Mercurial > repos > jeltje > jtest1
changeset 0:65489579eace draft
Uploaded
| author | jeltje |
|---|---|
| date | Wed, 07 Jan 2015 14:10:22 -0500 |
| parents | |
| children | a5f711786a86 |
| files | myTools/test-data/testinput.fa myTools/test-data/testoutput.txt myTools/toolExample.pl myTools/toolExample.xml |
| diffstat | 4 files changed, 58 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/myTools/test-data/testinput.fa Wed Jan 07 14:10:22 2015 -0500 @@ -0,0 +1,4 @@ +>gi|1731512|gb|U51349.1|TAU51349 +CTACGGCAGGAGAAGACATCCGAAGAAGCTGACACCTCTCGCCTACAAGCAGTTTATCCCTAATGTCGCG +GAGAAGACCTTAGGGGCCAGCGGCAGATACGAAGGCAAGATAACGCGCAATTCGGAGAGATTTAAAGAAC +TTACTCCAAATTACAATCCCGACATTATCTTTAAGGATGAGGAGAACACG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/myTools/test-data/testoutput.txt Wed Jan 07 14:10:22 2015 -0500 @@ -0,0 +1,1 @@ +0.471
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/myTools/toolExample.pl Wed Jan 07 14:10:22 2015 -0500 @@ -0,0 +1,23 @@ +#!/usr/local/bin/perl -w + +# usage : perl toolExample.pl <FASTA file> <output file> + +open (IN, "<$ARGV[0]"); +open (OUT, ">$ARGV[1]"); +while (<IN>) { + chop; + if (m/^>/) { + s/^>//; + if ($. > 1) { + print OUT sprintf("%.3f", $gc/$length) . "\n"; + } + $gc = 0; + $length = 0; + } else { + ++$gc while m/[gc]/ig; + $length += length $_; + } +} +print OUT sprintf("%.3f", $gc/$length) . "\n"; +close( IN ); +close( OUT );
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/myTools/toolExample.xml Wed Jan 07 14:10:22 2015 -0500 @@ -0,0 +1,30 @@ +<tool id="fa_gc_content_1" name="Compute GC content"> + <description>for each sequence in a file</description> + <command interpreter="perl">toolExample.pl $input $output</command> + <inputs> + <param format="fasta" name="input" type="data" label="Source file"/> + </inputs> + <outputs> + <data format="tabular" name="output" /> + </outputs> + + <tests> + <test> + <param name="input" value="input.fa"/> + <output name="out_file1" file="testoutput.txt"/> + </test> + </tests> + + <help> +This tool computes GC content from a FASTA file. + </help> + +<tests> + <test> + <param name="input1" value="in.fa" /> + <output name="output" file="out.txt" /> + </test> +</tests> + +</tool> +