Mercurial > repos > iuc > customize_metaphlan_database

changeset 2:487da152fb43 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 12:48:54 +0000
parents 025b0113ee97
children 4212f20315e5
files customize_metaphlan_database.xml formatoutput.py macros.xml test-data/no_taxon_input.fasta
diffstat 4 files changed, 21 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/customize_metaphlan_database.xml	Mon May 17 20:09:28 2021 +0000
+++ b/customize_metaphlan_database.xml	Mon Jun 14 12:48:54 2021 +0000
@@ -191,10 +191,14 @@
                 </repeat>
             </conditional>
             <output name="out_fasta" file="test-db.fasta" compare="sim_size">
+              <assert_contents>   
                 <has_text text="13076__A0A2I1PE66__CYJ72_10760" />
+              </assert_contents>
             </output>
             <output name="out_json" file="test-db.json" compare="sim_size">
+              <assert_contents>
                 <has_text text="13076__A0A2I1PE66__CYJ72_10760" />
+              </assert_contents>
             </output>
         </test>
         <test expect_num_outputs="2">
@@ -205,10 +209,14 @@
                 <param name="markers" value="marker.txt"/>
             </conditional>
             <output name="out_fasta" file="test-db-without-one-marker.fasta" compare="sim_size">
+              <assert_contents>
                 <not_has_text text="13076__A0A2I1PE66__CYJ72_10760" />
+              </assert_contents>
             </output>
             <output name="out_json" file="test-db-without-one-marker.json" compare="sim_size">
+              <assert_contents>
                 <not_has_text text="13076__A0A2I1PE66__CYJ72_10760" />
+              </assert_contents>
             </output>
         </test>
         <test expect_num_outputs="2">
@@ -219,10 +227,14 @@
                 <param name="markers" value="marker.txt"/>
             </conditional>
             <output name="out_fasta" file="test-db-with-one-marker.fasta" compare="sim_size">
+              <assert_contents>
                 <has_text text="13076__A0A2I1PE66__CYJ72_10760" />
+              </assert_contents>
             </output>
             <output name="out_json" file="test-db-with-one-marker.json" compare="sim_size">
+              <assert_contents>
                 <has_text text="13076__A0A2I1PE66__CYJ72_10760" />
+              </assert_contents> 
             </output>
         </test>
     </tests>
--- a/formatoutput.py	Mon May 17 20:09:28 2021 +0000
+++ b/formatoutput.py	Mon Jun 14 12:48:54 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 20:09:28 2021 +0000
+++ b/macros.xml	Mon Jun 14 12:48:54 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 12:48:54 2021 +0000
@@ -0,0 +1,4 @@
+> seq1
+ATTAGGGATTTTAGGGGGGGAGATTTAGAGAGAGAGAGAGAGAAGAAGAGAAGAAGAAGAAGAAAAAGGGGGAAGAGAGA
+> seq2
+ATTAGGGATTTTAGGGGGGGAGATTTAGAGAGAGAGAGAGAGAAGAAGAGAAGAAGAAGAAGAAAAAGGGGGAAGAGAGA