diff phavip.xml @ 0:f5dba8d92cf0 draft default tip

planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 3c8e23e1dea22f625fb6f77ae61e1f4b605aaae2

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phavip.xml	Tue Nov 12 09:32:52 2024 +0000
@@ -0,0 +1,93 @@
+<tool id="phabox_phavip" name="PhaBOX phavip" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.1" license="MIT">
+    <description>Protein annotation</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <xrefs>
+        <xref type="bio.tools">phabox</xref>
+    </xrefs>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">phabox</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        phabox2 --task phavip
+            @GENERAL@
+    ]]></command>
+    <inputs>
+        <expand macro="general"/>
+        <param name="supp_outputs" type="select" optional="true" label="Supplementary outputs">
+            <option value="gene_annotation">Gene annotation</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="out" format="tabular" from_work_dir="output/final_prediction/phavip_prediction.tsv"/>
+        <data name="phavip_annotation" format="tabular" from_work_dir="output/final_prediction/phavip_supplementary/gene_annotation.tsv" label="${tool.name} on ${on_string}: Gene annotation">
+            <filter>supp_outputs and "gene_annotation" in supp_outputs</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="dbdir" value="phaboxdb"/>
+            <param name="contigs" value="example_contigs.fa"/>
+            <output name="out">
+                <assert_contents>
+                    <has_line line="Accession&#9;Length&#9;Protein_num&#9;Annotated_num&#9;Annotation_rate"/>
+                    <has_n_lines n="11"/>
+                    <has_n_columns n="5"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="2">
+            <param name="dbdir" value="phaboxdb"/>
+            <param name="contigs" value="example_contigs.fa"/>
+            <param name="supp_outputs" value="gene_annotation"/>
+            <output name="out">
+                <assert_contents>
+                    <has_line line="Accession&#9;Length&#9;Protein_num&#9;Annotated_num&#9;Annotation_rate"/>
+                    <has_n_lines n="11"/>
+                    <has_n_columns n="5"/>
+                </assert_contents>
+            </output>
+            <output name="phavip_annotation">
+                <assert_contents>
+                    <has_line line="Genome&#9;ORF&#9;Start&#9;End&#9;Strand&#9;GC&#9;Annotation&#9;pident&#9;coverage"/>
+                    <has_n_lines n="171"/>
+                    <has_n_columns n="9"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+Please note that running task end_to_end, phamer, phagcn, phatyp, and cherry, will automatically run phavip.
+The output files are the same but the supplementary files will be dumped into the corresponding task.
+
+
+@COMMON_INPUT_DOC@
+
+**Output**
+
+@COMMON_OUTPUT_DOC@
+- Protein_num: total number of predicted proteins.
+- Annotated_num: number of proteins that have significant alignments.
+- Annotation_rate: percentage of proteins that have annotations.
+
+In addition the gene annotation itself can be produced:
+
+- Genome: the accession or the name of the input contigs.
+- ORF: the ID of the translated protein.
+- Start: start position on the genome.
+- End: end position on the genome.
+- Strand: forward (1) or backward(-1).
+- GC: GC content.
+- Annotation: the annotation of the proteins.
+
+Please note that there are two kinds of hypothetical protein:
+
+- hypothetical protein (no hit): a protein has no alignment results to the reference database.
+- hypothetical protein (no hit): a protein has alignment results but the annotation is "hypothetical protein"
+
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
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