Mercurial > repos > artbio > mircounts
diff mircounts.xml @ 10:de227b7307cf draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit af0f70b8156c078cc0d832c54ebb678af10c42a0
| author | artbio |
|---|---|
| date | Sun, 29 Apr 2018 18:57:13 -0400 |
| parents | 2a08a6eb471c |
| children | 7d50d8d0c8c4 |
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--- a/mircounts.xml Wed Apr 25 12:48:27 2018 -0400 +++ b/mircounts.xml Sun Apr 29 18:57:13 2018 -0400 @@ -1,18 +1,24 @@ -<tool id="mircounts" name="miRcounts" version="1.2.6"> +<tool id="mircounts" name="miRcounts" version="1.3.0"> <description> Counts miRNA alignments from small RNA sequence data</description> <requirements> - <requirement type="package" version="1.18">gnu-wget</requirement> <requirement type="package" version="1.2.0">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> + <stdio> + <exit_code range="1:" level="warning" description="Tool exception" /> + </stdio> <command detect_errors="exit_code"><![CDATA[ - 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 $gff3 && ## transcode the mature miR genome coordinates into coordinates relative to the corresponding "miRNA_primary_transcript". - wget --quiet ftp://mirbase.org/pub/mirbase/${mirbase_version}/hairpin.fa.gz && - sh '$__tool_directory__'/format_fasta_hairpins.sh $genomeKey && + tar -xvzf '$__tool_directory__'/mirbase.tar.gz && + python '$__tool_directory__'/mature_mir_gff_translation.py + --gff_path mirbase/${mirbase_version}/genomes/${genomeKey}.gff3 + --output $gff3 && ## transcode the mature miR genome coordinates into coordinates relative to the corresponding "miRNA_primary_transcript". + python '$__tool_directory__'/format_fasta_hairpins.py + --hairpins_path mirbase/${mirbase_version}/hairpin.fa.gz + --basename ${genomeKey} + --output hairpin.fa && #if $cutadapt.cutoption == "yes": python '$__tool_directory__'/yac.py --input $cutadapt.input --output clipped_input.fastq @@ -21,15 +27,15 @@ --min $cutadapt.min --max $cutadapt.max --Nmode $cutadapt.Nmode && - #else + #else: ln -f -s '$cutadapt.clipped_input' clipped_input.fastq && #end if - 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 && + bowtie-build hairpin.fa hairpin && + bowtie -v $v -M 1 --best --strata --norc -p \${GALAXY_SLOTS:-4} --sam hairpin -q clipped_input.fastq | samtools sort -O bam -o '$output' && 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 $coverage_dataframe; + python '$__tool_directory__'/mircounts.py --alignment $output --gff $gff3 --quality_threshold 10 --pre_mirs $pre_mir_count_file --mirs $mir_count_file --lattice $coverage_dataframe #if $plotting.plottingOption == 'yes': - Rscript '$__tool_directory__'/coverage_plotting.R --dataframe $coverage_dataframe --type $plotting.display --output $latticePDF + && Rscript '$__tool_directory__'/coverage_plotting.R --dataframe $coverage_dataframe --type $plotting.display --output $latticePDF #end if ]]></command> <inputs> @@ -141,8 +147,8 @@ <param name="plottingOption" value="no"/> <param name="output_premir_counts" value="True"/> <param name="output_mir_counts" value="True"/> - <output name="output" file="unclipped.out.22.bam" ftype="bam"/> - <output name="gff3" file="translated_dme.22.gff3" ftype="gff3" lines_diff="22"/> + <output name="output" file="unclipped.out.22.bam"/> + <output name="gff3" file="translated_dme.22.gff3" lines_diff="22"/> <output name="pre_mir_count_file" file="pre_mirs_unclipped_count.22.tab"/> <output name="mir_count_file" file="mirs_unclipped_count.22.tab"/> </test> @@ -159,8 +165,8 @@ <param name="plottingOption" value="no"/> <param name="output_premir_counts" value="True"/> <param name="output_mir_counts" value="True"/> - <output name="output" file="unclipped.out.bam" ftype="bam"/> - <output name="gff3" file="translated_dme.gff3" ftype="gff3" lines_diff="22"/> + <output name="output" file="unclipped.out.bam" /> + <output name="gff3" file="translated_dme.gff3" lines_diff="22"/> <output name="pre_mir_count_file" file="pre_mirs_unclipped_count.tab"/> <output name="mir_count_file" file="mirs_unclipped_count.tab"/> </test> @@ -178,11 +184,11 @@ <param name="display" value="relative"/> <param name="output_premir_counts" value="True"/> <param name="output_mir_counts" value="True"/> - <output name="output" file="unclipped.out.bam" ftype="bam"/> - <output name="gff3" file="translated_dme.gff3" ftype="gff3" lines_diff="22"/> + <output name="output" file="unclipped.out.bam"/> + <output name="gff3" file="translated_dme.gff3" lines_diff="22"/> <output name="pre_mir_count_file" file="pre_mirs_unclipped_count.tab"/> <output name="mir_count_file" file="mirs_unclipped_count.tab"/> - <output name="latticePDF" file="mir_unclipped_coverage.pdf" ftype="pdf"/> + <output name="latticePDF" file="mir_unclipped_coverage.pdf"/> <output name="coverage_dataframe" file="lattice_unclipped_dataframe.tab"/> </test> <test> @@ -195,11 +201,11 @@ <param name="display" value="absolute"/> <param name="output_premir_counts" value="True"/> <param name="output_mir_counts" value="True"/> - <output name="output" file="clipped.out.bam" ftype="bam"/> - <output name="gff3" file="translated_dme.gff3" ftype="gff3" lines_diff="22"/> + <output name="output" file="clipped.out.bam"/> + <output name="gff3" file="translated_dme.gff3" lines_diff="22"/> <output name="pre_mir_count_file" file="pre_mirs_clipped_count.tab"/> <output name="mir_count_file" file="mirs_clipped_count.tab"/> - <output name="latticePDF" file="mir_clipped_coverage.pdf" ftype="pdf"/> + <output name="latticePDF" file="mir_clipped_coverage.pdf"/> <output name="coverage_dataframe" file="lattice_clipped_dataframe.tab"/> </test> </tests>