Mercurial > repos > mcharles > rapsodyn
changeset 22:afaf2e8aedcc draft
Uploaded
| author | mcharles |
|---|---|
| date | Thu, 21 Aug 2014 08:18:05 -0400 |
| parents | 67ac3c7bcdeb |
| children | edddaa8ab855 |
| files | rapsodyn/Galaxy-Workflow-Rapsodyn_v1.31.ga rapsodyn/Galaxy-Workflow-Rapsodyn_v1.32.ga 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_v1.34.ga rapsodyn/Galaxy-Workflow-Rapsodyn_v1.34_-_Filtering.ga rapsodyn/Galaxy-Workflow-Rapsodyn_v1.34_-_Preparation___Mapping.ga rapsodyn/Galaxy-Workflow-Rapsodyn_v1.42.ga rapsodyn/extractseq.pl rapsodyn/extractseq.xml rapsodyn/fastaGroomerForMakeBlastdb.pl rapsodyn/fastaGroomerForMakeBlastdb.xml rapsodyn/rapsodyn_stats_filtering.pl rapsodyn/rapsodyn_stats_filtering.xml rapsodyn/rapsodyn_stats_mapping.pl rapsodyn/rapsodyn_stats_mapping.xml rapsodyn/repository_dependencies.xml rapsodyn/tempo2.pl rapsodyn/tempo2.xml |
| diffstat | 20 files changed, 1838 insertions(+), 3155 deletions(-) [+] |
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"id": 19, - "output_name": "output_file" - }, - "input_list_filtered_file": { - "id": 13, - "output_name": "output_file" - }, - "input_mpileup_filtered_file": { - "id": 12, - "output_name": "output_file" - }, - "input_mpileup_row_file": { - "id": 11, - "output_name": "output_mpileup" - }, - "input_read1_row_file": { - "id": 0, - "output_name": "output" - }, - "input_read1_trimmed_file": { - "id": 6, - "output_name": "output_paired1" - }, - "input_read1_trimmednoN_file": { - "id": 7, - "output_name": "output_paired1" - }, - "input_read2_row_file": { - "id": 1, - "output_name": "output" - }, - "input_read2_trimmed_file": { - "id": 6, - "output_name": "output_paired2" - }, - "input_read2_trimmednoN_file": { - "id": 7, - "output_name": "output_paired2" - }, - "input_sam_filtered_file": { - "id": 9, - "output_name": "output_file" - }, - "input_sam_row_file": { - "id": 8, - "output_name": "output" - } - }, - "inputs": [], - "name": "rapsodyn_stats", - "outputs": [ - { - "name": "output_file", - "type": "txt" - } - ], - "position": { - "left": 4964.0001220703125, - "top": 427.5 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "rapsodyn_stats", - "tool_state": "{\"input_read1_trimmed_file\": \"null\", \"input_read2_trimmednoN_file\": \"null\", \"input_read2_row_file\": \"null\", \"input_read2_trimmed_file\": \"null\", \"__page__\": 0, \"input_sam_row_file\": \"null\", \"__rerun_remap_job_id__\": null, \"input_mpileup_filtered_file\": \"null\", \"input_read1_trimmednoN_file\": \"null\", \"input_assembly_file\": \"null\", \"input_sam_filtered_file\": \"null\", \"input_read1_row_file\": \"null\", \"input_mpileup_row_file\": \"null\", \"input_list_filtered_file\": \"null\", \"input_blast_filtered_file\": \"null\"}", - "tool_version": "0.01", - "type": "tool", - "user_outputs": [] - } - } -} \ No newline at end of file
--- a/rapsodyn/extractseq.pl Wed Aug 20 12:37:55 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,132 +0,0 @@ -#!/usr/bin/perl -#V1.10 - -use strict; -use warnings; -use Getopt::Long; - -my $input_variant_file; -my $input_assembly_file; -my $WINDOWS_LENGTH = 50; - -GetOptions ( -"input_variant_file=s" => \$input_variant_file, -"input_assembly_file=s" => \$input_assembly_file, -"window_length=i" => \$WINDOWS_LENGTH -) or die("Error in command line arguments\n"); - -open(INV, $input_variant_file) or die ("Can't open $input_variant_file\n"); -open(INA, $input_assembly_file) or die ("Can't open $input_assembly_file\n"); - -my @variant_list; - - -### Retrieving the assembly -my %genome; - -my $current_header=""; -my $current_seq=""; -while (my $ligne = <INA>){ - if ($ligne =~ /^\>(.*?)\s*$/){ - if ($current_header){ - $genome{$current_header} = $current_seq; - } - $current_header=$1; - $current_seq = ""; - } - else { - if ($ligne=~/^([ATGCNXatgcnx]+)\s*$/){ - $current_seq .= $1; - } - else { - print STDERR "Erreur Parsing n°2\n$ligne\n"; - } - } -} -#TRAITEMENT DU DERNIER -if ($current_header){ - $genome{$current_header} = $current_seq; - undef($current_seq); -} -close (INA); - - -### Retrieving the variant -while (my $ligne=<INV>){ - if ($ligne !~ /^\s*$/){ - my %variant; - my @fields = split (/\s+/,$ligne); - $variant{"ref"}=$fields[0]; - $variant{"position"}=$fields[1]; - $variant{"baseref"}=$fields[2]; - $variant{"depth"}=$fields[3]; - $variant{"pileup"}=$fields[4]; - - - my $start = &max($variant{"position"} - $WINDOWS_LENGTH,1); - my $stop = &min ($variant{"position"} + $WINDOWS_LENGTH,length($genome{$variant{"ref"}})); - my $length = $stop-$start+1; - - #print $variant{"position"}," / ",length($genome{$variant{"ref"}})," / ","$start / $stop / $length \n"; - - $variant{"SEQ"} = substr $genome{$variant{"ref"}},$start-1,$length; - - my $pileup = $variant{"pileup"}; - $pileup =~ s/\$//g; #the read start at this position - $pileup =~ s/\^.//g; #the read end at this position - my $descriptor = $variant{"position"}."_".$variant{"depth"}."_"; - if ($pileup=~/\+([0-9]+)([ACGTNacgtn]+)/){ - $descriptor .="I".$1."_".$2; - } - elsif ($pileup=~/\-([0-9]+)([ACGTNacgtn]+)/){ - $descriptor .="D".$1."_".$2; - } - elsif ($pileup=~/([ACGTNacgtn])/){ - $descriptor.="M1"."_".$1; - } - else { - $descriptor.="?_?"; - } - $variant{"desc"}=$descriptor; - - print ">",$variant{"ref"},"_",$descriptor,"\n",$variant{"SEQ"},"\n"; - - - - #print ">",$variant{"ref"},"_",$variant{"position"},"_",$variant{"depth"},"\n",$variant{"SEQ"},"\n"; - - push(@variant_list,\%variant); - } -} -close (INV); - - - - - - - - - -#*********** -sub min{ - my $first = shift; - my $second = shift; - if ($first <= $second){ - return $first; - } - else { - return $second; - } -} - -sub max { - my $first = shift; - my $second = shift; - if ($first >= $second){ - return $first; - } - else { - return $second; - } -} \ No newline at end of file
--- a/rapsodyn/extractseq.xml Wed Aug 20 12:37:55 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,20 +0,0 @@ -<tool id="extractseq" name="extractseq" version="0.03"> -<description>Extract Sequence around variant position</description> -<command interpreter="perl"> - extractseq.pl -input_variant_file $input_variant_file -input_assembly_file $input_assembly_file -window_length $window_length > $output_file -</command> -<inputs> -<param name="input_variant_file" type="data" format="pileup" label="Select a suitable input VARIANT file from your history"/> -<param name="input_assembly_file" type="data" format="fasta" label="Select a suitable input ASSEMBLY file from your history"/> -<param name="window_length" type="integer" value="50" label="Number of bases extracted before and after the variant position"/> -</inputs> -<outputs> - <data name="output_file" format="fasta" label="${tool.name} on ${on_string}"/> -</outputs> - -<help> - - - -</help> -</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/fastaGroomerForMakeBlastdb.pl Thu Aug 21 08:18:05 2014 -0400 @@ -0,0 +1,22 @@ +#!/usr/bin/perl +my $inputfasta = $ARGV[0]; + +open(IB, $inputfasta) or die ("Can't open $inputfasta \n"); + +while (my $ligne = <IB>){ + if ($ligne=~/\[.*?\=.*?\]/){ + $ligne =~ s/[\[\]]//g; + print $ligne; + } + elsif ($ligne =~/^\>/){ + print $ligne; + $ligne = <IB>; + $ligne =~ s/N/a/g; + print $ligne; + } + else { + print $ligne; + } +} + +close (IB);
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/fastaGroomerForMakeBlastdb.xml Thu Aug 21 08:18:05 2014 -0400 @@ -0,0 +1,20 @@ +<tool id="fastaGroomerForMakeBlastdb" name="fastaGroomerForMakeBlastdb" version="0.01"> +<description>fasta Groomer For MakeBlastdb</description> +<command interpreter="perl"> + fastaGroomerForMakeBlastdb.pl $input_fasta > $output_fasta +</command> +<inputs> + <param name="input_fasta" type="data" format="fasta" label="Select a suitable input FASTA file from your history"/> +</inputs> +<outputs> + <data name="output_fasta" format="fasta" label="${tool.name} on ${on_string}"/> +</outputs> + +<help> +MakeBlastDb has several warning handled has error which is problematic on galaxyn This groomer ensure that the fasta file will not generate this warnings / error : + +- First line of the sequence is more than 40% of N => replace all the 'N' of the first line by 'a' (not elegant but low impact and efficient) + +- Header line should not have [xxx=xxx] kind of text because MakeBlastdb try to interpret it => remove the [] when this feature is detected +</help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/rapsodyn_stats_filtering.pl Thu Aug 21 08:18:05 2014 -0400 @@ -0,0 +1,90 @@ +#!/usr/bin/perl +use strict; +use warnings; + +my $mpileup_row = $ARGV[0]; + +my $mpileup_filtered = $ARGV[1]; + +my $list_filtered = $ARGV[2]; + +my $blast_filtered = $ARGV[3]; + + +print "\nMPILEUP row\n"; +open(MPR, $mpileup_row) or die ("Can't open $mpileup_row\n"); +my $basecovered=0; +my $nbvariant=0; +while (my $line=<MPR>){ + my @fields = split(/\s+/,$line); + if ($#fields >= 4){ + $basecovered++; + my $match = $fields[4]; + $match =~ s/\$//g; #the read start at this position + $match =~ s/\^.//g; #the read end at this position followed by quality char + if ($match =~/[ACGTNacgtn]+/){ + $nbvariant++; + } + } + else { + #print STDERR "Erreur : $line\n"; + } +} + +print "Base covered :\t$basecovered\n"; +print "Variant detected :\t$nbvariant\n"; +close (MPR); + +print "\nMPILEUP filered\n"; +open(MPF, $mpileup_filtered) or die ("Can't open $mpileup_filtered\n"); + +$basecovered=0; +$nbvariant=0; +while (my $line=<MPF>){ + my @fields = split(/\s+/,$line); + if ($#fields >= 4){ + $basecovered++; + my $match = $fields[4]; + $match =~ s/\$//g; #the read start at this position + $match =~ s/\^.//g; #the read end at this position followed by quality char + if ($match =~/[ACGTNacgtn]+/){ + $nbvariant++; + } + } + else { + #print STDERR "Erreur : $line\n"; + } +} + +print "Variant selected :\t$nbvariant\n"; +close (MPF); + +print "\nMPILEUP filered without dubious position\n"; +open(LF, $list_filtered) or die ("Can't open $list_filtered\n"); +$nbvariant=0; +while (my $line=<LF>){ + $nbvariant++; +} + +print "Variant selected :\t$nbvariant\n"; +close (LF); + +print "\nMPILEUP filered without dubious position and BLAST\n"; +open(BF, $blast_filtered) or die ("Can't open $blast_filtered\n"); +$nbvariant=0; +while (my $line=<BF>){ + $nbvariant++; +} + +print "Variant selected :\t$nbvariant\n"; +close (BF); + + + + + + + + + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/rapsodyn_stats_filtering.xml Thu Aug 21 08:18:05 2014 -0400 @@ -0,0 +1,20 @@ +<tool id="rapsodyn_stats_filtering" name="rapsodyn_stats_filtering" version="0.01"> +<description>Merge best results from Blast</description> +<command interpreter="perl"> + rapsodyn_stats_filtering.pl $input_mpileup_row_file $input_mpileup_filtered_file $input_list_filtered_file $input_blast_filtered_file > $output_file +</command> +<inputs> +<param name="input_mpileup_row_file" type="data" format="pileup" label="Select a suitable input MPILEUP file from your history"/> +<param name="input_mpileup_filtered_file" type="data" format="pileup" label="Select a suitable input MPILEUP FILTERED file from your history"/> +<param name="input_list_filtered_file" type="data" format="pileup" label="Select a suitable input LIST FILTERED file from your history"/> +<param name="input_blast_filtered_file" type="data" format="pileup" label="Select a suitable input BLAST FILTERED file from your history"/> +</inputs> +<outputs> + <data name="output_file" format="txt" label="STATS"/> +</outputs> + + +<help> + +</help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/rapsodyn_stats_mapping.pl Thu Aug 21 08:18:05 2014 -0400 @@ -0,0 +1,193 @@ +#!/usr/bin/perl +use strict; +use warnings; + +my $read1_row = $ARGV[0]; +my $read2_row = $ARGV[1]; + +my $read1_trimmed = $ARGV[2]; +my $read2_trimmed = $ARGV[3]; + +my $read1_trimmed_noN = $ARGV[4]; +my $read2_trimmed_noN = $ARGV[5]; + +my $sam_row = $ARGV[6]; + +my $sam_filtered = $ARGV[7]; + + + + + +open(INR1R, $read1_row) or die ("Can't open $read1_row\n"); +my $nbread=0; +my $nbbase =0; +while (my $line1=<INR1R>){ + my $line2 = <INR1R>; + my $line3 = <INR1R>; + my $line4 = <INR1R>; + if ($line1 =~ /^@/){ + $nbread++; + if ($line2=~/([ATGCNX]+)/i){ + $nbbase += length($1); + } + } +} +print "Row Reads 1\t\tNumber of reads : ",$nbread,"\tnumber of bases : ",$nbbase,"\n"; +close (INR1R); + +open(INR2R, $read2_row) or die ("Can't open $read2_row\n"); +$nbread=0; +$nbbase =0; +while (my $line1=<INR2R>){ + my $line2 = <INR2R>; + my $line3 = <INR2R>; + my $line4 = <INR2R>; + if ($line1 =~ /^@/){ + $nbread++; + if ($line2=~/([ATGCNX]+)/i){ + $nbbase += length($1); + } + } +} +print "Row Reads 2\t\tNumber of reads : ",$nbread,"\tnumber of bases : ",$nbbase,"\n"; +close (INR2R); + +open(INR1T, $read1_trimmed) or die ("Can't open $read1_trimmed\n"); +$nbread=0; +$nbbase =0; +while (my $line1=<INR1T>){ + my $line2 = <INR1T>; + my $line3 = <INR1T>; + my $line4 = <INR1T>; + if ($line1 =~ /^@/){ + $nbread++; + if ($line2=~/([ATGCNX]+)/i){ + $nbbase += length($1); + } + else { + print STDERR "$line1\n$line2\n"; + } + } +} +print "Trimmed Reads 1\t\tNumber of reads : ",$nbread,"\tnumber of bases : ",$nbbase,"\n"; +close (INR1T); + +open(INR2T, $read2_trimmed) or die ("Can't open $read2_trimmed\n"); +$nbread=0; +$nbbase =0; +while (my $line1=<INR2T>){ + my $line2 = <INR2T>; + my $line3 = <INR2T>; + my $line4 = <INR2T>; + if ($line1 =~ /^@/){ + $nbread++; + if ($line2=~/([ATGCNX]+)/i){ + $nbbase += length($1); + } + else { + print STDERR "$line1\n$line2\n"; + } + } +} +print "Trimmed Reads 2\t\tNumber of reads : ",$nbread,"\tnumber of bases : ",$nbbase,"\n"; +close (INR2T); + +open(INR1N, $read1_trimmed_noN) or die ("Can't open $read1_trimmed_noN\n"); +$nbread=0; +$nbbase =0; +while (my $line1=<INR1N>){ + my $line2 = <INR1N>; + my $line3 = <INR1N>; + my $line4 = <INR1N>; + if ($line1 =~ /^@/){ + $nbread++; + if ($line2=~/([ATGCNX]+)/i){ + $nbbase += length($1); + } + else { + print STDERR "$line1\n$line2\n"; + } + } +} +print "Trimmed (no N) Reads 1\tNumber of reads : ",$nbread,"\tnumber of bases : ",$nbbase,"\n"; +close (INR1N); + +open(INR2N, $read2_trimmed_noN) or die ("Can't open $read2_trimmed_noN\n"); +$nbread=0; +$nbbase =0; +while (my $line1=<INR2N>){ + my $line2 = <INR2N>; + my $line3 = <INR2N>; + my $line4 = <INR2N>; + if ($line1 =~ /^@/){ + $nbread++; + if ($line2=~/([ATGCNX]+)/i){ + $nbbase += length($1); + } + else { + print STDERR "$line1\n$line2\n"; + } + } +} +print "Trimmed (no N) Reads 2\tNumber of reads : ",$nbread,"\tnumber of bases : ",$nbbase,"\n"; +close (INR2N); + +print "\nSAM row\n"; +open(SAM, $sam_row) or die ("Can't open $sam_row\n"); +my %bitscore; +while (my $line=<SAM>){ + if (($line !~ /^\@SQ/)&&($line !~ /^\@PG/)){ + my @fields = split(/\s+/,$line); + my $bit = $fields[1]; + if ($bitscore{$bit}){ + $bitscore{$bit}++; + } + else { + $bitscore{$bit}=1; + } + } +} + +print "bitscore\t"; +foreach my $key (sort {$bitscore{$b} <=> $bitscore{$a}} keys %bitscore) { + print $key,"\t*\t"; +} +print "\n"; + +print " number \t"; +foreach my $key (sort {$bitscore{$b} <=> $bitscore{$a}} keys %bitscore) { + print $bitscore{$key},"\t*\t"; +} +print "\n"; +close (SAM); + +print "\nSAM filtered\n"; +open(SAMF, $sam_filtered) or die ("Can't open $sam_filtered\n"); +undef %bitscore; +while (my $line=<SAMF>){ + if (($line !~ /^\@SQ/)&&($line !~ /^\@PG/)){ + my @fields = split(/\s+/,$line); + my $bit = $fields[1]; + if ($bitscore{$bit}){ + $bitscore{$bit}++; + } + else { + $bitscore{$bit}=1; + } + } +} + +print "bitscore\t"; +foreach my $key (sort {$bitscore{$b} <=> $bitscore{$a}} keys %bitscore) { + print $key,"\t*\t"; +} +print "\n"; + +print " number \t"; +foreach my $key (sort {$bitscore{$b} <=> $bitscore{$a}} keys %bitscore) { + print $bitscore{$key},"\t*\t"; +} +print "\n"; +close (SAMF); +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/rapsodyn_stats_mapping.xml Thu Aug 21 08:18:05 2014 -0400 @@ -0,0 +1,24 @@ +<tool id="rapsodyn_stats_mapping" name="rapsodyn_stats_mapping" version="0.01"> +<description>Stats on the mapping</description> +<command interpreter="perl"> + rapsodyn_stats_mapping.pl $input_read1_row_file $input_read2_row_file $input_read1_trimmed_file $input_read2_trimmed_file $input_read1_trimmednoN_file $input_read2_trimmednoN_file $input_sam_row_file $input_sam_filtered_file > $output_file +</command> +<inputs> +<param name="input_read1_row_file" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ1 ROW file from your history"/> +<param name="input_read2_row_file" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ2 ROW file from your history"/> +<param name="input_read1_trimmed_file" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ1 TRIMMED file from your history"/> +<param name="input_read2_trimmed_file" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ2 TRIMMED file from your history"/> +<param name="input_read1_trimmednoN_file" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ1 TRIMMED noN file from your history"/> +<param name="input_read2_trimmednoN_file" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ2 TRIMMED noN file from your history"/> +<param name="input_sam_row_file" type="data" format="sam" label="Select a suitable input SAM file from your history"/> +<param name="input_sam_filtered_file" type="data" format="sam" label="Select a suitable input SAM FILTERED file from your history"/> +</inputs> +<outputs> + <data name="output_file" format="txt" label="STATS"/> +</outputs> + + +<help> + +</help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/repository_dependencies.xml Thu Aug 21 08:18:05 2014 -0400 @@ -0,0 +1,10 @@ +<?xml version="1.0"?> +<repositories description="Rapsodyn worflow needed repository"> + <repository changeset_revision="c70137414dcd" name="sickle" owner="nikhil-joshi" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="1298445c852b" name="fastq_groomer" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="b4427dbb6ced" name="bwa_wrappers" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="973fea5b4bdf" name="samtools_mpileup" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> + <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" /> +</repositories>
--- a/rapsodyn/tempo2.pl Wed Aug 20 12:37:55 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,28 +0,0 @@ -#!/usr/bin/perl -#V1.10 - -use strict; -use warnings; -use Getopt::Long; - -my $input1 = $ARGV[0]; -my $output1 = $ARGV[1]; -my $input2 = $ARGV[2]; -my $output2 = $ARGV[3]; - -open(IN1, $input1) or die ("Can't open $input1\n"); -open(OUT1, ">$output1") or die ("Can't open $output1\n"); -while (my $ligne = <IN1>){ - print OUT1 $ligne; -} -close (IN1); -close (OUT1); - -open(IN2, $input2) or die ("Can't open $input2\n"); -open(OUT2, ">$output2") or die ("Can't open $output2\n"); -while (my $ligne = <IN2>){ - print OUT2 $ligne; -} -close (IN2); -close (OUT2); -
--- a/rapsodyn/tempo2.xml Wed Aug 20 12:37:55 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,66 +0,0 @@ -<tool id="tempo2" name="tempo2" version="0.01"> -<description>Temporisation with 2 inputs</description> -<command interpreter="perl"> - tempo2.pl $input1 $output1 $input2 $output2 -</command> -<inputs> -<param name="input1" type="data" format="txt" label="Select a FILE1 from your history"/> -<param name="out1_format" type="select" label="Output1 data type"> - <option value="fasta">fasta</option> - <option value="fastq">fastq</option> - <option value="fastqillumina">fastq (ILLUMINA)</option> - <option value="fastqsanger">fastq (SANGER)</option> - <option value="pileup">pileup</option> - <option value="sam">sam</option> - <option value="bam">bam</option> - <option value="xml">xml</option> - <option value="txt">txt</option> -</param> -<param name="input2" type="data" format="txt" label="Select a FILE2 from your history"/> -<param name="out2_format" type="select" label="Output2 data type"> - <option value="fasta">fasta</option> - <option value="fastq">fastq</option> - <option value="fastqillumina">fastq (ILLUMINA)</option> - <option value="fastqsanger">fastq (SANGER)</option> - <option value="pileup">pileup</option> - <option value="sam">sam</option> - <option value="bam">bam</option> - <option value="xml">xml</option> - <option value="txt">txt</option> -</param> - -</inputs> -<outputs> - - -<data format="txt" name="output1" label="OUTPUT 1"> - <change_format> - <when input="out1_format" value="fasta" format="fasta" /> - <when input="out1_format" value="fastq" format="fastq,fastqillumina,fastqsanger,fastqsolexa" /> - <when input="out1_format" value="fastqillumina" format="fastqillumina" /> - <when input="out1_format" value="fastqsanger" format="fastqsanger" /> - <when input="out1_format" value="pileup" format="pileup" /> - <when input="out1_format" value="sam" format="sam" /> - <when input="out1_format" value="bam" format="bam" /> - <when input="out1_format" value="xml" format="xml" /> - </change_format> -</data> -<data format="txt" name="output2" label="OUTPUT 2"> - <change_format> - <when input="out2_format" value="fasta" format="fasta" /> - <when input="out2_format" value="fastq" format="fastq,fastqillumina,fastqsanger,fastqsolexa" /> - <when input="out2_format" value="fastqillumina" format="fastqillumina" /> - <when input="out2_format" value="fastqsanger" format="fastqsanger" /> - <when input="out2_format" value="pileup" format="pileup" /> - <when input="out2_format" value="sam" format="sam" /> - <when input="out2_format" value="bam" format="bam" /> - <when input="out2_format" value="xml" format="xml" /> - </change_format> -</data> - -</outputs> - -<help> - -</help> -</tool>