Mercurial > repos > artbio > mircounts
comparison mircounts.xml @ 12:6d3e98cba73a draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 6718f7c6a0dbb36210f85a65b2e1ae0269855bb5
| author | artbio |
|---|---|
| date | Sat, 12 May 2018 09:06:24 -0400 |
| parents | 7d50d8d0c8c4 |
| children | b045c30fb768 |
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| 11:7d50d8d0c8c4 | 12:6d3e98cba73a |
|---|---|
| 1 <tool id="mircounts" name="miRcounts" version="1.3.1"> | 1 <tool id="mircounts" name="miRcounts" version="1.3.2"> |
| 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="1.2.0">bowtie</requirement> |
| 5 <requirement type="package" version="1.6.0">samtools</requirement> | 5 <requirement type="package" version="1.6.0">samtools</requirement> |
| 6 <requirement type="package" version="0.11.2.2">pysam</requirement> | 6 <requirement type="package" version="0.11.2.2">pysam</requirement> |
| 134 </data> | 134 </data> |
| 135 </outputs> | 135 </outputs> |
| 136 <tests> | 136 <tests> |
| 137 <test> | 137 <test> |
| 138 <param name="cutoption" value="yes" /> | 138 <param name="cutoption" value="yes" /> |
| 139 <param name="min" value="18"/> | |
| 140 <param name="max" value="32"/> | |
| 141 <param name="Nmode" value="reject"/> | |
| 142 <param name="clip_sequence" value="TGGAATTCTCGGGTGCCAAG"/> | |
| 143 <param name="v" value="1"/> | |
| 144 <param name="genomeKey" value="mmu"/> | |
| 145 <param name="mirbase_version" value="19"/> | |
| 146 <param name="input" value="mouse.fastq" ftype="fastqsanger"/> | |
| 147 <param name="plottingOption" value="yes"/> | |
| 148 <param name="display" value="relative"/> | |
| 149 <param name="output_premir_counts" value="True"/> | |
| 150 <param name="output_mir_counts" value="True"/> | |
| 151 <output name="output" file="mouse.bam"/> | |
| 152 <output name="gff3" file="mouse.19.gff3" lines_diff="22"/> | |
| 153 <output name="pre_mir_count_file" file="mouse_pre_mirs_count.29.tab"/> | |
| 154 <output name="mir_count_file" file="mouse_mirs_count.29.tab"/> | |
| 155 <output name="latticePDF" file="mouse_mir_coverage.pdf"/> | |
| 156 <output name="coverage_dataframe" file="mouse_lattice_dataframe.tab"/> | |
| 157 </test> | |
| 158 <test> | |
| 159 <param name="cutoption" value="yes" /> | |
| 139 <param name="min" value="15"/> | 160 <param name="min" value="15"/> |
| 140 <param name="max" value="25"/> | 161 <param name="max" value="25"/> |
| 141 <param name="Nmode" value="reject"/> | 162 <param name="Nmode" value="reject"/> |
| 142 <param name="clip_sequence" value="TCGTATGCCGTCTTCTGCTTG"/> | 163 <param name="clip_sequence" value="TCGTATGCCGTCTTCTGCTTG"/> |
| 143 <param name="v" value="0"/> | 164 <param name="v" value="0"/> |