# HG changeset patch
# User iuc
# Date 1724401048 0
# Node ID 0fc8251d3d0b9d1baaf2e0f8354c3e88856d83e0
# Parent  8a30a4bd0aaa5d1f042a45b609e07217349ba3b2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 3234c3d93fa294fa9c2c5148eae4b399d42904d8

diff -r 8a30a4bd0aaa -r 0fc8251d3d0b dram_strainer.xml
--- a/dram_strainer.xml	Tue Jul 11 23:44:41 2023 +0000
+++ b/dram_strainer.xml	Fri Aug 23 08:17:28 2024 +0000
@@ -3,10 +3,11 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
 DRAM.py strainer
---input_annotations '$input_annotations'
+--input_tsv '$input_tsv'
 --input_fasta '$input_fasta'
 --output_fasta '$output_fasta'
 #if $advanced.fastas:
@@ -21,16 +22,15 @@
 #if $advanced.identifiers:
     --identifiers '$advanced.identifiers'
 #end if
-## Broken in 3.5.1 - https://github.com/WrightonLabCSU/DRAM/issues/194
-##if $advanced.categories:
-##    --categories '$advanced.categories'
-##end if
+#if $advanced.categories:
+    --categories '$advanced.categories'
+#end if
 #if $advanced.custom_distillate:
     --custom_distillate '$advanced.custom_distillate'
 #end if
     ]]></command>
     <inputs>
-        <param argument="--input_annotations" type="data" format="tabular" label="Annotations file" help="Produced by the DRAM annotate tool"/>
+        <param argument="--input_tsv" type="data" format="tabular" label="Annotations file" help="Produced by the DRAM annotate tool"/>
         <param argument="--input_fasta" type="data" format="fasta,fasta.gz" label="FASTA file to filter"/>
         <section name="advanced" title="Advanced options" expanded="false">
             <param argument="--fastas" type="text" value="" label="Space-separated list of fastas to keep" help="Optional, leave blank to ignore">
@@ -42,8 +42,7 @@
             <expand macro="genes_param"/>
             <expand macro="identifiers_param"/>
             <expand macro="custom_distillate_param"/>
-            <!-- Broken in 3.5.1, see above -->
-            <!-- <expand macro="categories_param"/> -->
+            <expand macro="categories_param"/>
         </section>
     </inputs>
     <outputs>
@@ -51,12 +50,12 @@
     </outputs>
     <tests>
         <test expect_num_outputs="1">
-            <param name="input_annotations" ftype="tabular" value="annotated1.tabular"/>
-            <param name="input_fasta" ftype="fasta.gz" value="strainer_input_fasta1.fasta.gz"/>
+            <param name="input_tsv" value="annotated1.tabular" ftype="tabular"/>
+            <param name="input_fasta" value="strainer_input_fasta1.fasta.gz" ftype="fasta.gz"/>
             <param name="fastas" value="dataset_"/>
             <param name="scaffolds" value="scaffold_"/>
             <param name="identifiers" value="K15023"/>
-            <param name="custom_distillate" ftype="tabular" value="distill_custom.tabular"/>
+            <param name="custom_distillate" value="distill_custom.tabular" ftype="tabular"/>
             <output name="output_fasta" ftype="fasta" value="strainer_output1.fasta"/>
        </test>
     </tests>
diff -r 8a30a4bd0aaa -r 0fc8251d3d0b macros.xml
--- a/macros.xml	Tue Jul 11 23:44:41 2023 +0000
+++ b/macros.xml	Fri Aug 23 08:17:28 2024 +0000
@@ -1,10 +1,16 @@
 <macros>
-    <token name="@TOOL_VERSION@">1.3.5</token>
+    <token name="@TOOL_VERSION@">1.5.0</token>
     <!-- token name="@VERSION_SUFFIX@">0</token -->
     <token name="@PROFILE@">20.09</token>
+    <xml name="bio_tools">
+        <xrefs>
+            <xref type="bio.tools">dram</xref>
+        </xrefs>
+    </xml>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">dram</requirement>
+            <yield/>
         </requirements>
     </xml>
     <xml name="stdio">