# HG changeset patch
# User devteam
# Date 1583065482 18000
# Node ID 8cacfcf96a5212ae030e163a08ec479dd21d0482
# Parent  e626b3ff9922e8b18c60ab199d0d61c0b3cc8e40
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"

diff -r e626b3ff9922 -r 8cacfcf96a52 fasta_filter_by_length.py
--- a/fasta_filter_by_length.py	Tue Dec 17 13:13:32 2019 -0500
+++ b/fasta_filter_by_length.py	Sun Mar 01 07:24:42 2020 -0500
@@ -5,48 +5,50 @@
 Return sequences whose lengths are within the range.
 """
 
-import sys, os
+import sys
 
-assert sys.version_info[:2] >= ( 2, 4 )
+assert sys.version_info[:2] >= (2, 4)
 
-def stop_err( msg ):
-    sys.stderr.write( msg )
-    sys.exit()
+
+def stop_err(msg):
+    sys.exit(msg)
+
 
 def __main__():
     input_filename = sys.argv[1]
     try:
-        min_length = int( sys.argv[2] )
-    except:
-        stop_err( "Minimal length of the return sequence requires a numerical value." )
+        min_length = int(sys.argv[2])
+    except Exception:
+        stop_err("Minimal length of the return sequence requires a numerical value.")
     try:
-        max_length = int( sys.argv[3] )
-    except:
-        stop_err( "Maximum length of the return sequence requires a numerical value." )
+        max_length = int(sys.argv[3])
+    except Exception:
+        stop_err("Maximum length of the return sequence requires a numerical value.")
     output_filename = sys.argv[4]
-    output_handle = open( output_filename, 'w' )
-    tmp_size = 0 #-1
+    tmp_size = 0  # -1
     tmp_buf = ''
     at_least_one = 0
-    for line in file(input_filename):
-        if not line or line.startswith('#'):
-            continue
-        if line[0] == '>':
-            if min_length <= tmp_size <= max_length or (min_length <= tmp_size and max_length == 0):
-                output_handle.write(tmp_buf)
-                at_least_one = 1
-            tmp_buf = line
-            tmp_size = 0                                                       
-        else:
-            if max_length == 0 or tmp_size <= max_length:
-                tmp_size += len(line.rstrip('\r\n'))
-                tmp_buf += line
-    # final flush of buffer
-    if min_length <= tmp_size <= max_length or (min_length <= tmp_size and max_length == 0):
-        output_handle.write(tmp_buf.rstrip('\r\n'))
-        at_least_one = 1
-    output_handle.close()
+    with open(output_filename, 'w') as output_handle, open(input_filename, 'r') as input_handle:
+        for line in input_handle:
+            if not line or line.startswith('#'):
+                continue
+            if line[0] == '>':
+                if min_length <= tmp_size <= max_length or (min_length <= tmp_size and max_length == 0):
+                    output_handle.write(tmp_buf)
+                    at_least_one = 1
+                tmp_buf = line
+                tmp_size = 0
+            else:
+                if max_length == 0 or tmp_size <= max_length:
+                    tmp_size += len(line.rstrip('\r\n'))
+                    tmp_buf += line
+        # final flush of buffer
+        if min_length <= tmp_size <= max_length or (min_length <= tmp_size and max_length == 0):
+            output_handle.write(tmp_buf.rstrip('\r\n'))
+            at_least_one = 1
     if at_least_one == 0:
-        print "There is no sequence that falls within your range."
+        print("There is no sequence that falls within your range.")
+
 
-if __name__ == "__main__" : __main__()
+if __name__ == "__main__":
+    __main__()
diff -r e626b3ff9922 -r 8cacfcf96a52 fasta_filter_by_length.xml
--- a/fasta_filter_by_length.xml	Tue Dec 17 13:13:32 2019 -0500
+++ b/fasta_filter_by_length.xml	Sun Mar 01 07:24:42 2020 -0500
@@ -1,35 +1,34 @@
-<tool id="fasta_filter_by_length" name="Filter sequences by length" version="1.1">
-	<description></description>
-	<command>
-		python $__tool_directory__/fasta_filter_by_length.py
-			'$input'
-			$min_length
-			$max_length
-			'$output'
-	</command>
-	<inputs>
-		<param name="input" type="data" format="fasta" label="Fasta file"/>
-		<param name="min_length" type="integer" value="0" label="Minimal length" />
-		<param name="max_length" type="integer" value="0" label="Maximum length" help="Setting to '0' will return all sequences longer than the 'Minimal length'"/> 
-	</inputs>
-	<outputs>
-		<data name="output" format="fasta"/>
-	</outputs>
-	<tests>
-		<test>
-			<param name="input" value="454.fasta" />
-			<param name="min_length" value="10" />
-			<param name="max_length" value="0" />
-			<output name="output" file="fasta_tool_filter_length_1.out" />
-		</test>
-		<test>
-			<param name="input" value="4.fasta" />
-			<param name="min_length" value="0" />
-			<param name="max_length" value="60" />
-			<output name="output" file="fasta_tool_filter_length_2.out" />
-		</test>
-	</tests>
-	<help>
+<tool id="fasta_filter_by_length" name="Filter sequences by length" version="1.2" profile="16.04">
+    <description></description>
+    <requirements>
+        <requirement type="package" version="3.7">python</requirement>
+    </requirements>
+    <command>
+python '$__tool_directory__/fasta_filter_by_length.py' '$input' $min_length $max_length '$output'
+    </command>
+    <inputs>
+        <param name="input" type="data" format="fasta" label="Fasta file"/>
+        <param name="min_length" type="integer" value="0" label="Minimal length" />
+        <param name="max_length" type="integer" value="0" label="Maximum length" help="Setting to '0' will return all sequences longer than the 'Minimal length'"/> 
+    </inputs>
+    <outputs>
+        <data name="output" format="fasta"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="454.fasta" />
+            <param name="min_length" value="10" />
+            <param name="max_length" value="0" />
+            <output name="output" file="fasta_tool_filter_length_1.out" />
+        </test>
+        <test>
+            <param name="input" value="4.fasta" />
+            <param name="min_length" value="0" />
+            <param name="max_length" value="60" />
+            <output name="output" file="fasta_tool_filter_length_2.out" />
+        </test>
+    </tests>
+    <help><![CDATA[
 
 .. class:: infomark
 
@@ -38,7 +37,7 @@
 -----
 
 **What it does**
-	
+
 Outputs sequences greater than or equal to *Minimal length* and less than or equal to *Maximum length*. 
  
 -----
@@ -47,22 +46,22 @@
 
 Suppose you have the following FASTA formatted sequences::
 
-	&gt;seq1
-	TCATTTAATGAC
-	&gt;seq2
-	ATGGC
-	&gt;seq3
-	TCACATGATGCCG
-	&gt;seq4
-	ATGGAAGC
+    >seq1
+    TCATTTAATGAC
+    >seq2
+    ATGGC
+    >seq3
+    TCACATGATGCCG
+    >seq4
+    ATGGAAGC
 
 Setting the **Minimal length** to **10**, and the **Maximum length** to **0** will return all sequences longer than 10 bp::
 
- 	&gt;seq1
-	TCATTTAATGAC
-	&gt;seq3
-	TCACATGATGCCG
+    >seq1
+    TCATTTAATGAC
+    >seq3
+    TCACATGATGCCG
 
 
-	</help>
+    ]]></help>
 </tool>