Mercurial > repos > artbio > mircounts
diff mircounts.xml @ 7:65befdc9925a draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3514091150570410ce32cbdfda26fd6e5591fef1
| author | artbio |
|---|---|
| date | Sat, 14 Oct 2017 18:53:02 -0400 |
| parents | 543472c9e272 |
| children | 3f62272192f9 |
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--- a/mircounts.xml Tue Sep 05 17:54:46 2017 -0400 +++ b/mircounts.xml Sat Oct 14 18:53:02 2017 -0400 @@ -1,17 +1,17 @@ -<tool id="mircounts" name="miRcounts" version="1.1.0"> +<tool id="mircounts" name="miRcounts" version="1.1.1"> <description> Counts miRNA alignments from small RNA sequence data</description> <requirements> <requirement type="package" version="1.18">gnu-wget</requirement> - <requirement type="package" version="1.2">bowtie</requirement> - <requirement type="package" version="1.4.1">samtools</requirement> - <requirement type="package" version="0.11.2.1">pysam</requirement> + <requirement type="package" version="1.2.0">bowtie</requirement> + <requirement type="package" version="1.6.0">samtools</requirement> + <requirement type="package" version="0.11.2.2">pysam</requirement> <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement> <requirement type="package" version="0.20_34=r3.3.2_0">r-lattice</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ - wget ftp://mirbase.org/pub/mirbase/${mirbase_version}/genomes/${genomeKey}.gff3 && ## download the gff3 file specified by the variable genomeKey + wget --quiet ftp://mirbase.org/pub/mirbase/${mirbase_version}/genomes/${genomeKey}.gff3 && ## download the gff3 file specified by the variable genomeKey python '$__tool_directory__'/mature_mir_gff_translation.py --input ${genomeKey}.gff3 --output $gff3 && ## transcode the mature miR genome coordinates into coordinates relative to the corresponding "miRNA_primary_transcript". - wget ftp://mirbase.org/pub/mirbase/${mirbase_version}/hairpin.fa.gz && + wget --quiet ftp://mirbase.org/pub/mirbase/${mirbase_version}/hairpin.fa.gz && sh '$__tool_directory__'/format_fasta_hairpins.sh $genomeKey && #if $cutadapt.cutoption == "yes": python '$__tool_directory__'/yac.py --input $cutadapt.input @@ -24,8 +24,8 @@ #else ln -f -s '$cutadapt.clipped_input' clipped_input.fastq && #end if - bowtie-build hairpin.fa hairpin && - bowtie -v $v -M 1 --best --strata --norc -p \${GALAXY_SLOTS:-4} --sam hairpin -q clipped_input.fastq 2>/dev/null | samtools sort -O bam -o '$output' && + bowtie-build hairpin.fa hairpin >/dev/null && + bowtie -v $v -M 1 --best --strata --norc -p \${GALAXY_SLOTS:-4} --sam hairpin -q clipped_input.fastq | samtools sort -O bam -o '$output' 2>&1 && samtools index $output && python '$__tool_directory__'/mircounts.py -pm --alignment $output --gff $gff3 --quality_threshold 10 --pre_mirs $pre_mir_count_file --mirs $mir_count_file --lattice $coverage_dataframe; #if $plotting.plottingOption == 'yes':