diff plasclass.xml @ 0:8a97b4648968 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasclass commit 8cec6b221914a96102b6d09b51e95626d43a9f8c
author iuc
date Thu, 31 Jul 2025 13:21:38 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/plasclass.xml	Thu Jul 31 13:21:38 2025 +0000
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+<tool id="plasclass" name="PlasClass" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
+    <description>for plasmid/chromosome classification</description>
+    <macros>
+        <token name="@TOOL_VERSION@">0.1.1</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@PROFILE@">24.1</token>
+    </macros>
+    <xrefs>
+        <xref type="bio.tools">PlasClass</xref>
+    </xrefs>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">plasclass</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+classify_fasta.py
+    --fasta '$fasta'
+    --outfile '$outfile'
+    --num_processes "\${GALAXY_SLOTS:-1}"
+    ]]></command>
+    <inputs>
+        <param argument="--fasta" type="data" format="fasta" label="Sequences to be classified"/>
+    </inputs>
+    <outputs>
+        <data name="outfile" format="tabular"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="fasta" value="test.fa"/>
+            <output name="outfile" ftype="tabular">
+                <assert_contents>
+                    <has_text text="EDGE_1998488_length_236_cov_0.817680"/>
+                    <has_n_lines n="62"/>
+                    <has_n_columns n="2"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+**What it does**
+
+PlasClass is a cutting-edge plasmid classifier designed to address the challenges of distinguishing between 
+plasmid and bacterial genome sequences in metagenomic and isolate assemblies. Many bacteria contain plasmids, 
+but identifying contigs that originate from plasmids can be particularly difficult in metagenomic assembly, 
+where the origin of contigs is often unknown. 
+
+**Input**
+
+- FASTA file with sequences to classify
+
+**Output**
+
+- A tabular separated file with each line containing a sequence header and the corresponding score. The sequences are in the same order as in the input FASTA file.
+
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1371/journal.pcbi.1007781</citation>
+    </citations>
+</tool>