From 30d10985433035d062ada03beb960e63c03031dc Mon Sep 17 00:00:00 2001
From: Dave B <dave@bx.psu.edu>
Date: Mon, 21 Jan 2019 10:05:04 -0500
Subject: [PATCH 1/2] Add converters between tabular and CSV.

---
 config/datatypes_conf.xml.sample              | 14 ++++--
 .../datatypes/converters/csv_to_tabular.xml   | 12 +++++
 .../datatypes/converters/tabular_csv.py       | 44 +++++++++++++++++++
 .../datatypes/converters/tabular_to_csv.xml   | 12 +++++
 4 files changed, 78 insertions(+), 4 deletions(-)
 create mode 100644 lib/galaxy/datatypes/converters/csv_to_tabular.xml
 create mode 100644 lib/galaxy/datatypes/converters/tabular_csv.py
 create mode 100644 lib/galaxy/datatypes/converters/tabular_to_csv.xml

diff --git a/config/datatypes_conf.xml.sample b/config/datatypes_conf.xml.sample
index 70ab3228653..8ca2e47859d 100644
--- a/config/datatypes_conf.xml.sample
+++ b/config/datatypes_conf.xml.sample
@@ -72,8 +72,12 @@
       <converter file="interval_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/>
       <converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/>
     </datatype>
-    <datatype extension="csv" type="galaxy.datatypes.tabular:CSV" display_in_upload="true"/>
-    <datatype extension="tsv" type="galaxy.datatypes.tabular:TSV" display_in_upload="true"/>
+    <datatype extension="csv" type="galaxy.datatypes.tabular:CSV" display_in_upload="true">
+      <converter file="csv_to_tabular.xml" target_datatype="tabular"/>
+    </datatype>
+    <datatype extension="tsv" type="galaxy.datatypes.tabular:TSV" display_in_upload="true">
+      <converter file="tabular_to_csv.xml" target_datatype="csv"/>
+    </datatype>
     <datatype extension="intermine_tabular" type="galaxy.datatypes.tabular:TSV" subclass="true" display_in_upload="true">
       <display file="intermine/intermine_simple.xml"/>
     </datatype>
@@ -96,7 +100,7 @@
       <converter file="fasta_to_fai.xml" target_datatype="fai"/>
       <display file="igv/genome_fasta.xml" inherit="true"/>
     </datatype>
-    <datatype extension="fastg" type="galaxy.datatypes.sequence:Fastg" display_in_upload="true" description="fastg format faithfully represents genome assemblies in the face of allelic polymorphism and assembly uncertainty" description_url="http://fastg.sourceforge.net/FASTG_Spec_v1.00.pdf"/> 
+    <datatype extension="fastg" type="galaxy.datatypes.sequence:Fastg" display_in_upload="true" description="fastg format faithfully represents genome assemblies in the face of allelic polymorphism and assembly uncertainty" description_url="http://fastg.sourceforge.net/FASTG_Spec_v1.00.pdf"/>
     <datatype extension="fastq" auto_compressed_types="gz,bz2" type="galaxy.datatypes.sequence:Fastq" display_in_upload="true" description="FASTQ format is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Fastq">
       <converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/>
     </datatype>
@@ -304,7 +308,9 @@
     <datatype extension="sra" type="galaxy.datatypes.binary:Sra" mimetype="application/octet-stream" display_in_upload="true" description="A binary file archive format from the NCBI Sequence Read Archive with a '.sra' file extension." description_url="http://www.ncbi.nlm.nih.gov/books/n/helpsra/SRA_Overview_BK/#SRA_Overview_BK.4_SRA_Data_Structure"/>
     <datatype extension="svg" type="galaxy.datatypes.xml:GenericXml" mimetype="image/svg+xml" subclass="true"/>
     <datatype extension="taxonomy" type="galaxy.datatypes.tabular:Taxonomy" display_in_upload="true"/>
-    <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true" description="Any data in tab delimited format (tabular)." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Tabular_.28tab_delimited.29"/>
+    <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true" description="Any data in tab delimited format (tabular)." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Tabular_.28tab_delimited.29">
+      <converter file="tabular_to_csv.xml" target_datatype="csv"/>
+    </datatype>
     <datatype extension="twobit" type="galaxy.datatypes.binary:TwoBit" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="sqlite" type="galaxy.datatypes.binary:SQlite" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="gemini.sqlite" type="galaxy.datatypes.binary:GeminiSQLite" mimetype="application/octet-stream" display_in_upload="true"/>
diff --git a/lib/galaxy/datatypes/converters/csv_to_tabular.xml b/lib/galaxy/datatypes/converters/csv_to_tabular.xml
new file mode 100644
index 00000000000..4a00b67e406
--- /dev/null
+++ b/lib/galaxy/datatypes/converters/csv_to_tabular.xml
@@ -0,0 +1,12 @@
+<tool id="csv_to_tabular" name="Convert CSV to tabular" version="1.0.0">
+    <description></description>
+    <command>python '$__tool_directory__/tabular_csv.py' -o '$tabular' -i '$csv'</command>
+    <inputs>
+        <param format="csv" name="csv" type="data" label="Choose file with comma-separated values"/>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="tabular"/>
+    </outputs>
+    <help>
+    </help>
+</tool>
diff --git a/lib/galaxy/datatypes/converters/tabular_csv.py b/lib/galaxy/datatypes/converters/tabular_csv.py
new file mode 100644
index 00000000000..53b3148f5a8
--- /dev/null
+++ b/lib/galaxy/datatypes/converters/tabular_csv.py
@@ -0,0 +1,44 @@
+#!/usr/bin/env python
+"""
+Uses the python csv library to convert to and from tabular
+
+usage: %prog [--from-tabular] -i in_file -o out_file
+"""
+
+import argparse
+import os.path
+
+import csv
+
+
+def main():
+    usage = "Usage: %prog [options]"
+    parser = argparse.ArgumentParser(usage=usage)
+    parser.add_argument('-f', '--from-tabular', action='store_true', default=False, dest='fromtabular')
+    parser.add_argument('-i', '--input', type=str, dest='input')
+    parser.add_argument('-o', '--output', type=str, dest='output')
+    args = parser.parse_args()
+    input_fname = args.input
+    output_fname = args.output
+    if args.fromtabular:
+        convert_to_csv(input_fname, output_fname)
+    else:
+        convert_to_tsv(input_fname, output_fname)
+
+def convert_to_tsv(input_fname, output_fname):
+    with open(input_fname, 'rb') as csvfile:
+        with open(output_fname, 'wb') as ofh:
+            reader = csv.reader(csvfile)
+            for line in reader:
+                ofh.write('\t'.join(line) + '\n')
+
+def convert_to_csv(input_fname, output_fname):
+    with open(input_fname, 'rb') as tabfile:
+        with open(output_fname, 'wb') as ofh:
+            writer = csv.writer(ofh, delimiter=',')
+            for line in tabfile.readlines():
+                writer.writerow(line.strip().split('\t'))
+
+
+if __name__ == "__main__":
+    main()
diff --git a/lib/galaxy/datatypes/converters/tabular_to_csv.xml b/lib/galaxy/datatypes/converters/tabular_to_csv.xml
new file mode 100644
index 00000000000..2c853109184
--- /dev/null
+++ b/lib/galaxy/datatypes/converters/tabular_to_csv.xml
@@ -0,0 +1,12 @@
+<tool id="tabular_to_csv" name="Convert tabular to CSV" version="1.0.0">
+    <description></description>
+    <command>python '$__tool_directory__/tabular_csv.py' --from-tabular -i '$tabular' -o '$csv'</command>
+    <inputs>
+        <param format="tsv,tabular" name="tabular" type="data" label="Choose file with tab-separated values"/>
+    </inputs>
+    <outputs>
+        <data format="csv" name="csv"/>
+    </outputs>
+    <help>
+    </help>
+</tool>

From f0ac15266aac6f8c3adcfce38e8aa49208e6ae87 Mon Sep 17 00:00:00 2001
From: Dave B <dave@bx.psu.edu>
Date: Mon, 21 Jan 2019 10:33:31 -0500
Subject: [PATCH 2/2] Fix imports, E302s

---
 lib/galaxy/datatypes/converters/tabular_csv.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/datatypes/converters/tabular_csv.py b/lib/galaxy/datatypes/converters/tabular_csv.py
index 53b3148f5a8..0b18e1571e5 100644
--- a/lib/galaxy/datatypes/converters/tabular_csv.py
+++ b/lib/galaxy/datatypes/converters/tabular_csv.py
@@ -6,8 +6,6 @@ usage: %prog [--from-tabular] -i in_file -o out_file
 """
 
 import argparse
-import os.path
-
 import csv
 
 
@@ -25,6 +23,7 @@ def main():
     else:
         convert_to_tsv(input_fname, output_fname)
 
+
 def convert_to_tsv(input_fname, output_fname):
     with open(input_fname, 'rb') as csvfile:
         with open(output_fname, 'wb') as ofh:
@@ -32,6 +31,7 @@ def convert_to_tsv(input_fname, output_fname):
             for line in reader:
                 ofh.write('\t'.join(line) + '\n')
 
+
 def convert_to_csv(input_fname, output_fname):
     with open(input_fname, 'rb') as tabfile:
         with open(output_fname, 'wb') as ofh: