Mercurial > repos > iuc > spades_rnaviralspades

changeset 5:b3490b036c5a 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 07:41:31 +0000
parents b65a43f70b99
children 48cf45a53456
files macros.xml rnaviralspades.xml write_tsv_script.py
diffstat 3 files changed, 5 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Mon Feb 21 10:54:21 2022 +0000
+++ b/macros.xml	Wed Jul 13 07:41:31 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/rnaviralspades.xml	Mon Feb 21 10:54:21 2022 +0000
+++ b/rnaviralspades.xml	Wed Jul 13 07:41:31 2022 +0000
@@ -117,9 +117,6 @@
                 <param name="input1" value="ecoli_1K_1.fastq.gz"/>
                 <param name="input2" value="ecoli_1K_2.fastq.gz"/>
             </conditional>
-            <conditional name="cov_cond">
-                <param name="cov_cutoff" value="auto"/>
-            </conditional>
             <param name="mode_sel" value="--disable-rr,--iontorrent"/>
             <param name="phred_offset" value="33"/>
             <param name="optional_output" value="ag,ags,cn,cp,cs,cr,sc,sp,ss,l"/>
@@ -146,7 +143,7 @@
                     <has_n_lines n="0"/>
                 </assert_contents>
             </output>
-            <output_collection name="out_cr" type="list" count="2">
+            <output_collection name="out_cr" type="list" count="4">
                 <element name="ecoli_1K_1.fastq.gz.fastq0_0.cor">
                     <assert_contents>
                         <has_size value="34468" delta="2000"/>
@@ -160,8 +157,9 @@
             </output_collection>
             <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;163.263933"/>
                 </assert_contents>
             </output>
             <output name="out_l">
--- a/write_tsv_script.py	Mon Feb 21 10:54:21 2022 +0000
+++ b/write_tsv_script.py	Wed Jul 13 07:41:31 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"