Mercurial > repos > nml > spades

changeset 20:78ced22d09a2 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a09a5e3ee3c76550526f082b97de8da75181a1dd
author iuc
date Wed, 13 Jul 2022 07:41:05 +0000
parents 9be710099b99
children a789e163a670
files macros.xml spades.xml write_tsv_script.py
diffstat 3 files changed, 19 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Mon May 09 22:49:43 2022 +0000
+++ b/macros.xml	Wed Jul 13 07:41:05 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/spades.xml	Mon May 09 22:49:43 2022 +0000
+++ b/spades.xml	Wed Jul 13 07:41:05 2022 +0000
@@ -161,8 +161,9 @@
             </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;1000&#009;225.723888"/>
                 </assert_contents>
             </output>
             <output name="out_l">
@@ -675,6 +676,21 @@
                 </assert_contents>
             </output>
         </test>
+        <!-- #17 Fix stats script -->
+        <test expect_num_outputs="1">
+            <conditional name="singlePaired">
+                <param name="sPaired" value="single"/>
+                <param name="input1" value="ecoli_1K.fastq.gz"/>
+            </conditional>
+            <param name="optional_output" value="ss"/>
+            <output name="out_ss">
+                <assert_contents>
+                    <has_n_lines n="2"/>
+                    <has_text text="NODE_1&#009;1000&#009;140.620106"/>
+                    <has_text_matching expression="#name&#009;length&#009;coverage"/>
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help><![CDATA[
 .. class:: infomark
--- a/write_tsv_script.py	Mon May 09 22:49:43 2022 +0000
+++ b/write_tsv_script.py	Wed Jul 13 07:41:05 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"