Mercurial > repos > p.lucas > megablast_tab_get_taxid_acc

changeset 1:fafa2c8d93d3 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Upload wrapper
author p.lucas
date Wed, 13 Dec 2023 10:52:32 +0000
parents e2df7c111004
children
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	Wed Dec 13 10:52:32 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>