Mercurial > repos > nml > fasta_extract
changeset 5:21888a4371d1 draft default tip
planemo upload for repository https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract commit df418d3445a03025bf38d27b1272fb913be548f1-dirty
| author | nml |
|---|---|
| date | Wed, 20 Sep 2017 13:25:29 -0400 |
| parents | c96a4314df39 |
| children | |
| files | fa-extract-few.pl fa-extract-sequence.xml test-data/input.fasta test-data/output.fasta |
| diffstat | 4 files changed, 35 insertions(+), 8 deletions(-) [+] |
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--- a/fa-extract-few.pl Mon Feb 06 16:35:50 2017 -0500 +++ b/fa-extract-few.pl Wed Sep 20 13:25:29 2017 -0400 @@ -1,4 +1,4 @@ -#!/usr/bin/perl -w +#!/usr/bin/env perl -w use strict; use Bio::SeqIO;
--- a/fa-extract-sequence.xml Mon Feb 06 16:35:50 2017 -0500 +++ b/fa-extract-sequence.xml Wed Sep 20 13:25:29 2017 -0400 @@ -1,11 +1,10 @@ -<tool id="fa-extract-sequence" name="Fasta Extract Sequence" version="1.0.0"> +<tool id="fa-extract-sequence" name="Fasta Extract Sequence" version="1.1.0"> <description>Extract a single sequence from a fasta file.</description> <requirements> - <requirement type="package" version="5.22.2.1">perl</requirement> <requirement type="package" version="1.6.924">perl-bioperl</requirement> </requirements> - <command interpreter="perl"> - fa-extract-few.pl + <command > + perl $__tool_directory__/fa-extract-few.pl -f $dataset $exact $inverse @@ -35,15 +34,16 @@ <param name="id" type="text" label="Sequence ID (or partial)" help="Name of the sequence to extract. Will also match partial names and return all matches." /> </when> </conditional> - - </inputs> <outputs> <data name="output" format="fasta" label="${tool.name} on ${on_string}: Fasta"/> </outputs> <tests> <test> - <output/> + <param name="dataset" value="input.fasta"/> + <param name="select" value="single"/> + <param name="id" value="B0R37_29930"/> + <output name="output" value="output.fasta"/> </test> </tests> <help>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.fasta Wed Sep 20 13:25:29 2017 -0400 @@ -0,0 +1,22 @@ +>lcl|MVOA01000203.1_cds_OON42627.1_1 [locus_tag=B0R37_29925] [protein=stress protein] [protein_id=OON42627.1] [location=join(181666..181684,1..410)] [gbkey=CDS] +ATGTTAAAAAAATTATCAGTATTTCTTATTGGTACTTTGCTATTGTTTGGTTTAGCAGCCTGTGATAGCA +TCAAATCGGTGGCTAGCGATGTTACAGTAGGAAAAGTAATTGAAGAATTTAAGGCTGCAGGACTTGAAGC +AGAACAGCCTAGTGATCTACCGGAAAAAGAATTTGGGAATACTAGAAAAGATGCGAAACGCATTCTTGTA +CCAGCACTAGGAGAAGATAGTGGTGGTAGAATATTTGAGTTTAAAAACAAACAAGATCTTGAACAAGCGA +AAAAGTACTATGACGATTTAGGTAACGGTAATCAAATGTTATTCTCTCATACTTACGCAAAAGGTAATTT +TCTTTTACAAATGAATGGTGACATGGAAGATGCCCAATTTAACAAATATAAAGAAGTAATGGACAAAATA +ATTAAGTAA +>lcl|MVOA01000203.1_cds_OON42628.1_2 [locus_tag=B0R37_29930] [protein=hypothetical protein] [protein_id=OON42628.1] [location=598..807] [gbkey=CDS] +GTGTATATCATAATTAATTTCGAGCCATTAAGTCCAGTTATGAATGACATAGCAATCAAGCTTGCCATGG +TACTATTTATACCGTTATTCCTAGCATTAATTGTCAAAGTTATACTTATGAAATTTATGAAAGAGTCGAT +TGCTGGCAGAATTGCAAGTCTATCTCTCTTATTTTTCATGTACTATGTATTTATATTTGTTACAGGGTAA +>lcl|MVOA01000203.1_cds_OON42630.1_3 [locus_tag=B0R37_29945] [protein=hypothetical protein] [protein_id=OON42630.1] [location=2291..2875] [gbkey=CDS] +ATGTTAAAACTTGTAGTAAATAATACCGGAACAGAACCAGAAGGTGATTCAGCTTTTTCAAACTATTTCA +CCTGCAAAGACTGTGTATATTATCTGTCAAAATCAGATTCTTGCAGTCTACAATTAGCAGCTGATTCAAA +TAATCCCCTTGTCCCTTATGAGTGTGGCAACTTTGAGGAAACCTATGAAATCGGAACGGAAGATCCATTG +AATTCACACATACACCAGCAACTTCGTGAAGAAAAAGCGCAAATACTAGCTGAAAGCTACCCAGCACAAC +CTTCTATTGATCCAATTCATAAAGACGCAATATGGTATGGGTCAGTAAACTATGGTTGTTGGATTATAAA +TGATTCGAAGAAACGTTTTGCACTTGCAGAACAGGTTCCTTTCGGTGATAATAATATGTCATCTAAAAAA +TACGCATCTCCTTTCCCTTTACATGACCATGGTGCAAAAGAAGGTATCCGGCACTATATGTGTTGGTACG +TAAATGAAAAAGGAATTGGCGAATACCATCTTCTTATTGGTGGTGTCATCATGAAAATTGCAGAAGGAGT +TAAGAAACTTGGATTCAATTACTAA \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.fasta Wed Sep 20 13:25:29 2017 -0400 @@ -0,0 +1,5 @@ +>lcl|MVOA01000203.1_cds_OON42628.1_2 [locus_tag=B0R37_29930] [protein=hypothetical protein] [protein_id=OON42628.1] [location=598..807] [gbkey=CDS] +GTGTATATCATAATTAATTTCGAGCCATTAAGTCCAGTTATGAATGACATAGCAATCAAG +CTTGCCATGGTACTATTTATACCGTTATTCCTAGCATTAATTGTCAAAGTTATACTTATG +AAATTTATGAAAGAGTCGATTGCTGGCAGAATTGCAAGTCTATCTCTCTTATTTTTCATG +TACTATGTATTTATATTTGTTACAGGGTAA