Mercurial > repos > chrisd > coverage_sampler
comparison gene_fraction.xml @ 0:72901052a829 draft
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
| author | chrisd |
|---|---|
| date | Wed, 23 Mar 2016 17:54:53 -0400 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:72901052a829 |
|---|---|
| 1 <tool id="gene_fraction" name="Coverage Sampler" version="0.1.0"> | |
| 2 <requirements> | |
| 3 <requirement type="package" version="0.1">csa</requirement> | |
| 4 </requirements> | |
| 5 <stdio> | |
| 6 <exit_code range="1:" /> | |
| 7 </stdio> | |
| 8 <description>Calculates the amount of a gene that is covered from a sample of reads</description> | |
| 9 <command><![CDATA[ | |
| 10 csa | |
| 11 -amr_fp $input1 | |
| 12 -sam_fp $input2 | |
| 13 -min $min | |
| 14 -max $max | |
| 15 -t $threshold | |
| 16 -skip $skip | |
| 17 -samples $samples | |
| 18 -out_fp $output1 | |
| 19 ]]></command> | |
| 20 <inputs> | |
| 21 <param type="data" name="input1" format="fasta" label="Reference sequence" /> | |
| 22 <param type="data" name="input2" format="sam" label="SAM file" /> | |
| 23 <param name="min" type="integer" label="Starting sample level" | |
| 24 value="1" min="1" max="100" help="(-min)" /> | |
| 25 <param name="max" type="integer" label="Ending sample level" | |
| 26 value="1" min="1" max="100" help="(-max)" /> | |
| 27 <param name="threshold" type="integer" label="Gene threshold" | |
| 28 value="0" min="0" max="100" help="(-t)" /> | |
| 29 <param name="skip" type="integer" label="Amount of levels to skip" | |
| 30 value="1" min="1" max="100" help="(-skip)" /> | |
| 31 <param name="samples" type="integer" label="Amount of samples per level" | |
| 32 value="1" min="1" max="100" help="(-samples)" /> | |
| 33 </inputs> | |
| 34 <outputs> | |
| 35 <data name="output1" format="tabular" /> | |
| 36 </outputs> | |
| 37 <tests> | |
| 38 <test> | |
| 39 <param name="input1" value="ref.fa"/> | |
| 40 <param name="input2" value="test.sam"/> | |
| 41 <output name="outfil1" file="out.txt"/> | |
| 42 </test> | |
| 43 </tests> | |
| 44 <help><![CDATA[ | |
| 45 This program takes iterative samples from a SAM file with the goal of identifying the amount of a gene that is covered by a sample of reads. | |
| 46 | |
| 47 Program: Coverage Sampler | |
| 48 | |
| 49 Contact: Chris Dean <cdean11@rams.colostate.edu> | |
| 50 | |
| 51 Usage: csa [options] | |
| 52 | |
| 53 Options: | |
| 54 -amr_fp amr database path | |
| 55 -sam_fp sam file path | |
| 56 -min starting level | |
| 57 -max ending level | |
| 58 -skip amount of levels to skip | |
| 59 -t gene fraction threshold | |
| 60 -samples amount of samples per level | |
| 61 -out_fp output file path | |
| 62 ]]></help> | |
| 63 </tool> |