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comparison mircounts.xml @ 7:65befdc9925a draft

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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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6:543472c9e272 7:65befdc9925a
1 <tool id="mircounts" name="miRcounts" version="1.1.0"> 1 <tool id="mircounts" name="miRcounts" version="1.1.1">
2 <description> Counts miRNA alignments from small RNA sequence data</description> 2 <description> Counts miRNA alignments from small RNA sequence data</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.18">gnu-wget</requirement> 4 <requirement type="package" version="1.18">gnu-wget</requirement>
5 <requirement type="package" version="1.2">bowtie</requirement> 5 <requirement type="package" version="1.2.0">bowtie</requirement>
6 <requirement type="package" version="1.4.1">samtools</requirement> 6 <requirement type="package" version="1.6.0">samtools</requirement>
7 <requirement type="package" version="0.11.2.1">pysam</requirement> 7 <requirement type="package" version="0.11.2.2">pysam</requirement>
8 <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement> 8 <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement>
9 <requirement type="package" version="0.20_34=r3.3.2_0">r-lattice</requirement> 9 <requirement type="package" version="0.20_34=r3.3.2_0">r-lattice</requirement>
10 </requirements> 10 </requirements>
11 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
12 wget ftp://mirbase.org/pub/mirbase/${mirbase_version}/genomes/${genomeKey}.gff3 && ## download the gff3 file specified by the variable genomeKey 12 wget --quiet ftp://mirbase.org/pub/mirbase/${mirbase_version}/genomes/${genomeKey}.gff3 && ## download the gff3 file specified by the variable genomeKey
13 python '$__tool_directory__'/mature_mir_gff_translation.py --input ${genomeKey}.gff3 --output $gff3 && ## transcode the mature miR genome coordinates into coordinates relative to the corresponding "miRNA_primary_transcript". 13 python '$__tool_directory__'/mature_mir_gff_translation.py --input ${genomeKey}.gff3 --output $gff3 && ## transcode the mature miR genome coordinates into coordinates relative to the corresponding "miRNA_primary_transcript".
14 wget ftp://mirbase.org/pub/mirbase/${mirbase_version}/hairpin.fa.gz && 14 wget --quiet ftp://mirbase.org/pub/mirbase/${mirbase_version}/hairpin.fa.gz &&
15 sh '$__tool_directory__'/format_fasta_hairpins.sh $genomeKey && 15 sh '$__tool_directory__'/format_fasta_hairpins.sh $genomeKey &&
16 #if $cutadapt.cutoption == "yes": 16 #if $cutadapt.cutoption == "yes":
17 python '$__tool_directory__'/yac.py --input $cutadapt.input 17 python '$__tool_directory__'/yac.py --input $cutadapt.input
18 --output clipped_input.fastq 18 --output clipped_input.fastq
19 --output_format fastq 19 --output_format fastq
22 --max $cutadapt.max 22 --max $cutadapt.max
23 --Nmode $cutadapt.Nmode && 23 --Nmode $cutadapt.Nmode &&
24 #else 24 #else
25 ln -f -s '$cutadapt.clipped_input' clipped_input.fastq && 25 ln -f -s '$cutadapt.clipped_input' clipped_input.fastq &&
26 #end if 26 #end if
27 bowtie-build hairpin.fa hairpin && 27 bowtie-build hairpin.fa hairpin >/dev/null &&
28 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' && 28 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 &&
29 samtools index $output && 29 samtools index $output &&
30 python '$__tool_directory__'/mircounts.py -pm --alignment $output --gff $gff3 --quality_threshold 10 --pre_mirs $pre_mir_count_file --mirs $mir_count_file --lattice $coverage_dataframe; 30 python '$__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;
31 #if $plotting.plottingOption == 'yes': 31 #if $plotting.plottingOption == 'yes':
32 Rscript '$__tool_directory__'/coverage_plotting.R --dataframe $coverage_dataframe --type $plotting.display --output $latticePDF 32 Rscript '$__tool_directory__'/coverage_plotting.R --dataframe $coverage_dataframe --type $plotting.display --output $latticePDF
33 #end if 33 #end if