diff dram_strainer.xml @ 0:5b577e90f822 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dram_strainer.xml	Sat Dec 10 21:15:23 2022 +0000
@@ -0,0 +1,83 @@
+<tool id="dram_strainer" name="DRAM strain annotations" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>down to genes of interest</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+DRAM.py strainer
+--input_annotations '$input_annotations'
+--input_fasta '$input_fasta'
+--output_fasta '$output_fasta'
+#if $advanced.fastas:
+    --fastas '$advanced.fastas'
+#end if
+#if $advanced.scaffolds:
+    --scaffolds '$advanced.scaffolds'
+#end if
+#if $advanced.genes:
+    --genes '$advanced.genes'
+#end if
+#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 $advanced.custom_distillate:
+    --custom_distillate '$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_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">
+                <expand macro="sanitizer"/>
+            </param>
+            <param argument="--scaffolds" type="text" value="" label="Space-separated list of scaffolds to keep" help="Optional, leave blank to ignore">
+                <expand macro="sanitizer"/>
+            </param>
+            <expand macro="genes_param"/>
+            <expand macro="identifiers_param"/>
+            <expand macro="custom_distillate_param"/>
+            <!-- Broken in 3.5.1, see above -->
+            <!-- <expand macro="categories_param"/> -->
+        </section>
+    </inputs>
+    <outputs>
+        <data name="output_fasta" format="fasta"/>
+    </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="fastas" value="dataset_"/>
+            <param name="scaffolds" value="scaffold_"/>
+            <param name="identifiers" value="K15023"/>
+            <param name="custom_distillate" ftype="tabular" value="distill_custom.tabular"/>
+            <output name="output_fasta" ftype="fasta" value="strainer_output1.fasta"/>
+       </test>
+    </tests>
+    <help>
+**What it does**
+ 
+@WHATITDOESHEADER@
+
+This tool accepts a tabular file with all gene annotations from Pfam, UniProt, dbCAN and MEROPS databases produced by the
+DRAM annotate tool and strains them, further analyzing genes of interest by making trees of functional models.
+
+@CUSTOMDISTILLATEFILES@
+
+**Options**
+
+ * **Space-separated list of fastas to keep** - space-separated list of fastas to keep
+ * **Space-separated list of scaffolds to keep** - space-separated list of scaffolds to keep
+ * **Space-separated list of genes to keep** - space-separated list of genes to keep
+ * **Database identifiers** - database identifiers to keep
+
+@WHATITDOESFOOTER@
+    </help>
+    <expand macro="citations"/>
+</tool>