diff blast2pxmfa.xml @ 1:c66d6978a5f8 draft

planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/blast2pxmfa.xml	Mon Jun 05 02:14:17 2023 +0000
@@ -0,0 +1,58 @@
+<tool id="edu.tamu.cpt.blast.blast2pxmfa" name="Blast TSV to Protein XMFA" version="1.0">
+  <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>