diff humann2_regroup_table.xml @ 1:1d141730ec69 draft

planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee

--- a/humann2_regroup_table.xml	Mon Mar 13 12:38:02 2017 -0400
+++ b/humann2_regroup_table.xml	Tue Aug 01 07:55:06 2017 -0400
@@ -1,25 +1,24 @@
 <tool id="humann2_regroup_table" name="Regroup" version="@WRAPPER_VERSION@.0">
-    <description> a HUMAnN2 generated table by features</description>
+    <description>a HUMAnN2 generated table by features</description>
     <macros>
         <import>humann2_macros.xml</import>
     </macros>
     <expand macro="requirements"/>
     <expand macro="version"/>
     <command detect_errors="exit_code"><![CDATA[
-        humann2_regroup_table
-            --input '$input'
-            -o '$output_table'
-            --function '$function'
-
-            #if $built_in.built_in_test == "true":
-                --groups '$built_in.gene_family_groups.groups'
-            #else:
-                --custom '$built_in.custom'
-                $built_in.reversed
-            #end if  
-
-            --ungrouped '$ungrouped'
-            --protected '$protected'
+humann2_regroup_table
+    --input '$input'
+    -o '$output_table'
+    --function '$function'
+    #if $built_in.built_in_test == "true":
+        --groups '$built_in.gene_family_groups.groups'
+    #else:
+        --custom '$built_in.custom'
+        $built_in.reversed
+    #end if
+    --precision '$precision'
+    --ungrouped '$ungrouped'
+    --protected '$protected'
     ]]></command>
     <inputs>
         <param argument="--input" type="data" format="tsv,tabular" label="Gene/pathway table"/>
@@ -40,23 +39,23 @@
                     </param>
                     <when value="uniref50">
                         <param name="groups" type="select" label="Grouping options" help="(--groups)">
-                            <option value="uniref50_go">UniRef50 gene families into GO</option>
+                            <!--<option value="uniref50_go">UniRef50 gene families into GO</option>
                             <option value="uniref50_ko">UniRef90 gene families into KEGG Orthogroups (KOs)</option>
                             <option value="uniref50_eggnog">UniRef50 gene families into eggNOG</option>
                             <option value="uniref50_pfam">UniRef50 gene families into PFAM</option>
                             <option value="uniref50_level4ec">UniRef50 gene families into level4ec</option>
-                            <option value="uniref50_infogo1000">UniRef50 gene families into InfoGO1000</option>
+                            <option value="uniref50_infogo1000">UniRef50 gene families into InfoGO1000</option>-->
                             <option value="uniref50_rxn">UniRef50 gene families into metacyc reactions</option>
                         </param>
                     </when>
                     <when value="uniref90">
                         <param name="groups" type="select" label="Grouping options" help="(--groups)">
-                            <option value="uniref90_go">UniRef90 gene families into GO</option>
+                            <!--<option value="uniref90_go">UniRef90 gene families into GO</option>
                             <option value="uniref90_ko">UniRef90 gene families into KEGG Orthogroups (KOs)</option>
                             <option value="uniref90_eggnog">UniRef90 gene families into eggNOG</option>
                             <option value="uniref90_pfam">UniRef90 gene families into PFAM</option>
                             <option value="uniref90_level4ec">UniRef90 gene families into level4ec</option>
-                            <option value="uniref90_infogo1000">UniRef90 gene families into InfoGO1000</option>
+                            <option value="uniref90_infogo1000">UniRef90 gene families into InfoGO1000</option>-->
                             <option value="uniref90_rxn">UniRef90 gene families into metacyc reactions</option>
                         </param>
                     </when>
@@ -75,32 +74,35 @@
         <data format="tsv" name="output_table" label="${tool.name} on ${on_string}: Regrouped table" />
     </outputs>
     <tests>
-        <test>
+        <!--<test>
             <param name="input" value="demo_genefamilies.tsv"/>
             <param name="function" value="sum"/>
             <param name="built_in_test" value="true"/>
             <param name="gene_family_type" value="uniref90"/>
             <param name="groups" value="uniref90_infogo1000"/>
+            <param name="precision" value="3"/>
             <param name="ungrouped" value="Y"/>
             <param name="protected" value="Y"/>
             <output name="output_table" file="regrouped_gene_families_to_infogo1000.tsv"/>
-        </test>
-        <test>
+        </test>-->
+        <!--<test>
             <param name="input" value="demo_genefamilies.tsv"/>
             <param name="function" value="mean"/>
             <param name="built_in_test" value="true"/>
             <param name="gene_family_type" value="uniref90"/>
             <param name="groups" value="uniref90_ko"/>
+            <param name="precision" value="3"/>
             <param name="ungrouped" value="Y"/>
             <param name="protected" value="Y"/>
             <output name="output_table" file="regrouped_gene_families_to_ko.tsv"/>
-        </test>
+        </test>-->
         <test>
             <param name="input" value="demo_genefamilies.tsv"/>
             <param name="function" value="sum"/>
             <param name="built_in_test" value="true"/>
             <param name="gene_family_type" value="uniref90"/>
             <param name="groups" value="uniref90_rxn"/>
+            <param name="precision" value="3"/>
             <param name="ungrouped" value="Y"/>
             <param name="protected" value="Y"/>
             <output name="output_table" file="regrouped_gene_families_to_rxn.tsv"/>