Mercurial > repos > iuc > macs2
comparison macs2_randsample.xml @ 35:2f7d0d0b5bd0 draft
Uploaded
| author | iuc |
|---|---|
| date | Wed, 29 Apr 2015 12:06:24 -0400 |
| parents | c82a1f154c60 |
| children | 8c8ae1e19b10 |
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| 34:2b358389a54a | 35:2f7d0d0b5bd0 |
|---|---|
| 1 <tool id="macs2_randsample" name="MACS2 randsample" version="@VERSION_STRING@.0"> | |
| 2 <description>Randomly sample number or percentage of total reads</description> | |
| 3 <expand macro="requirements" /> | |
| 4 <expand macro="version_command" /> | |
| 5 <macros> | |
| 6 <import>macs2_macros.xml</import> | |
| 7 </macros> | |
| 8 <command> | |
| 9 macs2 randsample | |
| 10 -t "${ infile }" | |
| 11 -o "${ outfile }" | |
| 12 | |
| 13 --format '${ infile.extension.upper() }' | |
| 14 | |
| 15 @tag_size@ | |
| 16 #if $method_options.method_options_selector == 'percentage': | |
| 17 --percentage "${ method_options.percentage }" | |
| 18 #else: | |
| 19 --number "${ method_options.number }" | |
| 20 #end if | |
| 21 </command> | |
| 22 <expand macro="stdio" /> | |
| 23 <inputs> | |
| 24 <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" /> | |
| 25 <expand macro="tag_size" /> | |
| 26 | |
| 27 <conditional name="method_options"> | |
| 28 <param name="method_options_selector" type="select" label="Select action to be performed"> | |
| 29 <option value="percentage" selected="true">Percentage</option> | |
| 30 <option value="number">Number</option> | |
| 31 </param> | |
| 32 <when value="percentage"> | |
| 33 <param name="percentage" type="float" value="80.0" label="Pvalue cutoff for binomial distribution test" help="(--percentage)" /> | |
| 34 </when> | |
| 35 <when value="number"> | |
| 36 <param name="number" type="integer" value="800000" label="Number of tags you want to keep" help="Note that the number of tags in output is approximate as the number specified here (--number)" /> | |
| 37 </when> | |
| 38 </conditional> | |
| 39 </inputs> | |
| 40 <outputs> | |
| 41 <data name="outfile" format="bed" label="${tool.name} on ${on_string}" /> | |
| 42 </outputs> | |
| 43 <tests> | |
| 44 <!-- No test, due to the randomness --> | |
| 45 </tests> | |
| 46 <help> | |
| 47 **What it does** | |
| 48 | |
| 49 randsample tool from macs2 | |
| 50 | |
| 51 @citation@ | |
| 52 </help> | |
| 53 <expand macro="citations" /> | |
| 54 </tool> |