# HG changeset patch
# User rplanel
# Date 1566308809 14400
# Node ID 7b509a1801e4e61024ea01481d1e49e0e167da1a
# Parent  3e33310a7082c4f54212560379375cc27630b071
"planemo upload for repository https://github.com/rplanel/galaxy-tools/tree/master/tools/sequence-splitter commit 85ffc2e3805940c0ebb21d5450b86524bd788d7b"

diff -r 3e33310a7082 -r 7b509a1801e4 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Aug 20 09:46:49 2019 -0400
@@ -0,0 +1,12 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<macros>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">
+                @UNPUBLISHED{None,
+                author = {Rémi Planel},
+                title = {None},
+            }</citation>
+        </citations>
+    </xml>
+</macros>
\ No newline at end of file
diff -r 3e33310a7082 -r 7b509a1801e4 sequence-splitter.py
--- a/sequence-splitter.py	Thu Aug 08 11:18:30 2019 -0400
+++ b/sequence-splitter.py	Tue Aug 20 09:46:49 2019 -0400
@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+#!/usr/bin/env python2
 # coding: utf-8
 
 import argparse
@@ -24,24 +24,25 @@
     chunk_size = args.chunk_size
     # split the sequences in chunks
     if chunk_size:
-        logger.info("%s = %s", "chunk size parameter", chunk_size)
+        logger.info(
+            "%s = %s", "Number of sequences per chunk parameter", chunk_size)
         sequences_record = gen_sequence_record(args.sequences, args.format)
-        chunks = gen_get_chunks_by_size(sequences_record, chunk_size)
+        chunks = gen_chunks_of_size(sequences_record, chunk_size)
     else:
         logger.info("%s = %s", "number of chunks parameter", args.nb_chunk)
-        chunks = gen_get_chunks(args.sequences, args.format, args.nb_chunk)
+        chunks = gen_chunks(args.sequences, args.format, args.nb_chunk)
 
     # Write the chunks in numbered files.
     write_chunks(chunks, args.output, filename, file_extension, args.format)
 
 
-def gen_get_chunks(sequences_path, sequences_format, nb_chunk):
+def gen_chunks(sequences_path, sequences_format, nb_chunk):
     """[summary]
-
+    Split sequences to have a number of chunks defined by nb_chunks
     Arguments:
-        sequences_path {[type]} -- [description]
-        sequences_format {[type]} -- [description]
-        nb_chunk {[type]} -- [description]
+        sequences_path {[type]} -- Path to the sequence file
+        sequences_format {[type]} -- Format the sequence
+        nb_chunk {int} -- Number of chunks we want to obtain
 
     Returns:
         [type] -- [description]
@@ -51,25 +52,50 @@
         sequences_path, sequences_format)
     # Get the number of sequences
     nb_sequences = get_nb_sequences(sequences_record_to_count)
-    logger.info("%s = %i", "Number of sequences per chunk", nb_sequences)
+    logger.info("%s = %i", "Number of sequences total", nb_sequences)
     # Second record to that will be splitted
     sequences_to_split = gen_sequence_record(sequences_path, sequences_format)
 
     # Get the size of the chunks
     chunk_size = int(nb_sequences / nb_chunk) if nb_sequences > nb_chunk else 1
-    return gen_get_chunks_by_size(sequences_to_split, chunk_size)
+    return gen_chunks_of_size(
+        sequences_to_split,
+        chunk_size,
+        nb_chunk,
+        nb_sequences
+    )
 
 
-def gen_get_chunks_by_size(iterable, size=10):
-    logger.info(
-        "%s = %i",
-        "chunk size got (could be different from parameter if more chunk asked \
-         than sequences in multifasta)",
-        size
-    )
+def gen_chunks_of_size(
+    iterable, size=10,
+    limit_nb_chunk=None,
+    nb_sequences=None
+):
+    """[summary]
+    Split sequences by size
+    Arguments:
+        iterable {[type]} -- [description]
+
+    Keyword Arguments:
+        size {int} -- [description] (default: {10})
+    """
     iterator = iter(iterable)
-    for first in iterator:
-        yield chain([first], islice(iterator, size - 1))
+    if limit_nb_chunk is not None and nb_sequences is not None:
+        nb_chunk_left = limit_nb_chunk
+        nb_sequences_left = nb_sequences
+        for first in iterator:
+            if (size + 1) * nb_chunk_left > nb_sequences_left:
+                nb_sequences_left -= size
+                nb_chunk_left -= 1
+                yield chain([first], islice(iterator, size - 1))
+            else:
+                nb_chunk_left -= 1
+                size += 1
+                nb_sequences_left -= size
+                yield chain([first], islice(iterator, size - 1))
+    else:
+        for first in iterator:
+            yield chain([first], islice(iterator, size - 1))
 
 
 def gen_sequence_record(sequences_path, sequence_format):
@@ -77,23 +103,54 @@
 
 
 def get_nb_sequences(sequences):
+    """[summary]
+        Compute the number of sequences
+    Arguments:
+        sequences {[type]} -- Iterable of sequences
+
+    Returns:
+        [type] -- Number of sequences
+    """
     return sum(1 for _ in sequences)
 
 
 def write_chunks(iterable, dirname, filename, file_extension, sequence_format):
+    sequence_total = 0
     for idx, chunk in enumerate(iterable):
         if not os.path.exists(dirname):
             os.mkdir(dirname)
         output_file = os.path.join(
             dirname, filename + "-chunk-" + str(idx + 1) + file_extension
         )
+
         with open(output_file, mode="w") as output_handle:
             count_seq, seq_to_write = tee(chunk, 2)
-            logger.info(
-                "%s : number of seuquences = %i", output_file, len(
-                    list(count_seq))
-            )
+            nb_seq = len(list(count_seq))
+            logger.info("%s : number of sequences = %i", output_file, nb_seq)
+            sequence_total += nb_seq
             SeqIO.write(seq_to_write, output_handle, sequence_format)
+    logger.info("%s = %i", "Total number of chunks", idx + 1)
+    logger.info("%s = %i", "Number of sequences total", sequence_total)
+
+
+def positive_integer(str_value):
+    """[summary]
+    Define a type for argparse in order to enforce integer greater than 0
+    Arguments:
+        str_value {[type]} -- Value got by argparse
+
+    Raises:
+        argparse.ArgumentTypeError: When the value is not an integer > 0
+
+    Returns:
+        [type] -- [description]
+    """
+    value = int(str_value)
+    if isinstance(value, int) and value > 0:
+        return value
+    else:
+        msg = "%r is not an integer > 0" % value
+        raise argparse.ArgumentTypeError(msg)
 
 
 def parse_arguments():
@@ -106,11 +163,14 @@
                         help="File format (fastq, fasta)")
     group = parser.add_mutually_exclusive_group(required=True)
     group.add_argument(
-        "-c", "--chunk-size",
-        type=int,
+        "-c", "--chunk-size", type=positive_integer,
         help="The number of sequences by chunks."
     )
-    group.add_argument("-n", "--nb-chunk", help="Number of chunks", type=int)
+    group.add_argument(
+        "-n", "--nb-chunk",
+        type=positive_integer,
+        help="Number of chunks"
+    )
 
     parser.add_argument(
         "-o",
diff -r 3e33310a7082 -r 7b509a1801e4 sequence-splitter.xml
--- a/sequence-splitter.xml	Thu Aug 08 11:18:30 2019 -0400
+++ b/sequence-splitter.xml	Tue Aug 20 09:46:49 2019 -0400
@@ -1,4 +1,7 @@
-<tool id="sequence-splitter" name="Sequence Splitter" version="0.1.0">
+<tool id="sequence-splitter" name="Sequence Splitter" version="0.1.1">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
     <requirements>
         <requirement type="package" version="2.7.11">python</requirement>
         <requirement type="package" version="1.73">biopython</requirement>
@@ -50,17 +53,7 @@
         <data format="text" name="logfile" from_work_dir="sequence-splitter.log" label="${tool.name} logfile on ${on_string}"/>
     </outputs>
     <tests>
-        <test>
-            <param name="sequences" value="sample.fasta"/>
-            <conditional name="split_mode">
-                <param name="selector" value="chunk_size"/>
-                <param name="chunk_size" value="2"/>
-            </conditional>
-            <output_collection name="split_output" type="list" count="2">
-                <element name="sequences-chunk-1" file="sample-chunk-1.fasta" ftype="fasta"/>
-                <element name="sequences-chunk-2" file="sample-chunk-2.fasta" ftype="fasta"/>
-            </output_collection>
-        </test>
+        <!-- CHUNK SIZE -->
         <test>
             <param name="sequences" value="sample.fastq"/>
             <conditional name="split_mode">
@@ -68,14 +61,24 @@
                 <param name="chunk_size" value="2"/>
             </conditional>
             <output_collection name="split_output" type="list" count="5">
-                <element name="sequences-chunk-1" file="sample-chunk-1.fastq" ftype="fastqsanger"/>
-                <element name="sequences-chunk-2" file="sample-chunk-2.fastq" ftype="fastqsanger"/>
-                <element name="sequences-chunk-3" file="sample-chunk-3.fastq" ftype="fastqsanger"/>
-                <element name="sequences-chunk-4" file="sample-chunk-4.fastq" ftype="fastqsanger"/>
-                <element name="sequences-chunk-5" file="sample-chunk-5.fastq" ftype="fastqsanger"/>
+                <element name="sequences-chunk-1" file="sample-chunk-1.fastq" ftype="fastqsanger" compare="diff"/>
+                <element name="sequences-chunk-2" file="sample-chunk-2.fastq" ftype="fastqsanger" compare="diff"/>
+                <element name="sequences-chunk-3" file="sample-chunk-3.fastq" ftype="fastqsanger" compare="diff"/>
+                <element name="sequences-chunk-4" file="sample-chunk-4.fastq" ftype="fastqsanger" compare="diff"/>
+                <element name="sequences-chunk-5" file="sample-chunk-5.fastq" ftype="fastqsanger" compare="diff"/>
             </output_collection>
         </test>
-
+        <test>
+            <param name="sequences" value="sample.fasta"/>
+            <conditional name="split_mode">
+                <param name="selector" value="chunk_size" />
+                <param name="chunk_size" value="5"/>
+            </conditional>
+            <output_collection name="split_output" type="list" count="1">
+                <element name="sequences-chunk-1" file="sample-5-chunk-1.fasta" ftype="fasta" compare="diff"/>
+            </output_collection>
+        </test>
+        <!-- NUMBER CHUNK -->
         <test>
             <param name="sequences" value="sample.fastq"/>
             <conditional name="split_mode">
@@ -83,8 +86,21 @@
                 <param name="nb_chunk" value="2"/>
             </conditional>
             <output_collection name="split_output" type="list" count="2">
-                <element name="sequences-chunk-1" file="sample-3-chunk-1.fastq" ftype="fastqsanger"/>
-                <element name="sequences-chunk-2" file="sample-3-chunk-2.fastq" ftype="fastqsanger"/>
+                <element name="sequences-chunk-1" file="sample-3-chunk-1.fastq" ftype="fastqsanger" compare="diff"/>
+                <element name="sequences-chunk-2" file="sample-3-chunk-2.fastq" ftype="fastqsanger" compare="diff"/>
+            </output_collection>
+        </test>
+        <test>
+            <param name="sequences" value="sample.fastq"/>
+            <conditional name="split_mode">
+                <param name="selector" value="nb_chunk" />
+                <param name="nb_chunk" value="4"/>
+            </conditional>
+            <output_collection name="split_output" type="list" count="4">
+                <element name="sequences-chunk-1" file="sample-4-chunk-1.fastq" ftype="fastqsanger" compare="diff"/>
+                <element name="sequences-chunk-2" file="sample-4-chunk-2.fastq" ftype="fastqsanger" compare="diff"/>
+                <element name="sequences-chunk-3" file="sample-4-chunk-3.fastq" ftype="fastqsanger" compare="diff"/>
+                <element name="sequences-chunk-4" file="sample-4-chunk-4.fastq" ftype="fastqsanger" compare="diff"/>
             </output_collection>
         </test>
         <test>
@@ -94,10 +110,10 @@
                 <param name="nb_chunk" value="10"/>
             </conditional>
             <output_collection name="split_output" type="list" count="4">
-                <element name="sequences-chunk-1" file="sample-2-chunk-1.fasta" ftype="fasta"/>
-                <element name="sequences-chunk-2" file="sample-2-chunk-2.fasta" ftype="fasta"/>
-                <element name="sequences-chunk-3" file="sample-2-chunk-3.fasta" ftype="fasta"/>
-                <element name="sequences-chunk-4" file="sample-2-chunk-4.fasta" ftype="fasta"/>
+                <element name="sequences-chunk-1" file="sample-2-chunk-1.fasta" ftype="fasta" compare="diff"/>
+                <element name="sequences-chunk-2" file="sample-2-chunk-2.fasta" ftype="fasta" compare="diff"/>
+                <element name="sequences-chunk-3" file="sample-2-chunk-3.fasta" ftype="fasta" compare="diff"/>
+                <element name="sequences-chunk-4" file="sample-2-chunk-4.fasta" ftype="fasta" compare="diff"/>
             </output_collection>
         </test>
 
@@ -129,4 +145,5 @@
 
 
     ]]>    </help>
+    <expand macro="citations" />
 </tool>
\ No newline at end of file
diff -r 3e33310a7082 -r 7b509a1801e4 test-data/sample-4-chunk-1.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample-4-chunk-1.fastq	Tue Aug 20 09:46:49 2019 -0400
@@ -0,0 +1,8 @@
+@cluster_2:UMI_ATTCCG
+TTTCCGGGGCACATAATCTTCAGCCGGGCGC
++
+9C;=;=<9@4868>9:67AA<9>65<=>591
+@cluster_8:UMI_CTTTGA
+TATCCTTGCAATACTCTCCGAACGGGAGAGC
++
+1/04.72,(003,-2-22+00-12./.-.4-
diff -r 3e33310a7082 -r 7b509a1801e4 test-data/sample-4-chunk-2.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample-4-chunk-2.fastq	Tue Aug 20 09:46:49 2019 -0400
@@ -0,0 +1,8 @@
+@cluster_12:UMI_GGTCAA
+GCAGTTTAAGATCATTTTATTGAAGAGCAAG
++
+?7?AEEC@>=1?A?EEEB9ECB?==:B.A?A
+@cluster_21:UMI_AGAACA
+GGCATTGCAAAATTTATTACACCCCCAGATC
++
+>=2.660/?:36AD;0<14703640334-//
diff -r 3e33310a7082 -r 7b509a1801e4 test-data/sample-4-chunk-3.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample-4-chunk-3.fastq	Tue Aug 20 09:46:49 2019 -0400
@@ -0,0 +1,12 @@
+@cluster_29:UMI_GCAGGA
+CCCCCTTAAATAGCTGTTTATTTGGCCCCAG
++
+8;;;>DC@DAC=B?C@9?B?CDCB@><<??A
+@cluster_34:UMI_AGCTCA
+TCTTGCAAAAACTCCTAGATCGGAAGAGCAC
++
+-/CA:+<599803./2065?6=<>90;?150
+@cluster_36:UMI_AACAGA
+TCCCCCCCCCAAATCGGAAAAACACACCCCC
++
+5?:5;<02:@977=:<0=9>@5>7>;>*3,-
diff -r 3e33310a7082 -r 7b509a1801e4 test-data/sample-4-chunk-4.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample-4-chunk-4.fastq	Tue Aug 20 09:46:49 2019 -0400
@@ -0,0 +1,12 @@
+@cluster_37:UMI_GAGGAG
+GTCTTTGTACAAAATTTTATTAAAGGTCTTT
++
+?B?DEC@A=?ADDAEEEC?EC@D6A@@>DE4
+@cluster_39:UMI_GAACCG
+CCTTCCATCACCAGATCGGAAAAACACACGC
++
+00>7;8@5<192?/8;0;;>=3=/3239713
+@cluster_43:UMI_GGATTG
+GAGTTATAATCCAATCTTTATTTAAAAATCT
++
+>=AEC?C@;??0A>?0DEB9EEB@DDC1?=6
diff -r 3e33310a7082 -r 7b509a1801e4 test-data/sample-5-chunk-1.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample-5-chunk-1.fasta	Tue Aug 20 09:46:49 2019 -0400
@@ -0,0 +1,8 @@
+>derice
+ACTGACTAGCTAGCTAACTG
+>sanka
+GCATCGTAGCTAGCTACGAT
+>junior
+CATCGATCGTACGTACGTAG
+>yul
+ATCGATCGATCGTACGATCG
diff -r 3e33310a7082 -r 7b509a1801e4 test-data/sample-chunk-1.fasta
--- a/test-data/sample-chunk-1.fasta	Thu Aug 08 11:18:30 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
->derice
-ACTGACTAGCTAGCTAACTG
->sanka
-GCATCGTAGCTAGCTACGAT