changeset 4:532a84f0de1e draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 3a3bb179f4f3c99b25ef082996720c62aedb6200"

--- a/gff_to_prot.py	Wed Oct 16 04:32:33 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,65 +0,0 @@
-#!/usr/bin/env python
-import csv
-import os
-import sys
-
-
-def get_description(line, parent):
-    cols = line.split('\t')
-    labels = {}
-    for pair in cols[8].split(";"):
-        k, v = pair.split('=')
-        labels[k] = v
-
-    if (cols[2]) == "CDS" and labels["Parent"] == parent:
-        return labels.get("Note", '-')
-    return '-'
-
-
-def convert_to_prot_table(fname, output_name):
-    gff_file = open(fname)
-    output_file = open(output_name, 'w')
-    writer = csv.writer(output_file, delimiter='\t')
-    lines = gff_file.readlines()
-    gff_file.close()
-    for i, line in enumerate(lines):
-        line = line.strip()
-        if line.startswith('#'):
-            continue
-        cols = line.split('\t')
-        if (len(cols) < 9):
-            print("Ignoring invalid row with entries: {0}".format(cols))
-        elif (cols[2]) == "region":
-            continue
-        elif (cols[2]) == "CDS":
-            continue
-        elif (cols[2]) == "gene":
-            start = int(cols[3])
-            end = int(cols[4])
-            strand = cols[6].strip()
-            labels = {}
-            diff = int(abs(end - start) / 3)  # What is this called?
-            for pair in cols[8].split(";"):
-                k, v = pair.split('=')
-                labels[k.strip()] = v.strip()
-
-            Rv = labels["locus_tag"].strip()  # error out if not found
-            gene = labels.get('Name', '')
-            desc = get_description(lines[i + 1], labels.get("ID", "")) if (i + 1) < len(lines) else '-'
-            vals = [desc, start, end, strand, diff, '-', '-', gene, Rv, '-']
-            writer.writerow(vals)
-    output_file.close()
-
-
-if __name__ == "__main__":
-    usage_string = "Usage: python gff-prot-converter.py <gff filename> <output filename>"
-
-    if len(sys.argv) < 3:
-        print(usage_string)
-        sys.exit(0)
-    file_name = sys.argv[1]
-    if not os.path.exists(file_name):
-        print("File not found. Exiting...")
-        print(usage_string)
-        sys.exit(0)
-    convert_to_prot_table(file_name, sys.argv[2])

--- a/macros.xml	Wed Oct 16 04:32:33 2019 -0400
+++ b/macros.xml	Fri Jan 31 10:48:38 2020 -0500
@@ -9,11 +9,10 @@
 	<xml name="requirements">
 		<requirements>
 			<requirement type="package" version="@VERSION@">transit</requirement>
-            <requirement type="package" version="3.7">python</requirement>
 			<yield />
 		</requirements>
 	</xml>
-	<token name="@VERSION@">3.0.1</token>
+	<token name="@VERSION@">3.0.2</token>
 	<xml name="outputs">
         <yield />
         <data name="sites" from_work_dir="transit_out.txt" format="tabular" label="${tool.name} on ${on_string} Sites" />

--- a/transit_hmm.xml	Wed Oct 16 04:32:33 2019 -0400
+++ b/transit_hmm.xml	Fri Jan 31 10:48:38 2020 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="transit_hmm" name="HMM" version="@VERSION@+galaxy2">
+<tool id="transit_hmm" name="HMM" version="@VERSION@+galaxy0">
     <description>- determine essentiality of a genome</description>
     <macros>
         <import>macros.xml</import>