Mercurial > repos > artbio > mircounts
comparison 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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| 9:2a08a6eb471c | 10:de227b7307cf |
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| 1 <tool id="mircounts" name="miRcounts" version="1.2.6"> | 1 <tool id="mircounts" name="miRcounts" version="1.3.0"> |
| 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> | |
| 5 <requirement type="package" version="1.2.0">bowtie</requirement> | 4 <requirement type="package" version="1.2.0">bowtie</requirement> |
| 6 <requirement type="package" version="1.6.0">samtools</requirement> | 5 <requirement type="package" version="1.6.0">samtools</requirement> |
| 7 <requirement type="package" version="0.11.2.2">pysam</requirement> | 6 <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> | 7 <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> | 8 <requirement type="package" version="0.20_34=r3.3.2_0">r-lattice</requirement> |
| 10 </requirements> | 9 </requirements> |
| 10 <stdio> | |
| 11 <exit_code range="1:" level="warning" description="Tool exception" /> | |
| 12 </stdio> | |
| 11 <command detect_errors="exit_code"><![CDATA[ | 13 <command detect_errors="exit_code"><![CDATA[ |
| 12 wget --quiet ftp://mirbase.org/pub/mirbase/${mirbase_version}/genomes/${genomeKey}.gff3 && ## download the gff3 file specified by the variable genomeKey | 14 tar -xvzf '$__tool_directory__'/mirbase.tar.gz && |
| 13 python '$__tool_directory__'/mature_mir_gff_translation.py --input ${genomeKey}.gff3 --output $gff3 && ## transcode the mature miR genome coordinates into coordinates relative to the corresponding "miRNA_primary_transcript". | 15 python '$__tool_directory__'/mature_mir_gff_translation.py |
| 14 wget --quiet ftp://mirbase.org/pub/mirbase/${mirbase_version}/hairpin.fa.gz && | 16 --gff_path mirbase/${mirbase_version}/genomes/${genomeKey}.gff3 |
| 15 sh '$__tool_directory__'/format_fasta_hairpins.sh $genomeKey && | 17 --output $gff3 && ## transcode the mature miR genome coordinates into coordinates relative to the corresponding "miRNA_primary_transcript". |
| 18 python '$__tool_directory__'/format_fasta_hairpins.py | |
| 19 --hairpins_path mirbase/${mirbase_version}/hairpin.fa.gz | |
| 20 --basename ${genomeKey} | |
| 21 --output hairpin.fa && | |
| 16 #if $cutadapt.cutoption == "yes": | 22 #if $cutadapt.cutoption == "yes": |
| 17 python '$__tool_directory__'/yac.py --input $cutadapt.input | 23 python '$__tool_directory__'/yac.py --input $cutadapt.input |
| 18 --output clipped_input.fastq | 24 --output clipped_input.fastq |
| 19 --output_format fastq | 25 --output_format fastq |
| 20 --adapter_to_clip $cutadapt.clip_source.clip_sequence | 26 --adapter_to_clip $cutadapt.clip_source.clip_sequence |
| 21 --min $cutadapt.min | 27 --min $cutadapt.min |
| 22 --max $cutadapt.max | 28 --max $cutadapt.max |
| 23 --Nmode $cutadapt.Nmode && | 29 --Nmode $cutadapt.Nmode && |
| 24 #else | 30 #else: |
| 25 ln -f -s '$cutadapt.clipped_input' clipped_input.fastq && | 31 ln -f -s '$cutadapt.clipped_input' clipped_input.fastq && |
| 26 #end if | 32 #end if |
| 27 bowtie-build hairpin.fa hairpin >/dev/null && | 33 bowtie-build hairpin.fa hairpin && |
| 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 && | 34 bowtie -v $v -M 1 --best --strata --norc -p \${GALAXY_SLOTS:-4} --sam hairpin -q clipped_input.fastq | samtools sort -O bam -o '$output' && |
| 29 samtools index $output && | 35 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 $coverage_dataframe; | 36 python '$__tool_directory__'/mircounts.py --alignment $output --gff $gff3 --quality_threshold 10 --pre_mirs $pre_mir_count_file --mirs $mir_count_file --lattice $coverage_dataframe |
| 31 #if $plotting.plottingOption == 'yes': | 37 #if $plotting.plottingOption == 'yes': |
| 32 Rscript '$__tool_directory__'/coverage_plotting.R --dataframe $coverage_dataframe --type $plotting.display --output $latticePDF | 38 && Rscript '$__tool_directory__'/coverage_plotting.R --dataframe $coverage_dataframe --type $plotting.display --output $latticePDF |
| 33 #end if | 39 #end if |
| 34 ]]></command> | 40 ]]></command> |
| 35 <inputs> | 41 <inputs> |
| 36 <conditional name="cutadapt"> | 42 <conditional name="cutadapt"> |
| 37 <param label="Remove adapter sequence before aligning" name="cutoption" type="select"> | 43 <param label="Remove adapter sequence before aligning" name="cutoption" type="select"> |
| 139 <param name="mirbase_version" value="22"/> | 145 <param name="mirbase_version" value="22"/> |
| 140 <param name="input" value="input.unclipped.fastqsanger" ftype="fastqsanger"/> | 146 <param name="input" value="input.unclipped.fastqsanger" ftype="fastqsanger"/> |
| 141 <param name="plottingOption" value="no"/> | 147 <param name="plottingOption" value="no"/> |
| 142 <param name="output_premir_counts" value="True"/> | 148 <param name="output_premir_counts" value="True"/> |
| 143 <param name="output_mir_counts" value="True"/> | 149 <param name="output_mir_counts" value="True"/> |
| 144 <output name="output" file="unclipped.out.22.bam" ftype="bam"/> | 150 <output name="output" file="unclipped.out.22.bam"/> |
| 145 <output name="gff3" file="translated_dme.22.gff3" ftype="gff3" lines_diff="22"/> | 151 <output name="gff3" file="translated_dme.22.gff3" lines_diff="22"/> |
| 146 <output name="pre_mir_count_file" file="pre_mirs_unclipped_count.22.tab"/> | 152 <output name="pre_mir_count_file" file="pre_mirs_unclipped_count.22.tab"/> |
| 147 <output name="mir_count_file" file="mirs_unclipped_count.22.tab"/> | 153 <output name="mir_count_file" file="mirs_unclipped_count.22.tab"/> |
| 148 </test> | 154 </test> |
| 149 <test> | 155 <test> |
| 150 <param name="cutoption" value="yes" /> | 156 <param name="cutoption" value="yes" /> |
| 157 <param name="mirbase_version" value="21"/> | 163 <param name="mirbase_version" value="21"/> |
| 158 <param name="input" value="input.unclipped.fastqsanger" ftype="fastqsanger"/> | 164 <param name="input" value="input.unclipped.fastqsanger" ftype="fastqsanger"/> |
| 159 <param name="plottingOption" value="no"/> | 165 <param name="plottingOption" value="no"/> |
| 160 <param name="output_premir_counts" value="True"/> | 166 <param name="output_premir_counts" value="True"/> |
| 161 <param name="output_mir_counts" value="True"/> | 167 <param name="output_mir_counts" value="True"/> |
| 162 <output name="output" file="unclipped.out.bam" ftype="bam"/> | 168 <output name="output" file="unclipped.out.bam" /> |
| 163 <output name="gff3" file="translated_dme.gff3" ftype="gff3" lines_diff="22"/> | 169 <output name="gff3" file="translated_dme.gff3" lines_diff="22"/> |
| 164 <output name="pre_mir_count_file" file="pre_mirs_unclipped_count.tab"/> | 170 <output name="pre_mir_count_file" file="pre_mirs_unclipped_count.tab"/> |
| 165 <output name="mir_count_file" file="mirs_unclipped_count.tab"/> | 171 <output name="mir_count_file" file="mirs_unclipped_count.tab"/> |
| 166 </test> | 172 </test> |
| 167 <test> | 173 <test> |
| 168 <param name="cutoption" value="yes" /> | 174 <param name="cutoption" value="yes" /> |
| 176 <param name="input" value="input.unclipped.fastqsanger" ftype="fastqsanger"/> | 182 <param name="input" value="input.unclipped.fastqsanger" ftype="fastqsanger"/> |
| 177 <param name="plottingOption" value="yes"/> | 183 <param name="plottingOption" value="yes"/> |
| 178 <param name="display" value="relative"/> | 184 <param name="display" value="relative"/> |
| 179 <param name="output_premir_counts" value="True"/> | 185 <param name="output_premir_counts" value="True"/> |
| 180 <param name="output_mir_counts" value="True"/> | 186 <param name="output_mir_counts" value="True"/> |
| 181 <output name="output" file="unclipped.out.bam" ftype="bam"/> | 187 <output name="output" file="unclipped.out.bam"/> |
| 182 <output name="gff3" file="translated_dme.gff3" ftype="gff3" lines_diff="22"/> | 188 <output name="gff3" file="translated_dme.gff3" lines_diff="22"/> |
| 183 <output name="pre_mir_count_file" file="pre_mirs_unclipped_count.tab"/> | 189 <output name="pre_mir_count_file" file="pre_mirs_unclipped_count.tab"/> |
| 184 <output name="mir_count_file" file="mirs_unclipped_count.tab"/> | 190 <output name="mir_count_file" file="mirs_unclipped_count.tab"/> |
| 185 <output name="latticePDF" file="mir_unclipped_coverage.pdf" ftype="pdf"/> | 191 <output name="latticePDF" file="mir_unclipped_coverage.pdf"/> |
| 186 <output name="coverage_dataframe" file="lattice_unclipped_dataframe.tab"/> | 192 <output name="coverage_dataframe" file="lattice_unclipped_dataframe.tab"/> |
| 187 </test> | 193 </test> |
| 188 <test> | 194 <test> |
| 189 <param name="cutoption" value="no" /> | 195 <param name="cutoption" value="no" /> |
| 190 <param name="v" value="1"/> | 196 <param name="v" value="1"/> |
| 193 <param name="clipped_input" value="input.clipped.fastqsanger" ftype="fastqsanger"/> | 199 <param name="clipped_input" value="input.clipped.fastqsanger" ftype="fastqsanger"/> |
| 194 <param name="plottingOption" value="yes"/> | 200 <param name="plottingOption" value="yes"/> |
| 195 <param name="display" value="absolute"/> | 201 <param name="display" value="absolute"/> |
| 196 <param name="output_premir_counts" value="True"/> | 202 <param name="output_premir_counts" value="True"/> |
| 197 <param name="output_mir_counts" value="True"/> | 203 <param name="output_mir_counts" value="True"/> |
| 198 <output name="output" file="clipped.out.bam" ftype="bam"/> | 204 <output name="output" file="clipped.out.bam"/> |
| 199 <output name="gff3" file="translated_dme.gff3" ftype="gff3" lines_diff="22"/> | 205 <output name="gff3" file="translated_dme.gff3" lines_diff="22"/> |
| 200 <output name="pre_mir_count_file" file="pre_mirs_clipped_count.tab"/> | 206 <output name="pre_mir_count_file" file="pre_mirs_clipped_count.tab"/> |
| 201 <output name="mir_count_file" file="mirs_clipped_count.tab"/> | 207 <output name="mir_count_file" file="mirs_clipped_count.tab"/> |
| 202 <output name="latticePDF" file="mir_clipped_coverage.pdf" ftype="pdf"/> | 208 <output name="latticePDF" file="mir_clipped_coverage.pdf"/> |
| 203 <output name="coverage_dataframe" file="lattice_clipped_dataframe.tab"/> | 209 <output name="coverage_dataframe" file="lattice_clipped_dataframe.tab"/> |
| 204 </test> | 210 </test> |
| 205 </tests> | 211 </tests> |
| 206 <help> | 212 <help> |
| 207 | 213 |