diff dram_distill.xml @ 0:f9a3ea1c618c 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_distill.xml	Sat Dec 10 21:15:05 2022 +0000
@@ -0,0 +1,93 @@
+<tool id="dram_distill" name="DRAM distill" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>metagenome-assembled-genomes (MAGs)</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <command detect_errors="exit_code"><![CDATA[
+DRAM.py distill
+--input_file '$input_file'
+--output_dir 'output_dir'
+#if $rrna_path:
+    --rrna_path '$rrna_path'
+#end if
+#if $trna_path:
+    --trna_path '$trna_path'
+#end if
+--groupby_column '$groupby_column'
+#if $custom_distillate:
+    --custom_distillate '$custom_distillate'
+#end if
+$distillate_gene_names
+--genomes_per_product $genomes_per_product
+&& test -f 'output_dir/genome_stats.tsv' && mv 'output_dir/genome_stats.tsv' '$output_genome_stats' || echo 'No genome_stats.tsv output produced'
+&& test -f 'output_dir/metabolism_summary.xlsx' && mv 'output_dir/metabolism_summary.xlsx' '$output_metabolism_summary' || echo 'No metabolism_summary.xlsx output produced'
+&& test -f 'output_dir/product.html' && mv 'output_dir/product.html' '$output_product_html' || echo 'No product.html output produced'
+&& test -f 'output_dir/product.tsv' && mv 'output_dir/product.tsv' '$output_product_tsv' || echo 'No product.tsv output produced'
+    ]]></command>
+    <inputs>
+        <expand macro="input_file_param"/>
+        <param argument="--rrna_path" type="data" format="tabular" optional="true" label="rRNA file" help="Produced by the DRAM annotate tool (optional, leave blank to ignore)"/>
+        <param argument="--trna_path" type="data" format="tabular" optional="true" label="tRNA file" help="Produced by the DRAM annotate tool (optional, leave blank to ignore)"/>
+        <param argument="--groupby_column" type="text" value="fasta" label="Column from annotations to group as organism units">
+            <expand macro="sanitizer"/>
+        </param>
+        <expand macro="custom_distillate_param"/>
+        <param argument="--distillate_gene_names" type="boolean" truevalue="--distillate_gene_names" falsevalue="" checked="false" label="Give names of genes instead of counts in genome metabolism summary?"/>
+        <param argument="--genomes_per_product" type="integer" value="1000" min="0" label="Number of genomes per product.html output"/>
+    </inputs>
+    <outputs>
+        <data name="output_genome_stats" format="tabular" label="${tool.name} on ${on_string}: genome stats"/>
+        <data name="output_metabolism_summary" format="xlsx" label="${tool.name} on ${on_string}: metabolism summary"/>
+        <data name="output_product_html" format="html" label="${tool.name} on ${on_string}: product html"/>
+        <data name="output_product_tsv" format="tabular" label="${tool.name} on ${on_string}: product_tsv"/>
+    </outputs>
+    <tests>
+        <!--
+        These tests succeed, but the outputs are empty because the DRAM
+        database is not available in the test environment. This warning
+        is displayed in the log...
+        warnings.warn('Database does not exist at path %s' % self.description_loc)
+        ...and this exception is raised:
+        ValueError: Invalid file path or buffer object type: <class 'NoneType'
+        -->
+        <test expect_failure="true">
+            <param name="input_file" ftype="tabular" value="annotated1.tabular"/>
+            <param name="rrna_path" ftype="tabular" value="input_distill_rrna1.tabular"/>
+            <param name="trna_path" ftype="tabular" value="input_distill_trna1.tabular"/>
+            <param name="custom_distillate" ftype="tabular" value="distill_custom.tabular"/>
+            <assert_stderr>
+                <has_text text="Traceback"/>
+            </assert_stderr>
+        </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 curates them into useful functional categories, creating genome statistics and metabolism summary
+files.  The genome statistics provides most genome quality information required for MIMAG standards, including GTDB-tk
+and checkM information if provided by the user. The summarised metabolism table includes the number of genes with specific
+metabolic function identifiers (KO, CAZY ID, etc) for each genome with information obtained from multiple databases.
+
+@CUSTOMDISTILLATEFILES@
+
+This tool produces the following outputs.
+
+* **Distillate**
+
+  * **genome stats** - a tabular file with genome statistics for all input genomes including all statistics required by recently defined MIMAG standards
+  * **metabolism summary** - an Excel file with metabolism summary of all input genomes which gives gene counts of functional and structural genes across a wide variety of metabolisms
+
+* **Liquor**
+
+  * **product html** - an html file containing an interactive heatmap showing coverage of pathways, the coverage of electron transport chain components and the presence of selected metabolic functions
+  * **product tsv** - a tabular file with corresponding genes for the html heatmap
+
+@WHATITDOESFOOTER@
+    </help>
+    <expand macro="citations"/>
+</tool>