Mercurial > repos > artbio > mircounts
comparison mircounts.xml @ 8:3f62272192f9 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 0eaefbad21786cabed6791a6d06e9a0de8af10b0
| author | artbio |
|---|---|
| date | Mon, 23 Apr 2018 13:21:16 -0400 |
| parents | 65befdc9925a |
| children | 2a08a6eb471c |
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| 7:65befdc9925a | 8:3f62272192f9 |
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| 1 <tool id="mircounts" name="miRcounts" version="1.1.1"> | 1 <tool id="mircounts" name="miRcounts" version="1.2.0"> |
| 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> | 4 <requirement type="package" version="1.18">gnu-wget</requirement> |
| 5 <requirement type="package" version="1.2.0">bowtie</requirement> | 5 <requirement type="package" version="1.2.0">bowtie</requirement> |
| 6 <requirement type="package" version="1.6.0">samtools</requirement> | 6 <requirement type="package" version="1.6.0">samtools</requirement> |
| 73 <column name="name" index="1"/> | 73 <column name="name" index="1"/> |
| 74 <column name="value" index="0"/> | 74 <column name="value" index="0"/> |
| 75 </options> | 75 </options> |
| 76 </param> | 76 </param> |
| 77 <param name="mirbase_version" type="select" label="Choose miRbase version"> | 77 <param name="mirbase_version" type="select" label="Choose miRbase version"> |
| 78 <option selected="true" value="CURRENT">Current</option> | 78 <!-- <option selected="true" value="22">22</option> # activate when gff parsing is fixed --> |
| 79 <option value="21">21</option> | |
| 79 <option value="20">20</option> | 80 <option value="20">20</option> |
| 80 <option value="19">19</option> | 81 <option value="19">19</option> |
| 81 </param> | 82 </param> |
| 82 <param help="command [ bowtie -v 0,1,2,3 -M 1 --best --strata --norc ] will be used. Specify a value for -v (number of mismatches allowed)" label="Number of mismatches allowed" name="v" type="select"> | 83 <param help="command [ bowtie -v 0,1,2,3 -M 1 --best --strata --norc ] will be used. Specify a value for -v (number of mismatches allowed)" label="Number of mismatches allowed" name="v" type="select"> |
| 83 <option value="0">0</option> | 84 <option value="0">0</option> |
| 133 <param name="max" value="25"/> | 134 <param name="max" value="25"/> |
| 134 <param name="Nmode" value="reject"/> | 135 <param name="Nmode" value="reject"/> |
| 135 <param name="clip_sequence" value="TCGTATGCCGTCTTCTGCTTG"/> | 136 <param name="clip_sequence" value="TCGTATGCCGTCTTCTGCTTG"/> |
| 136 <param name="v" value="0"/> | 137 <param name="v" value="0"/> |
| 137 <param name="genomeKey" value="dme"/> | 138 <param name="genomeKey" value="dme"/> |
| 138 <param name="mirbase_version" value="CURRENT"/> | 139 <param name="mirbase_version" value="21"/> |
| 139 <param name="input" value="input.unclipped.fastqsanger" ftype="fastqsanger"/> | 140 <param name="input" value="input.unclipped.fastqsanger" ftype="fastqsanger"/> |
| 140 <param name="plottingOption" value="no"/> | 141 <param name="plottingOption" value="no"/> |
| 141 <param name="output_premir_counts" value="True"/> | 142 <param name="output_premir_counts" value="True"/> |
| 142 <param name="output_mir_counts" value="True"/> | 143 <param name="output_mir_counts" value="True"/> |
| 143 <output name="output" file="unclipped.out.bam" ftype="bam"/> | 144 <output name="output" file="unclipped.out.bam" ftype="bam"/> |
| 151 <param name="max" value="25"/> | 152 <param name="max" value="25"/> |
| 152 <param name="Nmode" value="reject"/> | 153 <param name="Nmode" value="reject"/> |
| 153 <param name="clip_sequence" value="TCGTATGCCGTCTTCTGCTTG"/> | 154 <param name="clip_sequence" value="TCGTATGCCGTCTTCTGCTTG"/> |
| 154 <param name="v" value="0"/> | 155 <param name="v" value="0"/> |
| 155 <param name="genomeKey" value="dme"/> | 156 <param name="genomeKey" value="dme"/> |
| 156 <param name="mirbase_version" value="CURRENT"/> | 157 <param name="mirbase_version" value="21"/> |
| 157 <param name="input" value="input.unclipped.fastqsanger" ftype="fastqsanger"/> | 158 <param name="input" value="input.unclipped.fastqsanger" ftype="fastqsanger"/> |
| 158 <param name="plottingOption" value="yes"/> | 159 <param name="plottingOption" value="yes"/> |
| 159 <param name="display" value="relative"/> | 160 <param name="display" value="relative"/> |
| 160 <param name="output_premir_counts" value="True"/> | 161 <param name="output_premir_counts" value="True"/> |
| 161 <param name="output_mir_counts" value="True"/> | 162 <param name="output_mir_counts" value="True"/> |
| 168 </test> | 169 </test> |
| 169 <test> | 170 <test> |
| 170 <param name="cutoption" value="no" /> | 171 <param name="cutoption" value="no" /> |
| 171 <param name="v" value="1"/> | 172 <param name="v" value="1"/> |
| 172 <param name="genomeKey" value="dme"/> | 173 <param name="genomeKey" value="dme"/> |
| 173 <param name="mirbase_version" value="CURRENT"/> | 174 <param name="mirbase_version" value="21"/> |
| 174 <param name="clipped_input" value="input.clipped.fastqsanger" ftype="fastqsanger"/> | 175 <param name="clipped_input" value="input.clipped.fastqsanger" ftype="fastqsanger"/> |
| 175 <param name="plottingOption" value="yes"/> | 176 <param name="plottingOption" value="yes"/> |
| 176 <param name="display" value="absolute"/> | 177 <param name="display" value="absolute"/> |
| 177 <param name="output_premir_counts" value="True"/> | 178 <param name="output_premir_counts" value="True"/> |
| 178 <param name="output_mir_counts" value="True"/> | 179 <param name="output_mir_counts" value="True"/> |
| 193 + Computes pre-mir and mir counts using the pysam python package | 194 + Computes pre-mir and mir counts using the pysam python package |
| 194 + Plots pre-mir read coverages using R lattice package (optional) | 195 + Plots pre-mir read coverages using R lattice package (optional) |
| 195 | 196 |
| 196 This tool uses a species-specific GFF3 file generated from mirBase_ to guide the parsing of a bam file of small RNA alignments. | 197 This tool uses a species-specific GFF3 file generated from mirBase_ to guide the parsing of a bam file of small RNA alignments. |
| 197 | 198 |
| 198 .. _mirBase: ftp://mirbase.org/pub/mirbase/CURRENT/genomes/ | 199 .. _mirBase: ftp://mirbase.org/pub/mirbase/ |
| 199 | 200 |
| 200 ------ | 201 ------ |
| 201 | 202 |
| 202 | 203 |
| 203 **Inputs** | 204 **Inputs** |