Mercurial > repos > artbio > mircounts
comparison mircounts.xml @ 14:c163574c246f draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 51dc6c56c7d95fc229ffee958354211cd454fd36"
| author | artbio |
|---|---|
| date | Sun, 09 May 2021 17:10:07 +0000 |
| parents | b045c30fb768 |
| children | ffcd42f85b61 |
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| 13:b045c30fb768 | 14:c163574c246f |
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| 1 <tool id="mircounts" name="miRcounts" version="1.4.0"> | 1 <tool id="mircounts" name="miRcounts" version="1.5.1"> |
| 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="1.2.0">bowtie</requirement> | 4 <requirement type="package" version="1.34=ha1f6473_0">tar</requirement> |
| 5 <requirement type="package" version="1.9=h10a08f8_12">samtools</requirement> | 5 <requirement type="package" version="1.3.0=py39h176da8b_2">bowtie</requirement> |
| 6 <requirement type="package" version="0.15.3=py27hda2845c_1">pysam</requirement> | 6 <requirement type="package" version="1.12=h9aed4be_1">samtools</requirement> |
| 7 <requirement type="package" version="1.6.4=r36h6115d3f_0">r-optparse</requirement> | 7 <requirement type="package" version="0.16.0.1=py39h051187c_3">pysam</requirement> |
| 8 <requirement type="package" version="0.20_38=r36hcdcec82_1002">r-lattice</requirement> | 8 <requirement type="package" version="1.6.6=r40h6115d3f_1">r-optparse</requirement> |
| 9 <requirement type="package" version="0.20_44=r40hcfec24a_0">r-lattice</requirement> | |
| 9 </requirements> | 10 </requirements> |
| 10 <stdio> | 11 <stdio> |
| 11 <exit_code range="1:" level="warning" description="Tool exception" /> | 12 <exit_code range="1:" level="warning" description="Tool exception" /> |
| 12 </stdio> | 13 </stdio> |
| 13 <command detect_errors="exit_code"><![CDATA[ | 14 <command detect_errors="exit_code"><![CDATA[ |
| 14 tar -xvzf '$__tool_directory__'/mirbase.tar.gz && | 15 tar -xf '$__tool_directory__'/mirbase.tar.gz && |
| 15 python '$__tool_directory__'/mature_mir_gff_translation.py | 16 python '$__tool_directory__'/mature_mir_gff_translation.py |
| 16 --gff_path mirbase/${mirbase_version}/genomes/${genomeKey}.gff3 | 17 --gff_path mirbase/${mirbase_version}/genomes/${genomeKey}.gff3 |
| 17 --output $gff3 && ## transcode the mature miR genome coordinates into coordinates relative to the corresponding "miRNA_primary_transcript". | 18 --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 python '$__tool_directory__'/format_fasta_hairpins.py |
| 19 --hairpins_path mirbase/${mirbase_version}/hairpin.fa.gz | 20 --hairpins_path mirbase/${mirbase_version}/hairpin.fa.gz |
| 142 <param name="clipped_input" value="aga.fastqsanger" ftype="fastqsanger"/> | 143 <param name="clipped_input" value="aga.fastqsanger" ftype="fastqsanger"/> |
| 143 <param name="plottingOption" value="yes"/> | 144 <param name="plottingOption" value="yes"/> |
| 144 <param name="display" value="relative"/> | 145 <param name="display" value="relative"/> |
| 145 <param name="output_premir_counts" value="True"/> | 146 <param name="output_premir_counts" value="True"/> |
| 146 <param name="output_mir_counts" value="True"/> | 147 <param name="output_mir_counts" value="True"/> |
| 147 <output name="output" file="aga.bam"/> | 148 <output name="output" file="aga.bam" compare="sim_size" /> |
| 148 <output name="gff3" file="aga.22.gff3" lines_diff="22"/> | 149 <output name="gff3" file="aga.22.gff3" lines_diff="22" ftype="gff3" /> |
| 149 <output name="pre_mir_count_file" file="aga_pre_mirs_count.22.tab"/> | 150 <output name="pre_mir_count_file" file="aga_pre_mirs_count.22.tab" ftype="tabular" /> |
| 150 <output name="mir_count_file" file="aga_mirs_count.22.tab"/> | 151 <output name="mir_count_file" file="aga_mirs_count.22.tab" ftype="tabular" /> |
| 151 <output name="latticePDF" file="aga_mir_coverage.pdf"/> | 152 <output name="latticePDF" file="aga_mir_coverage.pdf" ftype="pdf" /> |
| 152 <output name="coverage_dataframe" file="aga_lattice_dataframe.tab"/> | 153 <output name="coverage_dataframe" file="aga_lattice_dataframe.tab" ftype="tabular" /> |
| 153 </test> | 154 </test> |
| 154 <test> | 155 <test> |
| 155 <param name="cutoption" value="yes" /> | 156 <param name="cutoption" value="yes" /> |
| 156 <param name="min" value="18"/> | 157 <param name="min" value="18"/> |
| 157 <param name="max" value="32"/> | 158 <param name="max" value="32"/> |
| 163 <param name="input" value="mouse.fastq" ftype="fastqsanger"/> | 164 <param name="input" value="mouse.fastq" ftype="fastqsanger"/> |
| 164 <param name="plottingOption" value="yes"/> | 165 <param name="plottingOption" value="yes"/> |
| 165 <param name="display" value="relative"/> | 166 <param name="display" value="relative"/> |
| 166 <param name="output_premir_counts" value="True"/> | 167 <param name="output_premir_counts" value="True"/> |
| 167 <param name="output_mir_counts" value="True"/> | 168 <param name="output_mir_counts" value="True"/> |
| 168 <output name="output" file="mouse.bam"/> | 169 <output name="output" file="mouse.bam" compare="sim_size"/> |
| 169 <output name="gff3" file="mouse.19.gff3" lines_diff="22"/> | 170 <output name="gff3" file="mouse.19.gff3" lines_diff="22" ftype="gff3" /> |
| 170 <output name="pre_mir_count_file" file="mouse_pre_mirs_count.29.tab"/> | 171 <output name="pre_mir_count_file" file="mouse_pre_mirs_count.29.tab" ftype="tabular" /> |
| 171 <output name="mir_count_file" file="mouse_mirs_count.29.tab"/> | 172 <output name="mir_count_file" file="mouse_mirs_count.29.tab" ftype="tabular" /> |
| 172 <output name="latticePDF" file="mouse_mir_coverage.pdf"/> | 173 <output name="latticePDF" file="mouse_mir_coverage.pdf" ftype="pdf" /> |
| 173 <output name="coverage_dataframe" file="mouse_lattice_dataframe.tab"/> | 174 <output name="coverage_dataframe" file="mouse_lattice_dataframe.tab" ftype="tabular" /> |
| 174 </test> | 175 </test> |
| 175 <test> | 176 <test> |
| 176 <param name="cutoption" value="yes" /> | 177 <param name="cutoption" value="yes" /> |
| 177 <param name="min" value="15"/> | 178 <param name="min" value="15"/> |
| 178 <param name="max" value="25"/> | 179 <param name="max" value="25"/> |
| 183 <param name="mirbase_version" value="22"/> | 184 <param name="mirbase_version" value="22"/> |
| 184 <param name="input" value="input.unclipped.fastqsanger" ftype="fastqsanger"/> | 185 <param name="input" value="input.unclipped.fastqsanger" ftype="fastqsanger"/> |
| 185 <param name="plottingOption" value="no"/> | 186 <param name="plottingOption" value="no"/> |
| 186 <param name="output_premir_counts" value="True"/> | 187 <param name="output_premir_counts" value="True"/> |
| 187 <param name="output_mir_counts" value="True"/> | 188 <param name="output_mir_counts" value="True"/> |
| 188 <output name="output" file="unclipped.out.22.bam"/> | 189 <output name="output" file="unclipped.out.22.bam" compare="sim_size" /> |
| 189 <output name="gff3" file="translated_dme.22.gff3" lines_diff="22"/> | 190 <output name="gff3" file="translated_dme.22.gff3" lines_diff="22" ftype="gff3" /> |
| 190 <output name="pre_mir_count_file" file="pre_mirs_unclipped_count.22.tab"/> | 191 <output name="pre_mir_count_file" file="pre_mirs_unclipped_count.22.tab" ftype="tabular" /> |
| 191 <output name="mir_count_file" file="mirs_unclipped_count.22.tab"/> | 192 <output name="mir_count_file" file="mirs_unclipped_count.22.tab" ftype="tabular" /> |
| 192 </test> | 193 </test> |
| 193 <test> | 194 <test> |
| 194 <param name="cutoption" value="yes" /> | 195 <param name="cutoption" value="yes" /> |
| 195 <param name="min" value="15"/> | 196 <param name="min" value="15"/> |
| 196 <param name="max" value="25"/> | 197 <param name="max" value="25"/> |
| 201 <param name="mirbase_version" value="21"/> | 202 <param name="mirbase_version" value="21"/> |
| 202 <param name="input" value="input.unclipped.fastqsanger" ftype="fastqsanger"/> | 203 <param name="input" value="input.unclipped.fastqsanger" ftype="fastqsanger"/> |
| 203 <param name="plottingOption" value="no"/> | 204 <param name="plottingOption" value="no"/> |
| 204 <param name="output_premir_counts" value="True"/> | 205 <param name="output_premir_counts" value="True"/> |
| 205 <param name="output_mir_counts" value="True"/> | 206 <param name="output_mir_counts" value="True"/> |
| 206 <output name="output" file="unclipped.out.bam" /> | 207 <output name="output" file="unclipped.out.bam" compare="sim_size" /> |
| 207 <output name="gff3" file="translated_dme.gff3" lines_diff="22"/> | 208 <output name="gff3" file="translated_dme.gff3" lines_diff="22" ftype="gff3" /> |
| 208 <output name="pre_mir_count_file" file="pre_mirs_unclipped_count.tab"/> | 209 <output name="pre_mir_count_file" file="pre_mirs_unclipped_count.tab" ftype="tabular" /> |
| 209 <output name="mir_count_file" file="mirs_unclipped_count.tab"/> | 210 <output name="mir_count_file" file="mirs_unclipped_count.tab" ftype="tabular" /> |
| 210 </test> | 211 </test> |
| 211 <test> | 212 <test> |
| 212 <param name="cutoption" value="yes" /> | 213 <param name="cutoption" value="yes" /> |
| 213 <param name="min" value="15"/> | 214 <param name="min" value="15"/> |
| 214 <param name="max" value="25"/> | 215 <param name="max" value="25"/> |
| 220 <param name="input" value="input.unclipped.fastqsanger" ftype="fastqsanger"/> | 221 <param name="input" value="input.unclipped.fastqsanger" ftype="fastqsanger"/> |
| 221 <param name="plottingOption" value="yes"/> | 222 <param name="plottingOption" value="yes"/> |
| 222 <param name="display" value="relative"/> | 223 <param name="display" value="relative"/> |
| 223 <param name="output_premir_counts" value="True"/> | 224 <param name="output_premir_counts" value="True"/> |
| 224 <param name="output_mir_counts" value="True"/> | 225 <param name="output_mir_counts" value="True"/> |
| 225 <output name="output" file="unclipped.out.bam"/> | 226 <output name="output" file="unclipped.out.bam" compare="sim_size" /> |
| 226 <output name="gff3" file="translated_dme.gff3" lines_diff="22"/> | 227 <output name="gff3" file="translated_dme.gff3" lines_diff="22" ftype="gff3" /> |
| 227 <output name="pre_mir_count_file" file="pre_mirs_unclipped_count.tab"/> | 228 <output name="pre_mir_count_file" file="pre_mirs_unclipped_count.tab" ftype="tabular" /> |
| 228 <output name="mir_count_file" file="mirs_unclipped_count.tab"/> | 229 <output name="mir_count_file" file="mirs_unclipped_count.tab" ftype="tabular" /> |
| 229 <output name="latticePDF" file="mir_unclipped_coverage.pdf"/> | 230 <output name="latticePDF" file="mir_unclipped_coverage.pdf" ftype="pdf"/> |
| 230 <output name="coverage_dataframe" file="lattice_unclipped_dataframe.tab"/> | 231 <output name="coverage_dataframe" file="lattice_unclipped_dataframe.tab" ftype="tabular" /> |
| 231 </test> | 232 </test> |
| 232 <test> | 233 <test> |
| 233 <param name="cutoption" value="no" /> | 234 <param name="cutoption" value="no" /> |
| 234 <param name="v" value="1"/> | 235 <param name="v" value="1"/> |
| 235 <param name="genomeKey" value="dme"/> | 236 <param name="genomeKey" value="dme"/> |
| 237 <param name="clipped_input" value="input.clipped.fastqsanger" ftype="fastqsanger"/> | 238 <param name="clipped_input" value="input.clipped.fastqsanger" ftype="fastqsanger"/> |
| 238 <param name="plottingOption" value="yes"/> | 239 <param name="plottingOption" value="yes"/> |
| 239 <param name="display" value="absolute"/> | 240 <param name="display" value="absolute"/> |
| 240 <param name="output_premir_counts" value="True"/> | 241 <param name="output_premir_counts" value="True"/> |
| 241 <param name="output_mir_counts" value="True"/> | 242 <param name="output_mir_counts" value="True"/> |
| 242 <output name="output" file="clipped.out.bam"/> | 243 <output name="output" file="clipped.out.bam" compare="sim_size" /> |
| 243 <output name="gff3" file="translated_dme.gff3" lines_diff="22"/> | 244 <output name="gff3" file="translated_dme.gff3" lines_diff="22" ftype="gff3" /> |
| 244 <output name="pre_mir_count_file" file="pre_mirs_clipped_count.tab"/> | 245 <output name="pre_mir_count_file" file="pre_mirs_clipped_count.tab" ftype="tabular" /> |
| 245 <output name="mir_count_file" file="mirs_clipped_count.tab"/> | 246 <output name="mir_count_file" file="mirs_clipped_count.tab" ftype="tabular" /> |
| 246 <output name="latticePDF" file="mir_clipped_coverage.pdf"/> | 247 <output name="latticePDF" file="mir_clipped_coverage.pdf" ftype="pdf" /> |
| 247 <output name="coverage_dataframe" file="lattice_clipped_dataframe.tab"/> | 248 <output name="coverage_dataframe" file="lattice_clipped_dataframe.tab" ftype="tabular" /> |
| 248 </test> | 249 </test> |
| 249 </tests> | 250 </tests> |
| 250 <help> | 251 <help> |
| 251 | 252 |
| 252 **What it does** | 253 **What it does** |