Mercurial > repos > iuc > spades_rnaviralspades

changeset 2:249f6a28c751 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
author iuc
date Tue, 25 Jan 2022 07:55:39 +0000
parents 11d7955eddf9
children d159735a6a9f
files rnaviralspades.xml write_tsv_script.py
diffstat 2 files changed, 18 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/rnaviralspades.xml	Mon Jan 24 18:44:03 2022 +0000
+++ b/rnaviralspades.xml	Tue Jan 25 07:55:39 2022 +0000
@@ -149,12 +149,12 @@
             <output_collection name="out_cr" type="list" count="2">
                 <element name="ecoli_1K_1.fastq.gz.fastq0_0.cor">
                     <assert_contents>
-                        <has_size value="34468" delta="1000"/>
+                        <has_size value="34468" delta="2000"/>
                     </assert_contents>
                 </element>
                 <element name="ecoli_1K_2.fastq.gz.fastq0_0.cor">
                     <assert_contents>
-                        <has_size value="34468" delta="1000"/>
+                        <has_size value="34468" delta="2000"/>
                     </assert_contents>
                 </element>
             </output_collection>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/write_tsv_script.py	Tue Jan 25 07:55:39 2022 +0000
@@ -0,0 +1,16 @@
+#!/usr/bin/env python
+
+import re
+import sys
+
+search_str = r"^>(NODE|\S+)_(\d+)(?:_|\s)length_(\d+)_cov_(\d+\.*\d*).*\$"
+
+replace_str = r"\1_\2\t\3\t\4"
+
+cmd = re.compile(search_str)
+
+sys.stdout.write("#name\tlength\tcoverage\n")
+
+for i, line in enumerate(sys.stdin):
+    if cmd.match(line):
+        sys.stdout.write(cmd.sub(replace_str, line))