>
+            <output name="classification_summary">
+                <assert_contents>
+                    <has_text text="Listeria" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+**CAT contigs**
+
+Classifiy metagenomics contigs.
+
+@COMMON_HELP@
+
+@OUTPUTS_HELP@
+
+
+**CAT contigs**
+
+Run Contig Annotation Tool (CAT).
+
+Required arguments:
+  -c, --contigs_fasta    Path to contigs fasta file.
+  -d, --database_folder  Path to folder that contains database files.
+  -t, --taxonomy_folder  Path to folder that contains taxonomy files.
+
+
+@OPTIONS_HELP@
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>