diff macros.xml @ 3:18ece3d5bcde draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 3febcc9ba3d3717877c36bf96742209012a13ac4-dirty

--- a/macros.xml	Mon Nov 25 15:09:24 2019 -0500
+++ b/macros.xml	Tue Nov 26 15:42:14 2019 -0500
@@ -19,7 +19,7 @@
             </param>
             <when value="cached">
                 <param name="cat_builtin" type="select" label="Use a built-in CAT database" help="If the CAT database of interest is not listed, contact your Galaxy administrator">
-                    <options from_data_table="cat_databases">
+                    <options from_data_table="cat_database">
                         <filter type="sort_by" column="2" />
                         <validator type="no_options" message="No CAT database is available." />
                     </options>
@@ -77,7 +77,6 @@
       #end if
       --out_prefix 'cat_output'
 ]]></token>
-
     <xml name="custom_settings">
         <param argument="--range" type="integer" value="10" min="0" max="49" label="range"/>
         <param argument="--fraction" type="float" value="0.5" min="0" max="0.99" label="fraction"/>
@@ -115,6 +114,7 @@
             </when>
         </conditional>
     </xml>
+    <token name="@TXT2TSV@">${__tool_directory__}/tabpad.py</token>
     <token name="@ADD_NAMES@"><![CDATA[
     #if $names.add_names in ['classification','both']:
         && CAT add_names $names.only_official $names.exclude_scores 
@@ -125,14 +125,14 @@
                 -i cat_output.bin2classification.tsv
             #end if
             -o classification_names.txt
-        && @TXT2TSV@ -i classification_names.txt -o $classification_names
+        && ${__tool_directory__}/tabpad.py -i classification_names.txt -o $classification_names
     #end if
     #if $names.add_names in ['orf2lca','both']:
         && CAT add_names $names.only_official $names.exclude_scores 
             @CAT_TAXONOMY@
             -i cat_output.ORF2LCA.tsv 
             -o orf2lca_names.txt
-        && @TXT2TSV@ -i orf2lca_names.txt -o $orf2lca_names
+        && ${__tool_directory__}/tabpad.py -i orf2lca_names.txt -o $orf2lca_names
     #end if
 ]]></token>
     <xml name="summarise">
@@ -162,7 +162,7 @@
             #end if
             -i $summary_input
             -o classification_summary.txt
-        && @TXT2TSV@ -i classification_summary.txt -o $classification_summary
+        && ${__tool_directory__}/tabpad.py -i classification_summary.txt -o $classification_summary
     #end if
 ]]></token>
     
@@ -194,10 +194,6 @@
             <option value="bin2classification" selected="true">bin2classification.txt</option>
         </expand>
     </xml>
-    
-    <token name="@TXT2TSV@"><![CDATA[
-    $__tool_directory__/tabpad.py 
-]]></token>
     <xml name="outputs">
         <data name="log" format="txt" label="${bcat}.log" from_work_dir="cat_output.log">
             <filter>'log' in select_outputs or not select_outputs</filter>
@@ -265,6 +261,8 @@
         <citations>
             <citation type="doi">https://doi.org/10.1101/072868</citation>
             <citation type="doi">https://doi.org/10.1186/s13059-019-1817-x</citation>
+            <citation type="doi">https://doi.org/10.1038/nmeth.3176</citation>
+            <citation type="doi">https://doi.org/10.1186/1471-2105-11-119</citation>
             <yield />
         </citations>
     </xml>