Mercurial > repos > nml > fasta_extract

changeset 5:21888a4371d1 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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(-) [+]
line wrap: on
line diff
--- 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