diff dram_strainer.xml @ 3:f081f73cc0be draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 3234c3d93fa294fa9c2c5148eae4b399d42904d8

--- a/dram_strainer.xml	Fri Feb 09 21:35:54 2024 +0000
+++ b/dram_strainer.xml	Fri Aug 23 08:18:27 2024 +0000
@@ -7,7 +7,7 @@
     <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:
@@ -22,16 +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">
@@ -43,8 +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>
@@ -52,12 +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>