Mercurial > repos > mcharles > rapsodyn
changeset 12:658acc3202dc draft
Uploaded
| author | mcharles |
|---|---|
| date | Tue, 19 Aug 2014 13:00:53 -0400 |
| parents | b7125d07b446 |
| children | f487491e1091 |
| files | rapsodyn/Galaxy-Workflow-Rapsodyn_v1.33_-_Filtering.ga rapsodyn/Galaxy-Workflow-Rapsodyn_v1.33_-_Mapping.ga rapsodyn/Galaxy-Workflow-Rapsodyn_v1.33_-_Preparation.ga rapsodyn/Galaxy-Workflow-Rapsodyn_v1.4.ga rapsodyn/repository_dependencies.xml rapsodyn/test.pl rapsodyn/test.xml rapsodyn/tool_dependencies.xml |
| diffstat | 8 files changed, 1556 insertions(+), 7 deletions(-) [+] |
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--- a/rapsodyn/repository_dependencies.xml Thu Aug 14 09:39:11 2014 -0400 +++ b/rapsodyn/repository_dependencies.xml Tue Aug 19 13:00:53 2014 -0400 @@ -7,4 +7,5 @@ <repository changeset_revision="8176b2575aa1" name="sam_to_bam" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> <repository changeset_revision="9710e9bcc5f3" name="samtools_filter" owner="jjohnson" toolshed="http://toolshed.g2.bx.psu.edu" /> <repository changeset_revision="623f727cdff1" name="ncbi_blast_plus" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="c70137414dcd" name="sickle" owner="nikhil-joshi" toolshed="http://toolshed.g2.bx.psu.edu" /> </repositories>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/test.pl Tue Aug 19 13:00:53 2014 -0400 @@ -0,0 +1,55 @@ +#!/usr/bin/perl +#V1.10 + +use strict; +use warnings; +use Getopt::Long; + +my $input_read1_file = $ARGV[0]; +my $input_read2_file = $ARGV[1]; +my $input_assembly_file = $ARGV[2]; +my $output_read1_file = $ARGV[3]; +my $output_read2_file = $ARGV[4]; +my $output_assembly_file = $ARGV[5]; + +#$output_read1_file = $input_read1_file.".tmp"; +#$output_read2_file = $input_read2_file.".tmp"; +#$output_assembly_file = $input_assembly_file.".tmp"; + + + +open(INR1, $input_read1_file) or die ("Can't open $input_read1_file\n"); +open(INR2, $input_read2_file) or die ("Can't open $input_read2_file\n"); +open(INAF, $input_assembly_file) or die ("Can't open $input_assembly_file\n"); + + +open(OUTR1, ">$output_read1_file") or die ("Can't open $output_read1_file\n"); +open(OUTR2, ">$output_read2_file") or die ("Can't open $output_read2_file\n"); +open(OUTAF, ">$output_assembly_file") or die ("Can't open $output_assembly_file\n"); + + + +while (my $ligne = <INR1>){ + print OUTR1 $ligne; +} + +close (INR1); +close (OUTR1); + +while (my $ligne = <INR2>){ + print OUTR2 $ligne; +} + +close (INR2); +close (OUTR2); + +while (my $ligne = <INAF>){ + print OUTAF $ligne; +} + +close (INAF); +close (OUTAF); + +print "Filler\n"; +print "$output_read1_file\n"; +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/test.xml Tue Aug 19 13:00:53 2014 -0400 @@ -0,0 +1,21 @@ +<tool id="test" name="test" version="0.01"> +<description>Merge best results from Blast</description> +<command interpreter="perl"> + test.pl $input_read1_file $input_read2_file $input_assembly_file $output_read1_file $output_read2_file $output_assembly_file > $output_stat_file +</command> +<inputs> +<param name="input_read1_file" type="data" format="fastq,fastqsolexa,fastqillumina,fastqsanger" label="Select a suitable input READ1 TRIMMED file from your history"/> +<param name="input_read2_file" type="data" format="fastq,fastqsolexa,fastqillumina,fastqsanger" label="Select a suitable input READ2 TRIMMED file from your history"/> +<param name="input_assembly_file" type="data" format="fasta" label="Select a suitable input ASSEMBLY file from your history"/> +</inputs> +<outputs> + <data name="output_read1_file" format="fastqsanger" label="${tool.name} READ1 TRIMMED"/> + <data name="output_read2_file" format="fastqsanger" label="${tool.name} READ2 TRIMMED"/> + <data name="output_assembly_file" format="fasta" label="${tool.name} ASSEMBLY"/> + <data name="output_stat_file" format="txt" label="${tool.name} STATS"/> +</outputs> + +<help> + +</help> +</tool>
--- a/rapsodyn/tool_dependencies.xml Thu Aug 14 09:39:11 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="sickle" version="1.210"> - <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="package_sickle_1_210" owner="jjohnson" changeset_revision="a78ad39d5ede" /> - </package> -</tool_dependency> -