Mercurial > repos > iuc > extract_metaphlan_database

changeset 2:b6ecdfac241f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55"
author iuc
date Mon, 14 Jun 2021 12:47:06 +0000
parents 1aaa9b943a83
children c11805a111ea
files formatoutput.py macros.xml test-data/no_taxon_input.fasta
diffstat 3 files changed, 9 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/formatoutput.py	Mon May 17 20:08:58 2021 +0000
+++ b/formatoutput.py	Mon Jun 14 12:47:06 2021 +0000
@@ -57,7 +57,9 @@
                 # skip headers
                 if line.startswith("#"):
                     continue
-
+                # skip UNKNOWN lines in Predicted taxon relative abundances
+                if "UNKNOWN" in line:
+                    continue
                 # spit lines
                 split_line = line[:-1].split('\t')
                 taxo_n = split_line[0].split('|')
--- a/macros.xml	Mon May 17 20:08:58 2021 +0000
+++ b/macros.xml	Mon Jun 14 12:47:06 2021 +0000
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">3.0.8</token>
+    <token name="@TOOL_VERSION@">3.0.9</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">20.01</token>
     <xml name="edam_ontology">
@@ -21,7 +21,7 @@
     </xml>
     <xml name="citations">
         <citations>
-            <citation type="doi">1101/2020.11.19.388223</citation>
+            <citation type="doi">10.7554/eLife.65088</citation>
         </citations>
     </xml>
 </macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/no_taxon_input.fasta	Mon Jun 14 12:47:06 2021 +0000
@@ -0,0 +1,4 @@
+> seq1
+ATTAGGGATTTTAGGGGGGGAGATTTAGAGAGAGAGAGAGAGAAGAAGAGAAGAAGAAGAAGAAAAAGGGGGAAGAGAGA
+> seq2
+ATTAGGGATTTTAGGGGGGGAGATTTAGAGAGAGAGAGAGAGAAGAAGAGAAGAAGAAGAAGAAAAAGGGGGAAGAGAGA