Mercurial > repos > iuc > spades_plasmidspades

changeset 5:6aad515a5270 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a09a5e3ee3c76550526f082b97de8da75181a1dd
author iuc
date Wed, 13 Jul 2022 07:42:22 +0000
parents 85fb02c43042
children 75405f5e2cc5
files macros.xml plasmidspades.xml write_tsv_script.py
diffstat 3 files changed, 7 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Mon Feb 21 10:21:50 2022 +0000
+++ b/macros.xml	Wed Jul 13 07:42:22 2022 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">3.15.4</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">spades</requirement>
--- a/plasmidspades.xml	Mon Feb 21 10:21:50 2022 +0000
+++ b/plasmidspades.xml	Wed Jul 13 07:42:22 2022 +0000
@@ -155,8 +155,9 @@
             </output>
             <output name="out_cs">
                 <assert_contents>
-                    <has_n_lines n="1"/>
+                    <has_n_lines n="2"/>
                     <has_text_matching expression="#name&#009;length&#009;coverage"/>
+                    <has_text_matching expression="NODE_1&#009;9689&#009;4.668331_component_0"/>
                 </assert_contents>
             </output>
             <output_collection name="out_cr" type="list" count="3">
@@ -193,7 +194,9 @@
             </output>
             <output name="out_ss">
                 <assert_contents>
-                    <has_n_lines n="1"/>
+                    <has_n_lines n="2"/>
+                    <has_text_matching expression="#name&#009;length&#009;coverage"/>
+                    <has_text_matching expression="NODE_1&#009;9689&#009;4.668331_component_0"/>
                 </assert_contents>
             </output>
         </test>
--- a/write_tsv_script.py	Mon Feb 21 10:21:50 2022 +0000
+++ b/write_tsv_script.py	Wed Jul 13 07:42:22 2022 +0000
@@ -3,7 +3,7 @@
 import re
 import sys
 
-search_str = r"^>(NODE|\S+)_(\d+)(?:_|\s)length_(\d+)_cov_(\d+\.*\d*).*\$"
+search_str = r"^>(NODE|\S+)_(\d+)(?:_|\s)length_(\d+)_cov_(\d+\.*\d*)(.*\$)?"
 
 replace_str = r"\1_\2\t\3\t\4"