Mercurial > repos > p.lucas > taxid_genusexpand_taxid2acc

changeset 3:4a907a27ca5a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded 13 03 23 Missing ".py" element when the script is called
author p.lucas
date Mon, 13 Mar 2023 13:20:51 +0000
parents 830e4f00d55b
children 9aed02bbc85c
files MEGABLAST_TAB_get_taxid_acc.xml
diffstat 1 files changed, 23 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/MEGABLAST_TAB_get_taxid_acc.xml	Mon Mar 13 13:20:51 2023 +0000
@@ -0,0 +1,23 @@
+<tool id="MEGABLAST_TAB_get_taxid_acc" name="Get taxid and acc from megablast" version="1">
+  <description>
+    From a megablast file of results (tabular 25 columns) and taxid(s) user is interested in, 
+    provide 1 file with 2 columns: taxids accfrom taxonomic profile
+  </description>
+  <requirements>
+    <requirement type="package" version="2.7">python</requirement>
+    <requirement type="package">krona</requirement>
+  </requirements>
+  <command detect_errors="exit_code"><![CDATA[
+    python2 '$__tool_directory__/MEGABLAST_TAB_get_taxid_acc.py' -r ${input} -o ${output}
+  ]]></command>
+  <inputs>
+    <param format="tsv,tabular" name="input" type="data" label="Select your megablast file."/>
+  </inputs> 
+  <outputs>
+    <data name="output" format="tsv" />
+  </outputs>
+  <help>
+  From a megablast file of results (tabular 25 columns) and taxid(s) user is interested in,
+  provide 1 file with 2 columns: taxids acc
+  </help>
+</tool>