| Previous changeset 3:1805b262c12d (2017-05-30) Next changeset 5:ea5bba2c569f (2017-05-30) |
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Commit message:
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 0ec9810f3c05456fa8f19329a56eb1db32e218e5 |
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modified:
edger-repenrich.xml repenrich.xml |
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| diff -r 1805b262c12d -r d359ec9f0fe1 edger-repenrich.xml --- a/edger-repenrich.xml Tue May 30 10:34:53 2017 -0400 +++ b/edger-repenrich.xml Tue May 30 19:52:36 2017 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="edger-repenrich" name="edgeR-repenrich" version="1.1.0"> +<tool id="edger-repenrich" name="edgeR-repenrich" version="1.2.0"> <description>Determines differentially expressed features from RepEnrich counts</description> <requirements> <requirement type="package" version="3.16.5">bioconductor-edger</requirement> |
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| diff -r 1805b262c12d -r d359ec9f0fe1 repenrich.xml --- a/repenrich.xml Tue May 30 10:34:53 2017 -0400 +++ b/repenrich.xml Tue May 30 19:52:36 2017 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="repenrich" name="RepEnrich" version="1.1.0"> +<tool id="repenrich" name="RepEnrich" version="1.2.0"> <description>Repeat Element Profiling</description> <requirements> <requirement type="package" version="1.2.0">bowtie</requirement> @@ -11,32 +11,56 @@ </stdio> <command detect_errors="exit_code"><![CDATA[ #import re - #set input_base = re.sub('\.fastq$', '', str($input_fastq.element_identifier)) - #set baseReference = re.sub('[^\w\-]', '_', str($genome.element_identifier)) - #set baseReference = re.sub('.fa$', '', $baseReference) + #set input_base = 'Sample' + #set baseReference = 'Genome' ln -f -s '$genome' '${baseReference}.fa' && ln -f -s '$input_fastq' '${input_base}.fastq' && + #if $seq_method.seq_method_list == "paired-end": + ln -f -s '$input2_fastq' '${input_base}_2.fastq' && + #end if bowtie-build '$genome' ${baseReference} && python $__tool_directory__/RepEnrich_setup.py $repeatmasker ${baseReference}.fa setup_folder_${baseReference} && - bowtie $baseReference -p \${GALAXY_SLOTS:-4} -t -m 1 -S --max ${input_base}_multimap.fastq ${input_base}.fastq ${input_base}_unique.sam 2>bowtie_alignments.txt && - ALIGNED=\$(grep 'reads with at least one' bowtie_alignments.txt | cut -d ' ' -f 9) && - NONALIGNED=\$(grep 'reads that failed to align:' bowtie_alignments.txt | cut -d ' ' -f 7) && - echo \$((\$ALIGNED-\$NONALIGNED)) > bowtie_aligned.numb && + #if $seq_method.seq_method_list == "single-read": + bowtie $baseReference -p \${GALAXY_SLOTS:-4} -t -m 1 -S --max ${input_base}_multimap.fastq ${input_base}.fastq ${input_base}_unique.sam 2>bowtie_alignments.txt && + TOTAL=\$(grep 'reads processed:' bowtie_alignments.txt | cut -d ' ' -f 4) && + NONALIGNED=\$(grep 'reads that failed to align:' bowtie_alignments.txt | cut -d ' ' -f 7) && + echo \$((\$TOTAL-\$NONALIGNED)) > bowtie_aligned.numb && + #else: + bowtie $baseReference -p \${GALAXY_SLOTS:-4} -t -m 1 -S --max ${input_base}_multimap.fastq -1 ${input_base}.fastq -2 ${input_base}_2.fastq ${input_base}_unique.sam 2>bowtie_alignments.txt && + TOTAL=\$(grep 'reads processed:' bowtie_alignments.txt | cut -d ' ' -f 4) && + NONALIGNED=\$(grep 'reads that failed to align:' bowtie_alignments.txt | cut -d ' ' -f 7) && + echo \$((\$TOTAL-\$NONALIGNED)) > bowtie_aligned.numb && + #end if samtools view -bS ${input_base}_unique.sam > ${input_base}_unique.bam && samtools sort ${input_base}_unique.bam ${input_base}_unique_sorted && mv ${input_base}_unique_sorted.bam ${input_base}_unique.bam && samtools index ${input_base}_unique.bam && rm ${input_base}_unique.sam && - python $__tool_directory__/RepEnrich.py $repeatmasker ${input_base} ${input_base} setup_folder_${baseReference} ${input_base}_multimap.fastq ${input_base}_unique.bam --cpus "\${GALAXY_SLOTS:-4}" && + #if $seq_method.seq_method_list == "single-read": + python $__tool_directory__/RepEnrich.py $repeatmasker ${input_base} ${input_base} setup_folder_${baseReference} ${input_base}_multimap.fastq ${input_base}_unique.bam --cpus "\${GALAXY_SLOTS:-4}" && + #else: + python $__tool_directory__/RepEnrich.py $repeatmasker ${input_base} ${input_base} setup_folder_${baseReference} ${input_base}_multimap_1.fastq --fastqfile2 ${input_base}_multimap_2.fastq ${input_base}_unique.bam --cpus "\${GALAXY_SLOTS:-4}" --pairedend TRUE && + #end if cp $input_base/${input_base}_class_fraction_counts.txt class_fraction_counts.tabular && cp $input_base/${input_base}_family_fraction_counts.txt family_fraction_counts.tabular && cp $input_base/${input_base}_fraction_counts.txt fraction_counts.tabular - ]]></command> <!-- basic error handling --> <inputs> + <conditional name="seq_method"> + <param help="Paired-end or single-read sequencing" label="Sequencing method" name="seq_method_list" type="select"> + <option selected="True" value="single-read">Single-read sequencing</option> + <option value="paired-end">Paired-end sequencing</option> + </param> + <when value="single-read"> + <param format="fastq,fastqsanger" label="Single-reads" name="input_fastq" type="data" help="accepted formats: fastq, fastqsanger" /> + </when> + <when value="paired-end"> + <param format="fastq,fastqsanger" label="1st paired-end sequencing dataset" name="input_fastq" type="data" help="accepted formats: fastq, fastqsanger" /> + <param format="fastq,fastqsanger" label="2nd paired-end sequencing dataset" name="input2_fastq" type="data" help="accepted formats: fastq, fastqsanger" /> + </when> + </conditional> <param format="fasta" label="Reference genome in fasta format" name="genome" type="data" /> - <param format="fastq,fastqsanger" label="Single-reads sequencing dataset" name="input_fastq" type="data" help="accepted formats: fastq, fastqsanger" /> <param format="txt" label="RepeatMasker description file" name="repeatmasker" type="data" help="see help section"/> </inputs> @@ -49,10 +73,13 @@ </data> <data format="tabular" name="fraction_counts" label="RepEnrich on ${on_string}: fraction counts" from_work_dir="fraction_counts.tabular"> </data> - </outputs> + <data format="tabular" name="bowtieoutput" label="bowtie aligments" from_work_dir="bowtie_alignments.txt"> + </data> + </outputs> <tests> <test> + <param name="seq_method_list" value="single-read"/> <param name="input_fastq" value="Samp.fastq" ftype="fastq"/> <param name="genome" value="chrM.fa" ftype="fasta"/> <param name="repeatmasker" value="chrM_repeatmasker.txt" ftype="txt"/> |