diff tn93_filter.xml @ 0:ba95715078c9 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tn93_filter.xml	Fri Apr 23 03:05:08 2021 +0000
@@ -0,0 +1,47 @@
+<tool id="tn93_filter" name="TN93 Filter" version="@VERSION@">
+    <description>- remove sequences from a reference that are within a given distance of of a cluster</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@VERSION@">tn93</requirement>
+        <requirement type="package" version="1.70">biopython</requirement>
+    </requirements>
+    <version_command><![CDATA[tn93 --version]]></version_command>
+    <command detect_errors="exit_code"><![CDATA[
+    cat '$reads' > filtered_msa.fa &&
+    tn93 -o pairwise.csv -s filtered_msa.fa -t $threshold '$clusters' &&
+    python '$__tool_directory__/tn93_filter.py' --reference '$reference'
+        --distances pairwise.csv
+        --reads filtered_msa.fa
+        --clusters '$clusters'
+    ]]></command>
+    <inputs>
+        <param name="reads" type="data" format="fasta" label="Aligned reads" />
+        <param name="reference" type="data" format="fasta" label="Reference sequence" />
+        <param name="clusters" type="data" format="fasta" label="FASTA file with compressed clusters" />
+        <param name="threshold" type="float" value="0.015" label="Pairwise distance threshold" />
+    </inputs>
+    <outputs>
+        <data name="filtered_reference" format="fasta" from_work_dir="filtered_msa.fa" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="reads" value="filter-in1-reads.fa" />
+            <param name="reference" value="filter-in1-reference.fa" />
+            <param name="clusters" value="filter-in1-clusters.fa" />
+            <param name="threshold" value="0.35" />
+            <output name="filtered_reference" file="filter-out1.fasta" ftype="fasta" />
+        </test>
+    </tests>
+    <help><![CDATA[
+TN93-Filter
+===========
+
+Removes aligned sequences that are within a given distance from a reference
+sequence using the 1993 Tamura-Nei distance calculation.
+]]></help>
+    <expand macro="citations">
+        <citation type="doi">10.1093/oxfordjournals.molbev.a040023</citation>
+    </expand>
+</tool>