changeset 0:965674d88d34 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/LICENSE	Tue Jul 07 04:20:40 2020 -0400
@@ -0,0 +1,674 @@
+                    GNU GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
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+IS WITH YOU.  SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+  16. Limitation of Liability.
+
+  IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+  17. Interpretation of Sections 15 and 16.
+
+  If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+                     END OF TERMS AND CONDITIONS
+
+            How to Apply These Terms to Your New Programs
+
+  If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+  To do so, attach the following notices to the program.  It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+    <one line to give the program's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+  If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
+
+    <program>  Copyright (C) <year>  <name of author>
+    This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License.  Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+  You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+<http://www.gnu.org/licenses/>.
+
+  The GNU General Public License does not permit incorporating your program
+into proprietary programs.  If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library.  If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.  But first, please read
+<http://www.gnu.org/philosophy/why-not-lgpl.html>.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Jul 07 04:20:40 2020 -0400
@@ -0,0 +1,11 @@
+<?xml version="1.0"?>
+<macros>
+  <xml name="requirements">
+    <requirements>
+      <requirement type="package" version="0.6.4">bcbiogff</requirement>
+      <yield/>
+    </requirements>
+  </xml>
+
+  <token name="@HELP@">If a numeric value is specified (e.g. 0.1, 1, -42), this column from the table will be used. If a non-numeric value (e.g. 2b, yeast) is used, then this text will be used instead</token>
+</macros>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tbl2gff3.py	Tue Jul 07 04:20:40 2020 -0400
@@ -0,0 +1,95 @@
+#!/usr/bin/env python
+import argparse
+import csv
+import sys
+
+from BCBio import GFF
+from Bio.Seq import Seq
+from Bio.SeqFeature import FeatureLocation, SeqFeature
+from Bio.SeqRecord import SeqRecord
+
+
+def c(row, v, default=None):
+    if v is None:
+        return default
+
+    try:
+        _ = int(v)
+        return row[int(v) - 1]
+    except ValueError:
+        return v
+
+
+def tbl2gff3(
+    table,
+    rid,
+    begin,
+    end,
+    source=None,
+    type=None,
+    score=None,
+    frame=None,
+    a=None,
+    strand_column=None,
+    strand_value=None,
+):
+
+    records = {}
+
+    for row in csv.reader(table, delimiter="\t"):
+        # print(', '.join(row))
+
+        # if we haven't seen this record before, populate it.
+        recid = c(row, rid)
+        if recid not in records:
+            records[recid] = SeqRecord(Seq("ACTG"), id=recid)
+
+        r = records[recid]
+        q = {}
+        if c(row, score) is not None:
+            q["score"] = float(c(row, score))
+
+        q["source"] = c(row, source, "tbl2gff3")
+
+        _str = None
+        if strand_column is not None:
+            _str = int(c(row, strand_column))
+        elif strand_value is not None:
+            _str = int(strand_value)
+
+        for x in a:
+            k, v = x.split(":", 1)
+            _v = c(row, v)
+            if k in q:
+                q[k].append(_v)
+            else:
+                q[k] = [_v]
+
+        f = SeqFeature(
+            FeatureLocation(int(c(row, begin)), int(c(row, end))),
+            type=c(row, type),
+            strand=_str,
+            qualifiers=q,
+        )
+        r.features.append(f)
+
+    return records
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="Convert tables to gff3", epilog="")
+    parser.add_argument("table", type=argparse.FileType("r"), help="Tabular Input")
+    parser.add_argument("rid", help="id column")
+    parser.add_argument("begin", help="begin column")
+    parser.add_argument("end", help="end column")
+    parser.add_argument("--type", help="feature type column")
+    parser.add_argument("--score", help="score column")
+    parser.add_argument("--source", help="source column")
+    parser.add_argument("--strand_column", help="strand column")
+    parser.add_argument("--strand_value", help="strand value")
+    # parser.add_argument('--frame', help='frame column')
+    parser.add_argument("-a", action="append", help="attribute column (-a k:v)")
+    args = parser.parse_args()
+
+    for rid, rec in tbl2gff3(**vars(args)).items():
+        GFF.write([rec], sys.stdout)

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tbl2gff3.xml	Tue Jul 07 04:20:40 2020 -0400
@@ -0,0 +1,117 @@
+<tool id="tbl2gff3" name="Table to GFF3" version="1.1">
+	<description></description>
+	<macros>
+		<import>macros.xml</import>
+	</macros>
+	<expand macro="requirements"/>
+	<command detect_errors="exit_code">
+	<![CDATA[
+		python '$__tool_directory__/tbl2gff3.py'
+			'$table'
+			'$rid'
+			'$begin'
+			'$end'
+
+			#if $type:
+				--type '$type'
+			#end if
+
+			#if $score:
+				--score '$score'
+			#end if
+
+			#if $source:
+				--source '$source'
+			#end if
+
+			#if str($strand.strand_select) != "none":
+				--strand_${strand.strand_select} '${strand.strand}'
+			#end if
+
+			#for $a in $attributes
+				-a '${a.key}:${a.val}'
+			#end for
+
+			> '$output'
+	]]></command>
+	<inputs>
+		<param label="Table" name="table" type="data" format="tabular"/>
+
+		<param name="rid" type="text" value="1" label="Record ID column or value" optional="false" help="@HELP@"/>
+		<param name="begin" type="text" value="" optional="false" label="Feature start column or value" help="@HELP@"/>
+		<param name="end" type="text" value="" optional="false" label="Feature end column or value" help="@HELP@"/>
+		<param name="type" type="text" value="sequence_feature" label="Feature type column or value" help="@HELP@"/>
+		<param name="score" type="text" value="" label="Feature score column or value" help="@HELP@"/>
+		<param name="source" type="text" value="tbl2gff3" label="Feature source column or value" help="@HELP@"/>
+
+
+		<conditional name="strand">
+			<param name="strand_select" type="select" label="Strand">
+				<option value="none">Not specified</option>
+				<option value="column">From Column</option>
+				<option value="value">Specify Value</option>
+			</param>
+			<when value="none" />
+			<when value="column" >
+				<param name="strand" type="text" value="" label="Strand column" />
+			</when>
+			<when value="value">
+				<param name="strand" type="integer" value="1" min="-1" max="1" label="Strand value" />
+			</when>
+		</conditional>
+
+		<repeat name="attributes" title="Qualifiers" help="Other columns can be turned into qualifiers with arbitrary keys and values">
+			<param name="key" type="text" value="key" label="Name of the qualifier"/>
+			<param name="val" type="text" value="" label="Qualifier value column or raw text" help="@HELP@"/>
+		</repeat>
+
+	</inputs>
+	<outputs>
+		<data format="gff3" name="output"/>
+	</outputs>
+	<tests>
+		<test>
+			<param name="table" ftype="tabular" value="input.tab" />
+			<param name="rid" value="1" />
+			<param name="begin" value="5" />
+			<param name="end" value="6" />
+			<param name="score" value="14" />
+			<conditional name="strand">
+				<param name="strand_select" value="value"/>
+				<param name="strand" value="1"/>
+			</conditional>
+			<repeat name="attributes">
+				<param name="key" value="e-value" />
+				<param name="val" value="7" />
+			</repeat>
+			<repeat name="attributes">
+				<param name="key" value="hit" />
+				<param name="val" value="9" />
+			</repeat>
+			<repeat name="attributes">
+				<param name="key" value="GI" />
+				<param name="val" value="11" />
+			</repeat>
+			<repeat name="attributes">
+				<param name="key" value="test" />
+				<param name="val" value="one" />
+			</repeat>
+			<repeat name="attributes">
+				<param name="key" value="test" />
+				<param name="val" value="two" />
+			</repeat>
+
+			<output name="output" file="blast.gff3" />
+
+		</test>
+	</tests>
+	<help><![CDATA[
+**What it does**
+
+Convert a table into GFF3. This is not a very complex or advanced tool, it won't produce GFF with hierarchy, just flat gff3 which may be sufficient for visualisation purposes.
+
+]]></help>
+	<citations>
+	</citations>
+</tool>
+

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/blast.gff3	Tue Jul 07 04:20:40 2020 -0400
@@ -0,0 +1,12 @@
+##gff-version 3
+##sequence-region contig_1 1 4
+contig_1	tbl2gff3	sequence_feature	351161	351269	0.00198687506457	+	.	GI=CP012743;e-value=4.61e-44;hit=Klebsiella pneumoniae subsp. pneumoniae strain TGH8%2C complete genome;test=one,two
+contig_1	tbl2gff3	sequence_feature	4335437	4335554	0.00214943756986	+	.	GI=CP012743;e-value=4.58e-49;hit=Klebsiella pneumoniae subsp. pneumoniae strain TGH8%2C complete genome;test=one,two
+contig_1	tbl2gff3	sequence_feature	4335437	4335556	0.00218556257103	+	.	GI=CP012743;e-value=3.54e-50;hit=Klebsiella pneumoniae subsp. pneumoniae strain TGH8%2C complete genome;test=one,two
+contig_1	tbl2gff3	sequence_feature	1707035	1707157	0.00223975007279	+	.	GI=CP012743;e-value=7.61e-52;hit=Klebsiella pneumoniae subsp. pneumoniae strain TGH8%2C complete genome;test=one,two
+contig_1	tbl2gff3	sequence_feature	3405237	3405359	0.00223975007279	+	.	GI=CP012743;e-value=7.61e-52;hit=Klebsiella pneumoniae subsp. pneumoniae strain TGH8%2C complete genome;test=one,two
+contig_1	tbl2gff3	sequence_feature	1707035	1707158	0.00225781257338	+	.	GI=CP012743;e-value=2.12e-52;hit=Klebsiella pneumoniae subsp. pneumoniae strain TGH8%2C complete genome;test=one,two
+contig_1	tbl2gff3	sequence_feature	2877174	2877297	0.00225781257338	+	.	GI=CP012743;e-value=2.12e-52;hit=Klebsiella pneumoniae subsp. pneumoniae strain TGH8%2C complete genome;test=one,two
+contig_1	tbl2gff3	sequence_feature	2877174	2877297	0.00225781257338	+	.	GI=CP012743;e-value=2.12e-52;hit=Klebsiella pneumoniae subsp. pneumoniae strain TGH8%2C complete genome;test=one,two
+contig_1	tbl2gff3	sequence_feature	2877819	2877942	0.00225781257338	+	.	GI=CP012743;e-value=2.12e-52;hit=Klebsiella pneumoniae subsp. pneumoniae strain TGH8%2C complete genome;test=one,two
+contig_1	tbl2gff3	sequence_feature	3404591	3404714	0.00225781257338	+	.	GI=CP012743;e-value=2.12e-52;hit=Klebsiella pneumoniae subsp. pneumoniae strain TGH8%2C complete genome;test=one,two

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input.tab	Tue Jul 07 04:20:40 2020 -0400
@@ -0,0 +1,10 @@
+contig_1	gi|1015484279|gb|CP012743.1|	100.000	110	351160	351269	4.61e-44	gi|1015484279|gb|CP012743.1|	Klebsiella pneumoniae subsp. pneumoniae strain TGH8, complete genome	1015484279	CP012743	Klebsiella pneumoniae subsp. pneumoniae strain TGH8, complete genome	5536332	0.00198687506457
+contig_1	gi|1015484279|gb|CP012743.1|	100.000	119	4335436	4335554	4.58e-49	gi|1015484279|gb|CP012743.1|	Klebsiella pneumoniae subsp. pneumoniae strain TGH8, complete genome	1015484279	CP012743	Klebsiella pneumoniae subsp. pneumoniae strain TGH8, complete genome	5536332	0.00214943756986
+contig_1	gi|1015484279|gb|CP012743.1|	100.000	121	4335436	4335556	3.54e-50	gi|1015484279|gb|CP012743.1|	Klebsiella pneumoniae subsp. pneumoniae strain TGH8, complete genome	1015484279	CP012743	Klebsiella pneumoniae subsp. pneumoniae strain TGH8, complete genome	5536332	0.00218556257103
+contig_1	gi|1015484279|gb|CP012743.1|	100.000	124	1707034	1707157	7.61e-52	gi|1015484279|gb|CP012743.1|	Klebsiella pneumoniae subsp. pneumoniae strain TGH8, complete genome	1015484279	CP012743	Klebsiella pneumoniae subsp. pneumoniae strain TGH8, complete genome	5536332	0.00223975007279
+contig_1	gi|1015484279|gb|CP012743.1|	100.000	124	3405236	3405359	7.61e-52	gi|1015484279|gb|CP012743.1|	Klebsiella pneumoniae subsp. pneumoniae strain TGH8, complete genome	1015484279	CP012743	Klebsiella pneumoniae subsp. pneumoniae strain TGH8, complete genome	5536332	0.00223975007279
+contig_1	gi|1015484279|gb|CP012743.1|	100.000	125	1707034	1707158	2.12e-52	gi|1015484279|gb|CP012743.1|	Klebsiella pneumoniae subsp. pneumoniae strain TGH8, complete genome	1015484279	CP012743	Klebsiella pneumoniae subsp. pneumoniae strain TGH8, complete genome	5536332	0.00225781257338
+contig_1	gi|1015484279|gb|CP012743.1|	100.000	125	2877173	2877297	2.12e-52	gi|1015484279|gb|CP012743.1|	Klebsiella pneumoniae subsp. pneumoniae strain TGH8, complete genome	1015484279	CP012743	Klebsiella pneumoniae subsp. pneumoniae strain TGH8, complete genome	5536332	0.00225781257338
+contig_1	gi|1015484279|gb|CP012743.1|	100.000	125	2877173	2877297	2.12e-52	gi|1015484279|gb|CP012743.1|	Klebsiella pneumoniae subsp. pneumoniae strain TGH8, complete genome	1015484279	CP012743	Klebsiella pneumoniae subsp. pneumoniae strain TGH8, complete genome	5536332	0.00225781257338
+contig_1	gi|1015484279|gb|CP012743.1|	100.000	125	2877818	2877942	2.12e-52	gi|1015484279|gb|CP012743.1|	Klebsiella pneumoniae subsp. pneumoniae strain TGH8, complete genome	1015484279	CP012743	Klebsiella pneumoniae subsp. pneumoniae strain TGH8, complete genome	5536332	0.00225781257338
+contig_1	gi|1015484279|gb|CP012743.1|	100.000	125	3404590	3404714	2.12e-52	gi|1015484279|gb|CP012743.1|	Klebsiella pneumoniae subsp. pneumoniae strain TGH8, complete genome	1015484279	CP012743	Klebsiella pneumoniae subsp. pneumoniae strain TGH8, complete genome	5536332	0.00225781257338