diff humann2_rename_table.xml @ 0:dd4b5b9daf6b draft

planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/humann2_rename_table.xml	Mon Mar 13 12:37:08 2017 -0400
@@ -0,0 +1,60 @@
+<tool id="humann2_rename_table" name="Rename" version="@WRAPPER_VERSION@.0">
+    <description>features of a HUMAnN2 generated table</description>
+    <macros>
+        <import>humann2_macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version"/>
+    <command detect_errors="exit_code"><![CDATA[
+        humann2_rename_table
+            --input '$input'
+            -o '$output_table'
+            --names '$names'
+            $simplify 
+            #if $custom
+                --custom '$custom'
+            #end if
+    ]]></command>
+    <inputs>
+        <param argument="--input" type="data" format="tsv,tabular" label="Gene/pathway table"/>
+        <param argument="--names" type="select" label="Table features that can be renamed">
+            <option value="metacyc-rxn" selected="true">MetaCyc reactions</option>
+            <option value="metacyc-pwy">MetaCyc pathways</option>
+            <option value="infogo1000">InfoGO1000</option>
+            <option value="uniref90">UniRef90</option>
+            <option value="kegg-module">KEGG Module</option>
+            <option value="ec">Enzyme commision (EC)</option>
+            <option value="go">Gene Ontology (GO)</option>
+            <option value="pfam">PFAM</option>
+            <option value="eggnog">eggNOG</option>
+            <option value="uniref50">UniRef50</option>
+            <option value="kegg-pathway">KEGG Pathway</option>
+            <option value="kegg-orthology">KEGG Orthology</option>
+        </param>
+        <param argument="--simplify" type="boolean" checked="false" truevalue="--simplify" falsevalue="" label="Remove non-alphanumeric characters from names?"/>
+        <param argument="--custom" type="data" format="tsv" label="Mapping file" help="The mapping file must be tabular format file with two tab-separated columns. The first column must contain the value you want to modify and the second contain the new value" optional="true"/>
+    </inputs>
+    <outputs>
+        <data format="tsv" name="output_table" label="${tool.name} on ${on_string}: Renamed table" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="demo_genefamilies.tsv"/>
+            <param name="names" value="uniref90" />
+            <param name="simplify" value=""/>
+            <output name="output_table">
+                <assert_contents>
+                    <has_text text="UniRef90_R6I0Z3: NO_NAME|g__Bacteroides.s__Bacteroides_vulgatus" />
+                    <has_text text="UniRef90_I9RGY5: Tape measure domain-containing protein|g__Bacteroides.s__Bacteroides_dorei" />
+                    <has_text text="UniRef90_C3RF26: HRDC domain protein" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+@HELP_HEADER@
+
+Rename HUMAnN2 table features is a tool for renaming table features given a custom mapping. The mapping file must be tabular format file with two tab-separated columns. The first column must contain the value you want to modify and the second contain the new valu
+    ]]></help>
+    <expand macro="citations"/>
+</tool>