| Previous changeset 3:98d99e51579a (2017-11-16) Next changeset 5:411b36116b7a (2017-11-17) |
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Commit message:
Deleted selected files |
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added:
alignTophat.pl alignTophat.xml bed_pipe.loc.sample |
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removed:
gred_rnaseq-2369cfe4f737/alignTophat.pl gred_rnaseq-2369cfe4f737/alignTophat.xml gred_rnaseq-2369cfe4f737/bed_pipe.loc.sample gred_rnaseq-2369cfe4f737/tool_data_table_conf.xml.sample gred_rnaseq-2369cfe4f737/tool_dependencies.xml tool_dependencies.xml |
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| diff -r 98d99e51579a -r 4d637ab9113e alignTophat.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/alignTophat.pl Fri Nov 17 03:33:56 2017 -0500 |
| [ |
| b'@@ -0,0 +1,334 @@\n+#!/usr/bin/perl\n+use strict;\n+use warnings;\n+use Getopt::Long;\n+\n+my $max_procs = 8;\n+\n+my ($ma, $fastq, $fastqN, $mis,$findSens, $contaminants, $directional, $build_contaminant, $ref, $build_ref, $annotation, $dirBam, $dirBam_cont,$dirBed, $dirBedgraph, $outText, $outSimple, $random_w);\n+\n+GetOptions (\n+"direction:s" => \\$directional,\n+"random_w:s" => \\$random_w,\n+"find:s" => \\$findSens,\n+"fastq=s" => \\$fastq,\n+"fastq_n=s" => \\$fastqN, \n+"ma=i" => \\$ma,\n+"mis=i" => \\$mis,\n+"contaminants=s" => \\$contaminants,\n+"anno=s" => \\$annotation,\n+"build_contaminant" => \\$build_contaminant,\n+"ref=s" => \\$ref,\n+"build_ref" => \\$build_ref,\n+"dirbamCont=s" => \\$dirBam_cont,\n+"dirbam=s" => \\$dirBam,\n+"dirbedgraph=s" => \\$dirBedgraph,\n+"text=s" => \\$outText,\n+);\n+\n+$directional = lc($directional);\n+$findSens = lc($findSens);\n+$random_w = lc($random_w);\n+\n+if ($build_ref)\n+{\n+ `(bowtie2-build $ref $ref) 2> /dev/null `;\n+}\n+\n+if ($build_contaminant)\n+{\n+ `(bowtie2-build $contaminants $contaminants) 2> /dev/null `;\n+}\n+\n+#"outsimple=s" => \\$outSimple\n+#"annotation=s" => \\$annotation,\n+\n+#$annotation = "/data/visiteur/annotation/ara/TAIR10_all_sorted.bed";\n+#$annotation = "/data/home/pogorelcnikr/SG/humanGenes.bed";\n+\n+# mapping against contaminants databases in: contaminants, fastq, # of mismatches, output_dir out: tophat dir\n+tophat2($fastq, $contaminants, $mis, 1, \'dir_contaminant\');\n+`bamToFastq -i dir_contaminant/unmapped.bam -fq clean.fastq`;\n+\n+# mapping against contaminants databases in: $ref, fastq, # of mismatches, output_dir out: tophat dir\n+tophat2(\'clean.fastq\', $ref, $mis, $max_procs, \'dir_reference\');\n+\n+my $repTot = 0;\n+if ($ma == 0)\n+{\n+ open (my $rT, \'dir_reference/align_summary.txt\');\n+ my @repT = <$rT>;\n+ $repTot = $1 if $repT[2] =~ /\\s+Mapped\\s+:\\s+(\\d+).*/;\n+ close $rT;\n+}\n+else\n+{\n+ $repTot = $ma;\n+}\n+\n+# Creation of bedgraphs\n+my $dir_bedgraph = $fastqN.\'_bedgraph/\';\n+findUnique(\'dir_reference/accepted_hits.bam\', $dir_bedgraph, $repTot);\n+\n+# count in: unique_mapped.bam out: raw_count_simple antisens_count\n+if ($random_w eq \'true\')\n+{\n+ reference(\'rand_sorted.bam\', $repTot);\n+ `mv rand_sorted.bam dir_reference/random_sorted.bam`;\n+}\n+else\n+{\n+ reference(\'ac_sorted.bam\', $repTot);\n+ `mv ac_sorted.bam dir_reference/unique_sorted.bam`;\n+}\n+\n+zip(\'dir_reference\', $dirBam);\n+zip(\'dir_contaminant\', $dirBam_cont);\n+zip( $dir_bedgraph , $dirBedgraph);\n+\n+#################################\n+# inputs:\n+# fastq $_[0]\n+# bowtie2_index $_[1]\n+# mismatches # $_[2]\n+# output directory $_[3]\n+# max_procs $_[4]\n+#################################\n+sub tophat2\n+{\n+ my ($fastq, $index, $mismtaches, $proc, $out_repertory) = @_;\n+ $out_repertory = $out_repertory.\'/\' unless $out_repertory =~ /\\/$/;\n+ # print STDERR "/data/visiteur/tophat-2.0.12.Linux_x86_64/tophat2 -p $proc -N $mismtaches --b2-very-sensitive -o $out_repertory $index $fastq\\n";\n+ `tophat2 -p $proc -N $mismtaches --b2-very-sensitive -o $out_repertory $index $fastq 2> /dev/stdin`;\n+}\n+############################################################################################\n+\n+#################################\n+# inputs:\n+# bam $_[0]\n+# output directory $_[1]\n+#################################\n+sub findUnique\n+{\n+ my ($bam, $out_bedgraph, $sc) = @_;\n+ \n+ mkdir $out_bedgraph;\n+\n+ my $bedg_uni = $out_bedgraph.\'/\'.$fastqN.\'_unique.bedgraph\' ;\n+ my $bedg_all_multi = $out_bedgraph.\'/\'.$fastqN.\'_all_multi.bedgraph\' ;\n+ my $bedg_random = $out_bedgraph.\'/\'.$fastqN.\'_random_multi.bedgraph\' ;\n+\n+ my $bedg_uni_p = $out_bedgraph.\'/\'.$fastqN.\'_unique_plusStrand.bedgraph\' ;\n+ my $bedg_all_multi_p = $out_bedgraph.\'/\'.$fastqN.\'_all_multi_plusStrand.bedgraph\' ;\n+ my $bedg_random_p = $out_bedgraph.\'/\'.$fastqN.\'_random_multi_plusStrand.bedgraph\' ;\n+\n+ my $bedg_uni_m = $out_bedgraph.\'/\'.$fastqN.\'_unique_minusStrand.bedgraph\' ;\n+ my $bedg_all_multi_m = $out_bedgraph.\'/\'.$fastqN.\'_all_multi_minusStrand.bedgraph\' ;\n+ my $bedg_random_m = $out_bedgraph'..b'if ($directional eq \'true\')\n+ {\n+ #Same strand\n+ `bedtools intersect -s -wao -b ac.bed -a $annotation> intersectStranded.bed`;\n+ #Different strand\n+ `bedtools intersect -S -wao -b ac.bed -a $annotation> intersectOppositeStrand.bed`;\n+ \n+ open (my $strand, \'intersectStranded.bed\') || die "cannot open intersectStranded.bed\\n";\n+ my $i = 0;\n+ my $firstLine = <$strand>; chomp $firstLine;\n+ my @split = split /\\t/, $firstLine;\n+ my $prevId = $split[3];\n+ if ($split[16] != 0 && $split[12] - $split[11] == $split[16])\n+ {\n+ $tabRef[$i]->[1] = 1;\n+ }\n+ while(<$strand>)\n+ {\n+ chomp $_;\n+ @split = split /\\t/, $_;\n+ if ($split[3] ne $prevId)\n+ {\n+ $i++;\n+ }\n+ if ($split[16] != 0 && $split[12] - $split[11] == $split[16])\n+ {\n+ $tabRef[$i]->[1] += 1;\n+ }\n+ $prevId = $split[3];\n+ }\n+ close $strand;\n+ \n+ open ($strand, \'intersectOppositeStrand.bed\') || die "cannot open intersectOppositeStrand.bed\\n";\n+ $i = 0;\n+ $firstLine = <$strand>; chomp $firstLine;\n+ @split = split /\\t/, $firstLine;\n+ $prevId = $split[3];\n+ if ($split[16] != 0 && $split[12] - $split[11] == $split[16])\n+ {\n+ $tabRef[$i]->[2] = 1;\n+ }\n+ while(<$strand>)\n+ {\n+ chomp $_;\n+ @split = split /\\t/, $_;\n+ if ($split[3] ne $prevId)\n+ {\n+ $i++;\n+ }\n+ if ($split[16] != 0 && $split[12] - $split[11] == $split[16])\n+ {\n+ $tabRef[$i]->[2] += 1;\n+ }\n+ $prevId = $split[3];\n+ }\n+ close $strand;\n+ }\n+\n+ else\n+ {\n+ `bedtools intersect -wao -b ac.bed -a $annotation> intersect.bed`;\n+\n+ open (my $strand, \'intersect.bed\') || die "cannot open intersect.bed\\n";\n+ my $i = 0;\n+ my $firstLine = <$strand>; chomp $firstLine;\n+ my @split = split /\\t/, $firstLine;\n+ my $prevId = $split[3];\n+ if ($split[16] != 0 && $split[12] - $split[11] == $split[16])\n+ {\n+ $tabRef[$i]->[1] = 1;\n+ }\n+ while(<$strand>)\n+ {\n+ chomp $_;\n+ @split = split /\\t/, $_;\n+ if ($split[3] ne $prevId)\n+ {\n+ $i++;\n+ }\n+ if ($split[16] != 0 && $split[12] - $split[11] == $split[16])\n+ {\n+ $tabRef[$i]->[1] += 1;\n+ }\n+ $prevId = $split[3];\n+ }\n+ close $strand; \n+ }\n+ \n+ my $totplus = 0; my $totminus = 0;\n+ foreach my $outPut (@tabRef)\n+ {\n+ $totplus += $outPut->[1];\n+ $totminus += $outPut->[2];\n+ }\n+ \n+ open (my $out, ">".$outText) || die "cannot open raw_count.txt\\n";\n+ print $out "Chr\\tstart\\tend\\tID\\tscore\\tstrand\\ttype\\tD1\\tD2\\tD3\\treads\\trpm\\treads on opposite strand\\trpm\\n";\n+ my ($Sr, $Rr) = (0,0);\n+ foreach my $outPut (@tabRef)\n+ {\n+ if ($totplus > $totminus || $findSens eq \'false\')\n+ {\n+ $Sr = rpm($outPut->[1],$mapnum);\n+ $Rr = rpm($outPut->[2],$mapnum);\n+ print $out $outPut->[0]."\\t".$outPut->[1]."\\t".$Sr."\\t".$outPut->[2]."\\t".$Rr."\\n";\n+ }\n+ else\n+ {\n+ $Rr = rpm($outPut->[1],$mapnum);\n+ $Sr = rpm($outPut->[2],$mapnum);\n+ print $out $outPut->[0]."\\t".$outPut->[2]."\\t".$Sr."\\t".$outPut->[1]."\\t".$Rr."\\n";\n+ }\n+ }\n+ close $out;\n+}\n+############################################################################################\n+\n+#################################\n+# inputs:\n+# bam $_[0]\n+# output directory $_[1]\n+#################################\n+sub rpm\n+{\n+ my $raw_count = shift;\n+ my $mapped_number = shift;\n+ my $RPM = 0;\n+ $RPM = ($raw_count * 1000000) / ($mapped_number) if $mapped_number != 0;\n+ return $RPM;\n+}\n+############################################################################################\n+\n+#################################\n+# inputs:\n+# bam $_[0]\n+# output directory $_[1]\n+#################################\n+sub zip\n+{\n+ my ($in_dir, $out_tar) = @_;\n+ `tar -cvf tmp.tar $in_dir/`;\n+ `mv tmp.tar $out_tar`;\n+ rmdir $in_dir;\n+}\n+############################################################################################\n+\n' |
| b |
| diff -r 98d99e51579a -r 4d637ab9113e alignTophat.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/alignTophat.xml Fri Nov 17 03:33:56 2017 -0500 |
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| @@ -0,0 +1,151 @@ +<tool id="alignTophat" name="align RNAseq" version="0.0.1"> + <description>Align directionnal RNAseq to obtain bedgraphs and raw count file</description> + <command interpreter="perl"> + + ./alignTophat.pl + + --fastq ${first_input} + --fastq_n ${first_input.name} + + #if $Genome.refGenomeSource == "history": + --ref "${Genome.ownFile}" + --build_ref + #else: + --ref "${Genome.indices.fields.path}" + #end if + + #if $contaminants.refGenomeSource == "history": + --contaminants "${contaminants.ownFile}" + --build_contaminant + #else: + --contaminants "${contaminants.indices.fields.path}" + #end if + #if $anno.bedpipe == "history": + --annot "${anno.ownFile}" + #else: + --anno "${anno.indices.fields.path}" + #end if + + --mis $mis + --ma $ma + + --dirbam $dirbam + --dirbamCont $dirbamcont + --dirbedgraph $dirbedgraph + + --text $text + + --random_w $rand + --find $idDir.find + --direction $idDir.direc + </command> + <inputs> + + <param format="fastqsanger" name="first_input" type="data" label="fastq produced by fasteris" help=""/> + + + <conditional name="Genome"> + <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?"> + <option value="indexed">Use a built-in index</option> + <option value="history">Use one from the history</option> + </param> + <when value="indexed"> + <param name="indices" type="select" label="Select a reference genome"> + <options from_data_table="bowtie2_indexes"> + <filter type="sort_by" column="2" /> + <validator type="no_options" message="No indexes are available" /> + </options> + </param> + </when> + <when value="history"> + <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" /> + </when> + </conditional> + + + <conditional name="Genome"> + <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?"> + <option value="indexed">Use a built-in index</option> + <option value="history">Use one from the history</option> + </param> + <when value="indexed"> + <param name="indices" type="select" label="Select a reference genome"> + <options from_data_table="bowtie2_indexes"> + <filter type="sort_by" column="2" /> + <validator type="no_options" message="No indexes are available" /> + </options> + </param> + </when> + <when value="history"> + <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" /> + </when> + </conditional> + + <conditional name="contaminants"> + <param name="refGenomeSource" type="select" label="Will you select contaminants database from your history or use a built-in index?"> + <option value="indexed">Use a built-in index</option> + <option value="history">Use one from the history</option> + </param> + <when value="indexed"> + <param name="indices" type="select" label="Select contaminants reference"> + <options from_data_table="bowtie2_indexes"> + <filter type="sort_by" column="2" /> + <validator type="no_options" message="No indexes are available" /> + </options> + </param> + </when> + <when value="history"> + <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" /> + </when> + </conditional> + + <conditional name="anno"> + <param name="bedpipe" type="select" label="Will you select an annotation file from your history or use a built-in index?" help="tab file format, (chr start end id score strand type description1 description2 description3"> + <option value="indexed">Use a built-in index</option> + <option value="history">Use one from the history</option> + </param> + <when value="indexed"> + <param name="indices" type="select" label="Select annotation file"> + <options from_data_table="bed_pipe"> + <filter type="sort_by" column="2" /> + <validator type="no_options" message="No indexes are available" /> + </options> + </param> + </when> + <when value="history"> + <param name="ownFile" type="data" format="bed" metadata_name="dbkey" label="Select a reference from history" /> + </when> + </conditional> + + + <param name="mis" type="integer" value="0" label="mismatches"/> + <param name="ma" type="integer" value="0" label="normalization value" help="e.g number of mappers (if 0 auto)"/> + <param name="rand" type="boolean" checked="false" label="work on multi-mappers randomly assigned"/> + + + <conditional name="idDir"> + <param name="direc" type="boolean" checked="true" label="directional library"/> + <when value="false"> + <param name="find" type="hidden" value="false"/> + </when> + <when value="true"> + <param name="find" type="boolean" checked="true" label="auto sens finder"/> + </when> + </conditional> + </inputs> + + <outputs> + <data format="tar" name="dirbam" label="alignement_zip_${first_input.name}"/> + <data format="tar" name="dirbamcont" label="contaminant_zip_${first_input.name}"/> + <data format="tar" name="dirbedgraph" label="bedgraph_zip_${first_input.name}"/> + <data format="tabular" name="text" label="raw_count_tabular_${first_input.name}_rand_${rand}"/> + </outputs> + + <requirements> + <requirement type="package" version="2.2.6">bowtie2</requirement> + <requirement type="package" version="2.1.0">tophat</requirement> + <requirement type="package" version="2.17.0">bedtools</requirement> + <requirement type="package" version="0.1.19">samtools</requirement> + </requirements> + +</tool> |
| b |
| diff -r 98d99e51579a -r 4d637ab9113e bed_pipe.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bed_pipe.loc.sample Fri Nov 17 03:33:56 2017 -0500 |
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| @@ -0,0 +1,2 @@ +#<unique_id> <database_caption> <base_name_path> +dmel dmel_annotation /path/to/annotation/dmel/dmel_gene.bed |
| b |
| diff -r 98d99e51579a -r 4d637ab9113e gred_rnaseq-2369cfe4f737/alignTophat.pl --- a/gred_rnaseq-2369cfe4f737/alignTophat.pl Thu Nov 16 10:33:42 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,334 +0,0 @@\n-#!/usr/bin/perl\n-use strict;\n-use warnings;\n-use Getopt::Long;\n-\n-my $max_procs = 8;\n-\n-my ($ma, $fastq, $fastqN, $mis,$findSens, $contaminants, $directional, $build_contaminant, $ref, $build_ref, $annotation, $dirBam, $dirBam_cont,$dirBed, $dirBedgraph, $outText, $outSimple, $random_w);\n-\n-GetOptions (\n-"direction:s" => \\$directional,\n-"random_w:s" => \\$random_w,\n-"find:s" => \\$findSens,\n-"fastq=s" => \\$fastq,\n-"fastq_n=s" => \\$fastqN, \n-"ma=i" => \\$ma,\n-"mis=i" => \\$mis,\n-"contaminants=s" => \\$contaminants,\n-"anno=s" => \\$annotation,\n-"build_contaminant" => \\$build_contaminant,\n-"ref=s" => \\$ref,\n-"build_ref" => \\$build_ref,\n-"dirbamCont=s" => \\$dirBam_cont,\n-"dirbam=s" => \\$dirBam,\n-"dirbedgraph=s" => \\$dirBedgraph,\n-"text=s" => \\$outText,\n-);\n-\n-$directional = lc($directional);\n-$findSens = lc($findSens);\n-$random_w = lc($random_w);\n-\n-if ($build_ref)\n-{\n- `(bowtie2-build $ref $ref) 2> /dev/null `;\n-}\n-\n-if ($build_contaminant)\n-{\n- `(bowtie2-build $contaminants $contaminants) 2> /dev/null `;\n-}\n-\n-#"outsimple=s" => \\$outSimple\n-#"annotation=s" => \\$annotation,\n-\n-#$annotation = "/data/visiteur/annotation/ara/TAIR10_all_sorted.bed";\n-#$annotation = "/data/home/pogorelcnikr/SG/humanGenes.bed";\n-\n-# mapping against contaminants databases in: contaminants, fastq, # of mismatches, output_dir out: tophat dir\n-tophat2($fastq, $contaminants, $mis, 1, \'dir_contaminant\');\n-`bamToFastq -i dir_contaminant/unmapped.bam -fq clean.fastq`;\n-\n-# mapping against contaminants databases in: $ref, fastq, # of mismatches, output_dir out: tophat dir\n-tophat2(\'clean.fastq\', $ref, $mis, $max_procs, \'dir_reference\');\n-\n-my $repTot = 0;\n-if ($ma == 0)\n-{\n- open (my $rT, \'dir_reference/align_summary.txt\');\n- my @repT = <$rT>;\n- $repTot = $1 if $repT[2] =~ /\\s+Mapped\\s+:\\s+(\\d+).*/;\n- close $rT;\n-}\n-else\n-{\n- $repTot = $ma;\n-}\n-\n-# Creation of bedgraphs\n-my $dir_bedgraph = $fastqN.\'_bedgraph/\';\n-findUnique(\'dir_reference/accepted_hits.bam\', $dir_bedgraph, $repTot);\n-\n-# count in: unique_mapped.bam out: raw_count_simple antisens_count\n-if ($random_w eq \'true\')\n-{\n- reference(\'rand_sorted.bam\', $repTot);\n- `mv rand_sorted.bam dir_reference/random_sorted.bam`;\n-}\n-else\n-{\n- reference(\'ac_sorted.bam\', $repTot);\n- `mv ac_sorted.bam dir_reference/unique_sorted.bam`;\n-}\n-\n-zip(\'dir_reference\', $dirBam);\n-zip(\'dir_contaminant\', $dirBam_cont);\n-zip( $dir_bedgraph , $dirBedgraph);\n-\n-#################################\n-# inputs:\n-# fastq $_[0]\n-# bowtie2_index $_[1]\n-# mismatches # $_[2]\n-# output directory $_[3]\n-# max_procs $_[4]\n-#################################\n-sub tophat2\n-{\n- my ($fastq, $index, $mismtaches, $proc, $out_repertory) = @_;\n- $out_repertory = $out_repertory.\'/\' unless $out_repertory =~ /\\/$/;\n- # print STDERR "/data/visiteur/tophat-2.0.12.Linux_x86_64/tophat2 -p $proc -N $mismtaches --b2-very-sensitive -o $out_repertory $index $fastq\\n";\n- `tophat2 -p $proc -N $mismtaches --b2-very-sensitive -o $out_repertory $index $fastq 2> /dev/stdin`;\n-}\n-############################################################################################\n-\n-#################################\n-# inputs:\n-# bam $_[0]\n-# output directory $_[1]\n-#################################\n-sub findUnique\n-{\n- my ($bam, $out_bedgraph, $sc) = @_;\n- \n- mkdir $out_bedgraph;\n-\n- my $bedg_uni = $out_bedgraph.\'/\'.$fastqN.\'_unique.bedgraph\' ;\n- my $bedg_all_multi = $out_bedgraph.\'/\'.$fastqN.\'_all_multi.bedgraph\' ;\n- my $bedg_random = $out_bedgraph.\'/\'.$fastqN.\'_random_multi.bedgraph\' ;\n-\n- my $bedg_uni_p = $out_bedgraph.\'/\'.$fastqN.\'_unique_plusStrand.bedgraph\' ;\n- my $bedg_all_multi_p = $out_bedgraph.\'/\'.$fastqN.\'_all_multi_plusStrand.bedgraph\' ;\n- my $bedg_random_p = $out_bedgraph.\'/\'.$fastqN.\'_random_multi_plusStrand.bedgraph\' ;\n-\n- my $bedg_uni_m = $out_bedgraph.\'/\'.$fastqN.\'_unique_minusStrand.bedgraph\' ;\n- my $bedg_all_multi_m = $out_bedgraph.\'/\'.$fastqN.\'_all_multi_minusStrand.bedgraph\' ;\n- my $bedg_random_m = $out_bedgraph'..b'if ($directional eq \'true\')\n- {\n- #Same strand\n- `bedtools intersect -s -wao -b ac.bed -a $annotation> intersectStranded.bed`;\n- #Different strand\n- `bedtools intersect -S -wao -b ac.bed -a $annotation> intersectOppositeStrand.bed`;\n- \n- open (my $strand, \'intersectStranded.bed\') || die "cannot open intersectStranded.bed\\n";\n- my $i = 0;\n- my $firstLine = <$strand>; chomp $firstLine;\n- my @split = split /\\t/, $firstLine;\n- my $prevId = $split[3];\n- if ($split[16] != 0 && $split[12] - $split[11] == $split[16])\n- {\n- $tabRef[$i]->[1] = 1;\n- }\n- while(<$strand>)\n- {\n- chomp $_;\n- @split = split /\\t/, $_;\n- if ($split[3] ne $prevId)\n- {\n- $i++;\n- }\n- if ($split[16] != 0 && $split[12] - $split[11] == $split[16])\n- {\n- $tabRef[$i]->[1] += 1;\n- }\n- $prevId = $split[3];\n- }\n- close $strand;\n- \n- open ($strand, \'intersectOppositeStrand.bed\') || die "cannot open intersectOppositeStrand.bed\\n";\n- $i = 0;\n- $firstLine = <$strand>; chomp $firstLine;\n- @split = split /\\t/, $firstLine;\n- $prevId = $split[3];\n- if ($split[16] != 0 && $split[12] - $split[11] == $split[16])\n- {\n- $tabRef[$i]->[2] = 1;\n- }\n- while(<$strand>)\n- {\n- chomp $_;\n- @split = split /\\t/, $_;\n- if ($split[3] ne $prevId)\n- {\n- $i++;\n- }\n- if ($split[16] != 0 && $split[12] - $split[11] == $split[16])\n- {\n- $tabRef[$i]->[2] += 1;\n- }\n- $prevId = $split[3];\n- }\n- close $strand;\n- }\n-\n- else\n- {\n- `bedtools intersect -wao -b ac.bed -a $annotation> intersect.bed`;\n-\n- open (my $strand, \'intersect.bed\') || die "cannot open intersect.bed\\n";\n- my $i = 0;\n- my $firstLine = <$strand>; chomp $firstLine;\n- my @split = split /\\t/, $firstLine;\n- my $prevId = $split[3];\n- if ($split[16] != 0 && $split[12] - $split[11] == $split[16])\n- {\n- $tabRef[$i]->[1] = 1;\n- }\n- while(<$strand>)\n- {\n- chomp $_;\n- @split = split /\\t/, $_;\n- if ($split[3] ne $prevId)\n- {\n- $i++;\n- }\n- if ($split[16] != 0 && $split[12] - $split[11] == $split[16])\n- {\n- $tabRef[$i]->[1] += 1;\n- }\n- $prevId = $split[3];\n- }\n- close $strand; \n- }\n- \n- my $totplus = 0; my $totminus = 0;\n- foreach my $outPut (@tabRef)\n- {\n- $totplus += $outPut->[1];\n- $totminus += $outPut->[2];\n- }\n- \n- open (my $out, ">".$outText) || die "cannot open raw_count.txt\\n";\n- print $out "Chr\\tstart\\tend\\tID\\tscore\\tstrand\\ttype\\tD1\\tD2\\tD3\\treads\\trpm\\treads on opposite strand\\trpm\\n";\n- my ($Sr, $Rr) = (0,0);\n- foreach my $outPut (@tabRef)\n- {\n- if ($totplus > $totminus || $findSens eq \'false\')\n- {\n- $Sr = rpm($outPut->[1],$mapnum);\n- $Rr = rpm($outPut->[2],$mapnum);\n- print $out $outPut->[0]."\\t".$outPut->[1]."\\t".$Sr."\\t".$outPut->[2]."\\t".$Rr."\\n";\n- }\n- else\n- {\n- $Rr = rpm($outPut->[1],$mapnum);\n- $Sr = rpm($outPut->[2],$mapnum);\n- print $out $outPut->[0]."\\t".$outPut->[2]."\\t".$Sr."\\t".$outPut->[1]."\\t".$Rr."\\n";\n- }\n- }\n- close $out;\n-}\n-############################################################################################\n-\n-#################################\n-# inputs:\n-# bam $_[0]\n-# output directory $_[1]\n-#################################\n-sub rpm\n-{\n- my $raw_count = shift;\n- my $mapped_number = shift;\n- my $RPM = 0;\n- $RPM = ($raw_count * 1000000) / ($mapped_number) if $mapped_number != 0;\n- return $RPM;\n-}\n-############################################################################################\n-\n-#################################\n-# inputs:\n-# bam $_[0]\n-# output directory $_[1]\n-#################################\n-sub zip\n-{\n- my ($in_dir, $out_tar) = @_;\n- `tar -cvf tmp.tar $in_dir/`;\n- `mv tmp.tar $out_tar`;\n- rmdir $in_dir;\n-}\n-############################################################################################\n-\n' |
| b |
| diff -r 98d99e51579a -r 4d637ab9113e gred_rnaseq-2369cfe4f737/alignTophat.xml --- a/gred_rnaseq-2369cfe4f737/alignTophat.xml Thu Nov 16 10:33:42 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,151 +0,0 @@ -<tool id="alignTophat" name="align RNAseq" version="0.0.1"> - <description>Align directionnal RNAseq to obtain bedgraphs and raw count file</description> - <command interpreter="perl"> - - ./alignTophat.pl - - --fastq ${first_input} - --fastq_n ${first_input.name} - - #if $Genome.refGenomeSource == "history": - --ref "${Genome.ownFile}" - --build_ref - #else: - --ref "${Genome.indices.fields.path}" - #end if - - #if $contaminants.refGenomeSource == "history": - --contaminants "${contaminants.ownFile}" - --build_contaminant - #else: - --contaminants "${contaminants.indices.fields.path}" - #end if - #if $anno.bedpipe == "history": - --annot "${anno.ownFile}" - #else: - --anno "${anno.indices.fields.path}" - #end if - - --mis $mis - --ma $ma - - --dirbam $dirbam - --dirbamCont $dirbamcont - --dirbedgraph $dirbedgraph - - --text $text - - --random_w $rand - --find $idDir.find - --direction $idDir.direc - </command> - <inputs> - - <param format="fastqsanger" name="first_input" type="data" label="fastq produced by fasteris" help=""/> - - - <conditional name="Genome"> - <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?"> - <option value="indexed">Use a built-in index</option> - <option value="history">Use one from the history</option> - </param> - <when value="indexed"> - <param name="indices" type="select" label="Select a reference genome"> - <options from_data_table="bowtie2_indexes"> - <filter type="sort_by" column="2" /> - <validator type="no_options" message="No indexes are available" /> - </options> - </param> - </when> - <when value="history"> - <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" /> - </when> - </conditional> - - - <conditional name="Genome"> - <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?"> - <option value="indexed">Use a built-in index</option> - <option value="history">Use one from the history</option> - </param> - <when value="indexed"> - <param name="indices" type="select" label="Select a reference genome"> - <options from_data_table="bowtie2_indexes"> - <filter type="sort_by" column="2" /> - <validator type="no_options" message="No indexes are available" /> - </options> - </param> - </when> - <when value="history"> - <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" /> - </when> - </conditional> - - <conditional name="contaminants"> - <param name="refGenomeSource" type="select" label="Will you select contaminants database from your history or use a built-in index?"> - <option value="indexed">Use a built-in index</option> - <option value="history">Use one from the history</option> - </param> - <when value="indexed"> - <param name="indices" type="select" label="Select contaminants reference"> - <options from_data_table="bowtie2_indexes"> - <filter type="sort_by" column="2" /> - <validator type="no_options" message="No indexes are available" /> - </options> - </param> - </when> - <when value="history"> - <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" /> - </when> - </conditional> - - <conditional name="anno"> - <param name="bedpipe" type="select" label="Will you select an annotation file from your history or use a built-in index?" help="tab file format, (chr start end id score strand type description1 description2 description3"> - <option value="indexed">Use a built-in index</option> - <option value="history">Use one from the history</option> - </param> - <when value="indexed"> - <param name="indices" type="select" label="Select annotation file"> - <options from_data_table="bed_pipe"> - <filter type="sort_by" column="2" /> - <validator type="no_options" message="No indexes are available" /> - </options> - </param> - </when> - <when value="history"> - <param name="ownFile" type="data" format="bed" metadata_name="dbkey" label="Select a reference from history" /> - </when> - </conditional> - - - <param name="mis" type="integer" value="0" label="mismatches"/> - <param name="ma" type="integer" value="0" label="normalization value" help="e.g number of mappers (if 0 auto)"/> - <param name="rand" type="boolean" checked="false" label="work on multi-mappers randomly assigned"/> - - - <conditional name="idDir"> - <param name="direc" type="boolean" checked="true" label="directional library"/> - <when value="false"> - <param name="find" type="hidden" value="false"/> - </when> - <when value="true"> - <param name="find" type="boolean" checked="true" label="auto sens finder"/> - </when> - </conditional> - </inputs> - - <outputs> - <data format="tar" name="dirbam" label="alignement_zip_${first_input.name}"/> - <data format="tar" name="dirbamcont" label="contaminant_zip_${first_input.name}"/> - <data format="tar" name="dirbedgraph" label="bedgraph_zip_${first_input.name}"/> - <data format="tabular" name="text" label="raw_count_tabular_${first_input.name}_rand_${rand}"/> - </outputs> - - <requirements> - <requirement type="package" version="2.2.6">bowtie2</requirement> - <requirement type="package" version="2.1.0">tophat</requirement> - <requirement type="package" version="2.17.0">bedtools</requirement> - <requirement type="package" version="0.1.19">samtools</requirement> - </requirements> - -</tool> |
| b |
| diff -r 98d99e51579a -r 4d637ab9113e gred_rnaseq-2369cfe4f737/bed_pipe.loc.sample --- a/gred_rnaseq-2369cfe4f737/bed_pipe.loc.sample Thu Nov 16 10:33:42 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -#<unique_id> <database_caption> <base_name_path> -dmel dmel_annotation /path/to/annotation/dmel/dmel_gene.bed |
| b |
| diff -r 98d99e51579a -r 4d637ab9113e gred_rnaseq-2369cfe4f737/tool_data_table_conf.xml.sample --- a/gred_rnaseq-2369cfe4f737/tool_data_table_conf.xml.sample Thu Nov 16 10:33:42 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,6 +0,0 @@ -<tables> - <table name="bed_pipe" comment_char="#"> - <columns>value, name, path</columns> - <file path="${__HERE__}/test-data/bed_pipe.loc" /> - </table> -</tables> \ No newline at end of file |
| b |
| diff -r 98d99e51579a -r 4d637ab9113e gred_rnaseq-2369cfe4f737/tool_dependencies.xml --- a/gred_rnaseq-2369cfe4f737/tool_dependencies.xml Thu Nov 16 10:33:42 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,11 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="bowtie2" version="2.2.6"> - </package> - <package name="tophat" version="2.1.0"> - </package> - <package name="bedtools" version="2.24.0"> - </package> - <package name="samtools" version="1.3.1"> - </package> -</tool_dependency> |
| b |
| diff -r 98d99e51579a -r 4d637ab9113e tool_dependencies.xml --- a/tool_dependencies.xml Thu Nov 16 10:33:42 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,14 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="bowtie2" version="2.2.6"> - <repository changeset_revision="0d9cd7487cc9" name="package_bowtie_2_2_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="tophat" version="2.1.0"> - <repository changeset_revision="ed92d4c8e7f6" name="package_tophat_2_1_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="bedtools" version="2.24.0"> - <repository changeset_revision="3416a1d4a582" name="package_bedtools_2_24" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="samtools" version="1.3.1"> - </package> -</tool_dependency> \ No newline at end of file |