--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Wed Apr 12 17:43:55 2017 -0400
@@ -0,0 +1,33 @@
+gbToFasta
+==========================================================
+Galaxy wrapper for UCSC tools gbToFasta and raToTab. Convert GenBank records to fasta and create table with coding regions information for each mRNA record.
+
+gbToFasta
+---------
+
+gbToFaRa - Convert GenBank flat format file to an fa file containing
+the sequence data, an ra file containing other relevant info and
+a ta file containing summary statistics.
+
+usage:
+  gbToFaRa filterFile faFile raFile taFile genBankFile(s)
+  where filterFile is definition of which records and fields
+  use /dev/null if you want no filtering.
+
+  $ gbToFaRa /dev/null gbfile.fa gbfile.ra gbfile.ta gbfile
+
+raToTab
+--------
+raToTab - Create table with coding regions information for each mRNA record
+
+usage:
+  raToTab -cols=acc,cds gbfile.ra gbfile.cds
+
+Source code:
+============
+
+http://hgdownload.cse.ucsc.edu/admin/exe/
+
+Licence
+-------
+Please note that commercial download and installation of the Blat and In-Silico PCR software may be licensed through Kent Informatics (http://www.kentinformatics.com).

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gbToFasta.xml	Wed Apr 12 17:43:55 2017 -0400
@@ -0,0 +1,96 @@
+<?xml version="1.0"?>
+<tool id="gbtofasta" name="gbToFasta" version="1.0">
+    <description>Convert GenBank records to fasta and Create table with coding regions information for each mRNA record</description>
+    <requirements>
+      <requirement type="package" version="1.0">ucsc_tools_340_for_BLAT</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+    gbToFaRa
+            /dev/null
+            '${outputfa}'
+            outputra
+            outputta
+            '${gbfile}'
+      #if $cds == "yes"
+            && raToTab
+                  -cols=acc,cds
+                  outputra
+                  '${outputcds}'
+      #end if
+]]></command>
+      <inputs>
+            <param type="data" name="gbfile" format="genbank" />
+            <param type="select" name="cds" label="Create table with coding regions information for each mRNA record" >
+                  <option value="yes">Yes</option>
+                  <option value="no">No</option>
+            </param>
+                  
+      </inputs>
+      <outputs>
+            <data format="fasta" name="outputfa" label="${tool.name} on ${on_string}:fasta"></data>
+            <data format="tabular" name="outputcds" label="${tool.name} on ${on_string}:cds">
+                  <filter>cds == "yes"</filter>
+            </data>
+      </outputs>
+  <tests>
+      <test>
+            <param name="gbfile" value="Gallus_gallus_RefSeq.gb" />
+            <param name="cds" value="yes" />
+            <output name="outputfa" value="Gallus_gallus_RefSeq.fa" />
+            <output name="outputcds" value="Gallus_gallus_RefSeq.cds" />
+      </test>
+      <test>
+            <param name="gbfile" value="Gallus_gallus_RefSeq.gb" />
+            <param name="cds" value="no" />
+            <output name="outputfa" value="Gallus_gallus_RefSeq.fa" />
+      </test>
+  </tests> 
+  <help>
+        <![CDATA[
+gbToFasta
+=========
+
+Convert GenBank records to fasta
+---------------------------------
+
+gbToFaRa - Convert GenBank flat format file to an fa file containing
+the sequence data, an ra file containing other relevant info and
+a ta file containing summary statistics.
+usage:
+   gbToFaRa filterFile faFile raFile taFile genBankFile(s)
+where filterFile is definition of which records and fields
+use /dev/null if you want no filtering.
+
+gbToFaRa /dev/null gbfile.fa \
+  gbfile.ra gbfile.ta gbfile
+
+Create table with coding regions information for each mRNA record
+-----------------------------------------------------------------
+raToTab - Convert ra file to table.
+raToTab -cols=acc,cds gbfile.ra gbfile.cds
+
+Source code:
+============
+
+http://hgdownload.cse.ucsc.edu/admin/exe/
+
+]]></help> 
+ <citations>
+            <citation type="bibtex">@article{kent2002blat,
+                  title={BLAT—the BLAST-like alignment tool},
+                  author={Kent, W James},
+                  journal={Genome research},
+                  volume={12},
+                  number={4},
+                  pages={656--664},
+                  year={2002},
+                  publisher={Cold Spring Harbor Lab}
+            }</citation>
+      </citations> 
+      
+</tool>
+             
+            
+
+               
+    
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Gallus_gallus_RefSeq.cds	Wed Apr 12 17:43:55 2017 -0400
@@ -0,0 +1,100 @@
+NM_001199713	95..1546
+NM_001199712	95..1618
+NM_001030697	100..2745
+NM_001277797	1..2943
+NM_001184757	1..468
+NM_205038	272..1336
+NM_204727	406..966
+NM_001031150	220..2043
+NM_204996	56..3379
+NM_001005808	216..1316
+NM_205405	26..4981
+NM_205387	19..312
+NM_001115017	48..2060
+NM_204843	170..1840
+NM_001347710	32..1513
+NM_001328355	99..1328
+NM_001328354	87..530
+NM_001278102	156..524
+NM_001278100	320..688
+NM_001278104	91..459
+NM_001006176	347..3118
+NM_001281486	21..248
+NM_001278545	42..728
+NM_001277657	250..774
+NM_001277490	21..818
+NM_001277477	81..569
+NM_001277476	81..569
+NM_001199231	141..365
+NM_001031013	121..822
+NM_001195562	1..2664
+NM_001194996	58..1314
+NM_001006577	58..1293
+NM_001145430	217..420
+NM_001110060	1..714
+NM_001044640	16..642
+NM_001030706	43..1413
+NM_001030974	38..1090
+NM_001031172	33..2396
+NM_001031536	99..3497
+NM_001012804	68..2092
+NM_001006355	64..684
+NM_204172	65..1531
+NM_204212	1..2751
+NM_001348012	162..2225
+NM_204182	61..1314
+NM_204788	86..1264
+NM_001347945	34..1248
+NM_204471	162..3470
+NM_001006211	40..792
+NM_001318995	35..826
+NM_001322804	30..2675
+NM_001257371	191..829
+NM_001292086	17..1990
+NM_204766	50..5863
+NM_001318982	36..1613
+NM_001318432	1..969
+NM_001317736	78..812
+NM_001305110	67..969
+NM_001305109	71..973
+NM_001305111	63..740
+NM_001305112	64..597
+NM_001305089	1..3510
+NM_205501	87..1487
+NM_001293169	122..2614
+NM_001030587	20..1669
+NM_001293103	1..1086
+NM_001290554	77..2845
+NM_205054	17..1168
+NM_001277841	51..1013
+NM_001277715	58..930
+NM_001277631	13..933
+NM_001277630	13..1053
+NM_001271966	144..521
+NM_001271965	144..524
+NM_001271964	144..560
+NM_001113708	75..491
+NM_001271936	95..484
+NM_001271894	50..1765
+NM_205450	39..530
+NM_204650	3..245
+NM_205307	71..2014
+NM_001257373	16..1005
+NM_001128828	191..3520
+NM_001252284	300..881
+NM_001006305	30..788
+NM_001024456	6..2228
+NM_001242604	191..2770
+NM_001004378	103..1056
+NM_001201399	152..346
+NM_204992	88..282
+NM_001199613	1..498
+NM_001199429	179..2224
+NM_001195561	16..540
+NM_001195424	13..636
+NM_001111014	216..2867
+NM_001001775	216..2867
+NM_001167726	113..1909
+NM_001167759	22..1290
+NM_001167758	22..1287
+NM_001163651	189..1229

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Gallus_gallus_RefSeq.fa	Wed Apr 12 17:43:55 2017 -0400
@@ -0,0 +1,4595 @@
+>NM_001199713
+cccttcctcttccttcctcctcctcctcccccttccctccctgccccccc
+aacaccgaagggaagagacaattctcctccgagcagcagcaaacatgatg
+gcggcagctcccatccagcagaacgggactcacaccggggttcccataga
+cctggacccgccggactcccggaaaagaccgctggaagccccccccgaag
+cgggcagcaccaagaggaccaacacgggcgaggatggccaatattttcta
+aaggtcctcatacctagttatgctgctggatctataattgggaagggagg
+acagacaattgttcagttgcagaaagagaccggggccaccatcaagctgt
+ctaaatccaaagatttttacccaggtactacggagcgcgtgtgtctgatc
+cagggaacagttgaagcactaaatgcagttcatggcttcattgcagagaa
+gattcgagaaatgcctcaaaatgtggccaagacagagcctgtcagcatcc
+tacaacctcagaccactgttaatccagaccgcatcaaacaagtaaagatt
+atagttcccaacagcacagcaggtctgataatagggaagggaggtgctac
+agtgaaggctataatggagcagtcaggggcttgggtgcagctttcccaga
+aacctgatgggatcaacttgcaagagagggttgtcactgtgagtggagaa
+cctgaacaaaaccgaaaagctgtcgaacttatcatccagaagatacaaga
+ggatccacagagtggcagctgtctcaatatcagttatgccaatgtcacag
+gtccagtggccaattccaatccaaccggatctccttatgcaaacactgct
+gaagtgttaccaactgctgcagctgctgcagggctattaggacatgctaa
+ccttgctggagtggcagcctttccagcagttttatctggctttacaggca
+atgacctggtggccatcacctctgcacttaatacattagccagctatgga
+tataatctcaatacattaggtttaggcctaagtcaggcagcagctacagg
+ggctttggctgcagcagctgccagtgccaacccagcagcagcagcagcca
+acttgttggccacctatgcgagtgaagcctcagccagtggcagcactgct
+ggtggtacggcggggacatttgcattaggtagcctggctgctgctactgc
+tgcaaccaatggatattttggagctgcttctcccctagctgccagtgcca
+tcctaggaacagaaaaatccacagatggatcaaaggatgtagttgaaata
+gcagtgccagaaaacttagttggtgcaatacttggaaaaggagggaaaac
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+acaccagctgcaacccaggccgcacagtatttaattacacaacggatcac
+atatgagcaaggagttcgggctgccaatccacagaaagtgggttgagagc
+ccctgttaaacatgagattgttttaacccctccttaccctattttcaaga
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+tgtgttttaccagatgtttcatagagagaattttttcttgatctgttttg
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+ttaactactgttaggttgggtatggtggggtcagtgacctaaaatggagt
+gaggccaaagcactgtcatgtcagtcttacttcctgcttagggcacagtg
+aagtaggaaacaatattttgaaaataagttttaaaatttaaaatgatcaa
+aaagcaatatagttgcataaaagcactgtaaaatatttaaaaaggttaaa
+actgtggaaaattatattggtaagtttacagatcaataaaagcacctgtt
+ctccatctgaactagacaatggaaataatgctgcatgctggccatggccc
+attcttcaccatttgtaagttcaacaaaagttctcacatggagtcccacc
+tctaactgaggtttgtacatttgtttttaagcactgaaatcactactgat
+cccatcgcctggccagtagaacagtcattactccattaacattctcactg
+tttagacacataactgtggtacagtgtattggaaattttatatacaaaaa
+gtgaaagtgccaacaaattattgatagctgataatgtttcattatctgca
+actgcttgataagtatgttgcattttaagagcttataattgtgtataatt
+tgttaacactagaaacctattagtattgtgaatgtagattttactgtgaa
+gctatctgtgatttagctgtttgctcccatgaaggagtctttgcagcatg
+gcgctagcagccaatgcagtttctaatactcagtaatttgcatgttttgt
+ggagcatttttatgtcaccaaccagacagtatttcctgcatgcttattta
+gaagaggcagttttccttgagaggtagtggtctacctttgccaggctttt
+tgacaggtcatttcagagtaagcctttgttcccaagacccaacaactgtc
+accctcttctgtacctctcctgagtgccaactgcccaggccattgaccca
+ccatctgttaacctctgagtttgcccgctcaaggccactcataggggcat
+ccataaccaagcacctcctcatgctgtgcatgcagtcttaaattcaatgg
+acaaaaataaaatgctggctacctctggatcatctggctgagcaactgaa
+tttcaaaagagaattacttccatctcaacttcaacccattgattacgtcc
+atcctagcaagctaaatggcatcccagctgctcctttctgtgcaaccaat
+taaagaacaatgagtgtgatgctccatgtctgaatttcgtccagcctctc
+tctgaactgtgatctttgtcctcatgaactttcccttttgttcattgaac
+tatatggactcttcatttcatattgatttactgtgcaatttacttttgga
+cattgagaacttgaaataattccctgatcccttcccccttcactattaat
+aactcatttctgtcaaactgtaagagtagactcattttttttagttttta
+acattggattgttatttcatttagagttctctatctctaaatatttaatt
+tagagaatgattaaaaagggaatgatatgcttgtttaaaatgaaagagaa
+aagctgtagtaaactgtgttacttggtaatgactatttatcgtcgatact
+ctgtagctgtgtaagttttgacaaatagtgtatctcgtgaaatcagtggt
+tagcattgccgctattatatttactcattttatcattataaatgtgctta
+gttcatcatgtag
+>NM_001199712
+cccttcctcttccttcctcctcctcctcccccttccctccctgccccccc
+aacaccgaagggaagagacaattctcctccgagcagcagcaaacatgatg
+gcggcagctcccatccagcagaacgggactcacaccggggttcccataga
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+ctaaatccaaagatttttacccaggtactacggagcgcgtgtgtctgatc
+cagggaacagttgaagcactaaatgcagttcatggcttcattgcagagaa
+gattcgagaaatgcctcaaaatgtggccaagacagagcctgtcagcatcc
+tacaacctcagaccactgttaatccagaccgcatcaaacaaacattgcca
+tcttccccaactaccaccaagtcctctccatctgatcccatgaccacctc
+cagagccaatcaggtaaagattatagttcccaacagcacagcaggtctga
+taatagggaagggaggtgctacagtgaaggctataatggagcagtcaggg
+gcttgggtgcagctttcccagaaacctgatgggatcaacttgcaagagag
+ggttgtcactgtgagtggagaacctgaacaaaaccgaaaagctgtcgaac
+ttatcatccagaagatacaagaggatccacagagtggcagctgtctcaat
+atcagttatgccaatgtcacaggtccagtggccaattccaatccaaccgg
+atctccttatgcaaacactgctgaagtgttaccaactgctgcagctgctg
+cagggctattaggacatgctaaccttgctggagtggcagcctttccagca
+gttttatctggctttacaggcaatgacctggtggccatcacctctgcact
+taatacattagccagctatggatataatctcaatacattaggtttaggcc
+taagtcaggcagcagctacaggggctttggctgcagcagctgccagtgcc
+aacccagcagcagcagcagccaacttgttggccacctatgcgagtgaagc
+ctcagccagtggcagcactgctggtggtacggcggggacatttgcattag
+gtagcctggctgctgctactgctgcaaccaatggatattttggagctgct
+tctcccctagctgccagtgccatcctaggaacagaaaaatccacagatgg
+atcaaaggatgtagttgaaatagcagtgccagaaaacttagttggtgcaa
+tacttggaaaaggagggaaaacattagttgaataccaggagttgactggt
+gcaaggatacagatctctaaaaagggagaattcgtacctggcacaagaaa
+tcgcaaggtaaccattactggaacaccagctgcaacccaggccgcacagt
+atttaattacacaacggatcacatatgagcaaggagttcgggctgccaat
+ccacagaaagtgggttgagagcccctgttaaacatgagattgttttaacc
+cctccttaccctattttcaagaaggatgtactgtactttgcagaagtgaa
+gtttttctgttattaatatataattatgcaaatgaatgcgactatgttga
+caatgtgtatatgtaaatataatgtgttttaccagatgtttcatagagag
+aattttttcttgatctgttttgttctctatactttgcttgtgtatatttg
+tcagaggtgtttctagtgtaagatttaagcctgccattttaccagcatta
+ttgtagtttaatgattgaatgtagacagggatatgcgtatagttttcagt
+attagttctagataacactaaattaactactgttaggttgggtatggtgg
+ggtcagtgacctaaaatggagtgaggccaaagcactgtcatgtcagtctt
+acttcctgcttagggcacagtgaagtaggaaacaatattttgaaaataag
+ttttaaaatttaaaatgatcaaaaagcaatatagttgcataaaagcactg
+taaaatatttaaaaaggttaaaactgtggaaaattatattggtaagttta
+cagatcaataaaagcacctgttctccatctgaactagacaatggaaataa
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+tgaatgtagattttactgtgaagctatctgtgatttagctgtttgctccc
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+tgctcctttctgtgcaaccaattaaagaacaatgagtgtgatgctccatg
+tctgaatttcgtccagcctctctctgaactgtgatctttgtcctcatgaa
+ctttcccttttgttcattgaactatatggactcttcatttcatattgatt
+tactgtgcaatttacttttggacattgagaacttgaaataattccctgat
+cccttcccccttcactattaataactcatttctgtcaaactgtaagagta
+gactcattttttttagtttttaacattggattgttatttcatttagagtt
+ctctatctctaaatatttaatttagagaatgattaaaaagggaatgatat
+gcttgtttaaaatgaaagagaaaagctgtagtaaactgtgttacttggta
+atgactatttatcgtcgatactctgtagctgtgtaagttttgacaaatag
+tgtatctcgtgaaatcagtggttagcattgccgctattatatttactcat
+tttatcattataaatgtgcttagttcatcatgtag
+>NM_001030697
+gccgcccggcggggagcggcgcggagcggagcccggcggggcgcggcgag
+gatgggcagggggccccggcggctgccgccctccaggagatgaattaaaa
+tgcagcacaccacgtgcacagaggacaggatctatcatgcactggagaga
+tgtctgcacgggcttagcagagatgctgtctccagcagatgggctgcagg
+gctgtgcctgaactgctggagcctgcaggagctggtgagcagggatgcag
+gtaactacctcatcctggtggagaaaatcctcggcaaggccagggaggtg
+caggagaagtgtgactacgacctggtgatgcccctggccctgcttttcta
+ctacgcggtcctctatgctccccacatcccaccagactccgagctgctcc
+tgaaagctgccagcatctaccacagcttcctcacctggcccgtgccctac
+tgcgacgtcttccgtgagctgctcaccttcatcagtgatgagctcaaggc
+gccagggatttccttccagaggttggtgaggacggagcaggggctgcctg
+tgaagaactaccagagctccactgtgacggtgctgctgctgaaccgctcc
+gaggtgcagagtgagttcctctccatcgcagagaagctgagcagcactga
+gcccccccggcacgccacgctcgtcctgctgctggagcacctctaccagg
+tcaccttcggcacccgctgcgacctgggcagcctgcaccacctcctgaag
+gccaagacactggaagagctctctgagatctacaccagcgctgctgaagc
+gcaggagatcgcagccgccagcagtgaccctgtgttggcccgggagcggc
+tgcagagcgctctgcgggacattgccggggcagcagcacttcctaccatt
+gcaggagatgcgcagccccgcaggctgcagcccatccccatccctacttc
+gcgctgctacacctacagctgggaccaggataactttgatgtcctcaatg
+atgtcctcagcaaggagtgcagtgttgttgagcctgtggcctcagagaat
+gaggaggacgaggaagaggaggaggaggatgtggaaacagacggctgttc
+cccagagagggactcgctgctgtcccccatctcctccatttccaaggact
+ccgtgtactcagcgctgtcagaggatggacccaagcactcctgcgtgtcc
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+gagctgaaggtggagaagacccaccacaaatacagacacacgctgaccaa
+caagatctacaagctcttcaagagcaaaagccagctggtcctgaggagag
+acctgaaggactgtgtggatacaggctcgctcccactgcgccgtgctgag
+agcctgtgccacccccaggccaagccccgcatcccggcacgctcccggcg
+cgctcactcattgccacagcacgggctgggccagaagctgcagaccccgc
+agaccccgcagctgctcagcctgccccgccggcccttcctcagctacgac
+gaggatgccaaagtggccaccatgcgcgtggtggtcttcggctccgaccg
+catctcagggaaagtagcccgagcctacagcaacctgaggctgaaggaga
+gcacctgccctacactgacaaggtacttcaagctgcagtttttctacgtc
+cccgtgaagaggagctgcctgctgccagcagccctgctgatgcatcctcc
+tccatccccaagcgacctgcagctccgcgccttggcacaggcggagccca
+ccttggctggggcggagagcagcaccaatgacatctcccactacatcggc
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+g
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+gttcgcctcgccggtgcccgccctcctggtcttcatcctcatcttcctcg
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