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changeset 0:1b3c339fd390 draft default tip

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planemo upload for repository https://github.com/phac-nml/galaxy_tools commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
author nml
date Wed, 11 Oct 2017 11:46:25 -0400
parents
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files fasta_to_bed.pl fasta_to_bed.xml test-data/contigs.fasta test-data/results.bed
diffstat 4 files changed, 95 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fasta_to_bed.pl	Wed Oct 11 11:46:25 2017 -0400
@@ -0,0 +1,25 @@
+#!/usr/bin/env perl
+use strict;
+use warnings;
+use Bio::SeqIO;
+use Bio::Seq;
+use Getopt::Long;
+
+my ($fasta_file, $out);
+
+GetOptions(
+	"i|input=s" => \$fasta_file, #contigs fasta file
+	"o|output=s" => \$out
+);
+
+my $seqio_object= Bio::SeqIO->new (-format =>'fasta', -file=>$fasta_file);
+open(my $out_fh, ">", $out) || die "Could write to file '$out'\n";
+
+while (my $seq_object = $seqio_object->next_seq()) {
+	my $seq_id = $seq_object->display_id();
+	my $length = $seq_object->length();
+	print $out_fh $seq_id . "\t" . "1" . "\t" . $length . "\t" . $seq_id . "\n";
+
+}
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fasta_to_bed.xml	Wed Oct 11 11:46:25 2017 -0400
@@ -0,0 +1,28 @@
+<tool id="fasta2bed" name="Fasta to Bed File" version="1.0.0">
+  <description>Create Bed file from Multiple fasta file</description>
+    <requirements>
+      <requirement type="package" version="1.6.924">perl-bioperl</requirement>
+      <requirement type="package" version="2.49">perl-getopt-long</requirement>
+    </requirements>  
+    <command detect_errors="exit_code"><![CDATA[      
+        perl $__tool_directory__/fasta_to_bed.pl 
+        -i '$dataset'
+        -o '$output'
+    ]]></command>        
+    <inputs>
+        <param name="dataset" type="data" format="fasta" label="fasta or multifasta file" help="fasta to convert to bed file."/> 
+    </inputs>
+    <outputs>
+        <data name="output" format="bed"/>
+    </outputs>
+    <tests>
+      <test>
+            <param name="dataset" value="contigs.fasta"/>
+            <output name="output" value="results.bed"/>
+      </test>
+    </tests>
+    <help>
+    Create a bed file format using the start and end position of one or more fata record in a fasta file.
+
+    </help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/contigs.fasta	Wed Oct 11 11:46:25 2017 -0400
@@ -0,0 +1,40 @@
+>lcl|AF319579.1_cds_AAN14420.1_1 [gene=dnaA] [protein=DnaA] [protein_id=AAN14420.1] [location=1090..2430] [gbkey=CDS]
+TTGGAAAATATCTCTGATTTATGGAATAGTGCCTTAAAAGAATTAGAAAAAAAGGTAAGCAAGCCAAGTT
+ATGAAACCTGGTTAAAATCAACAACTGCTCATAACTTAAAAAAAGATGTATTAACTATTACAGCTCCAAA
+TGAATTCGCTCGTGACTGGCTAGAATCTCATTATTCGGAACTAATCTCCGAAACACTTTATGATTTAACA
+GGGGCAAAACTAGCTATTCGTTTTATCATTCCCCAAAGTCAGGCAGAAGAGGATATAGATCTCCCTTCTG
+TTAAGCAAAAACACGCACATGATGAGTCTAATCACTTACCACAGAGTATGTTAAACCCAAAATATACATT
+TGATACATTTGTTATTGGCTCTGGTAATCGTTTTGCACATGCTGCTTCTTTAGCTGTAGCTGAAGCACCA
+GCTAAAGCCTATAATCCGCTCTTTATTTACGGGGGCGTTGGACTTGGAAAAACACATTTAATGCACGCAA
+TTGGGCATTATGTAATTGAACACAACCCAAATGCAAAAGTTGTATATTTATCATCTGAAAAATTTACAAA
+TGAATTTATTAATTCAATTCGTGATAATAAAGCTGTCGATTTTCGTAATAAATATCGTAATGTAGATGTC
+TTATTGATAGATGATATTCAATTTCTTGCTGGAAAAGAACAAACACAGGAAGAGTTTTTCCATACATTTA
+ATGCGTTACATGAAGAAAGTAAACAAATTGTGATTTCAAGCGATAGACCACCAAAAGAAATCCCAACTTT
+AGAAGATCGCCTTCGTTCTCGCTTTGAATGGGGGTTAATTACGGACATTACGCCACCAGATTTAGAAACC
+AGAATCGCAATTTTACGTAAAAAAGCAAAAGCAGAAGGTCTTGATATACCAAATGAAGTTATGCTTTATA
+TCGCAAATCAAATCGATTCAAATATTCGTGAACTAGAGGGTGCACTTATTCGAGTTGTAGCTTATTCATC
+TTTAATTAATAAAGATATGAATGCTGATTTAGCGGCTGAAGCGCTTAAAAATATTATTCCAAACTCTATA
+CCTAGAATTATTTCTATTTCTGATATTCAAAAGGCTGTTGGGGGCGTCTATCAAGTAAAATTAGAAGATT
+TCAAAGCAAAAAAACGGACAAAATCCGTTGCATTCCCTCGCCAAATTGCGATGTATTTATCACGTGAACT
+TACGGACTCATCTTTGCCAAAAATAGGTGAAGAATTTGGTGGCCGCGATCATACAACAGTAATCCATGCT
+CACGAAAAAATTTCGAAGCTATTAAAAACGGATACTCAATTACAAAAACACGTTGAAGAAGTTAAGGATA
+TTTTAAAATAG
+>lcl|AF319579.1_cds_AAN14421.1_2 [gene=dnaN] [protein=DNA polymerase III beta chain] [protein_id=AAN14421.1] [location=2613..3758] [gbkey=CDS]
+ATGCGTTTTACAATACAAAAAGACTATCTTGTAAGAAGTGTACAAGATGTAATGAAGGCAGTTTCTTCTC
+GTACAACAATTCCAATTCTTACAGGGATTAAAGTTGTAGCAACTGAAGAAGGAGTTACTTTAACAGGTAG
+TGATGCAGACATCTCTATCGAATCATTTATCCCAGTCGAAGATGCTGGAAAAGAAATTGTGGAAATTGAA
+CAAACAGGAAGTATTATTTTACAAGCAAAATATTTTAGTGAGATCGTAAAAAAATTACCTAAAGAAACTG
+TCGAAATTTCTGTAGAAAATCATTTTATGACAAAAATAAAATCTGGAAAATCAGAGTTCAACTTAAATGG
+TTTAGATGCTGCTGAATATCCGTTATTACCACAAATCGAAGAACATCATGTATTTAAGATTCCAACAGAT
+TTACTAAAGCACATGATTCGTCAAACAGTATTTGCAGTTTCAAGTTCTGAAACAAGACCGATCTTGACAG
+GTGTAAACTGGAAGGTATATAACAGCGAGCTAACTTGTATTGCAACAGATAGTCACAGACTAGCACTTCG
+TAAAGCAAAAATCGAAGGGTATAATATTGCCGATGAATTTCAAGCGAATGTCGTTATTCCTGGTAAGAGC
+TTAAGTGAATTAAGTAAAATTCTAGATGAATCTGAAGAAATGGTAGATATCGTTATTACGGAGTATCAAG
+TATTATTCCGTACAAAACATTTATTATTCTTCTCAAGATTATTAGAAGGAAATTATCCAGATACAACGCG
+TTTAATTCCAGCTGAAAGTAAAACTGATATATTTGTAAATACAAAAGAATTTTTACAAGCGATTGATCGT
+GCGTCGCTGTTAGCAAGAGATGGTCGTAACAACGTTGTTAAATTATCGACATTAGAACAACAGATGTTAG
+AGATTTCTTCGAATGCACCAGAAATCGGAAAAGTAGTAGAAGAGGTTCAATGTGAAAATGTAGATGGAGA
+AGAATTAAAAATATCTTTTAGTGCAAAATATATGATGGACGCATTAAAGGCTTTAGACAGTACAGAAATT
+AAAGTTAGTTTTACTGGAGCGATGAGACCGTTTTTAATTCGCACAGTAAATGATAATTCCATTATCCAAT
+TAATTTTACCAGTCCGTACTTACTAA
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/results.bed	Wed Oct 11 11:46:25 2017 -0400
@@ -0,0 +1,2 @@
+lcl|AF319579.1_cds_AAN14420.1_1	1	1341	lcl|AF319579.1_cds_AAN14420.1_1
+lcl|AF319579.1_cds_AAN14421.1_2	1	1146	lcl|AF319579.1_cds_AAN14421.1_2