diff cpt_blast_to_xmfa/blast2pxmfa.xml @ 0:84761ea60231 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cpt_blast_to_xmfa/blast2pxmfa.xml	Fri Jul 01 13:36:11 2022 +0000
@@ -0,0 +1,59 @@
+<?xml version="1.0"?>
+<tool id="edu.tamu.cpt.blast.blast2pxmfa" name="Blast TSV to Protein XMFA" version="1.0">
+  <description></description>
+  <macros>
+    <import>macros.xml</import>
+    <import>cpt-macros.xml</import>
+  </macros>
+  <expand macro="requirements">
+    <requirement type="package" version="2.1">clustalw</requirement>
+  </expand>
+  <command detect_errors="aggressive"><![CDATA[
+$__tool_directory__/blast2pxmfa.py
+@BLAST_TSV@
+$fasta
+$gff3
+$output
+]]></command>
+  <inputs>
+    <expand macro="blast_tsv" />
+    <expand macro="gff3_with_fasta" />
+  </inputs>
+  <outputs>
+    <data format="pxmfa" name="output"/>
+  </outputs>
+  <tests>
+      <test>
+          <param name="blast_tsv" value="results.tsv"/>
+          <param name="fasta" value="related.fa"/>
+          <param name="gff3" value="related.gbk.gff"/>
+          <output name="output" file="cbk.xmfa">
+                <assert_contents>
+			    <has_n_lines n="7547" delta="100"/>
+		</assert_contents>
+          </output>
+      </test>
+  </tests>
+  <help><![CDATA[
+.. class:: warningmark
+
+You likely should first filter your data first using the `Blast Tabular Dice
+Filter tool <root?tool_id=edu.tamu.cpt.blast.blasttab_dice_filter>`__.
+
+**What it does**
+
+This tool processes BLAST Tabular results into a *protein* XMFA file. This
+permits visualizing the data with CPT developed XMFA based tooling.
+
+**How it works**
+
+The tool works by:
+
+- taking the set of blast results
+- clustering them according to relationships detected by blast
+- running ClustalW to generate a set of alignments for each cluster
+- outputting those clusters in the XMFA format
+]]></help>
+    <citations>
+    </citations>
+</tool>