Mercurial > repos > chrisd > testing
comparison gene_fraction.xml @ 0:f95150c37d38 draft default tip
planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
| author | chrisd |
|---|---|
| date | Sun, 21 Feb 2016 23:31:55 -0500 |
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| children |
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| -1:000000000000 | 0:f95150c37d38 |
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| 1 <tool id="gene_fraction" name="Coverage sampler" version="0.1.0"> | |
| 2 <requirements> | |
| 3 </requirements> | |
| 4 <stdio> | |
| 5 <exit_code range="1:" /> | |
| 6 </stdio> | |
| 7 <command><![CDATA[ | |
| 8 $__tool_directory__/csa | |
| 9 -amr_fp $input1 | |
| 10 -sam_fp $input2 | |
| 11 -min $min | |
| 12 -max $max | |
| 13 -t $threshold | |
| 14 -skip $skip | |
| 15 -samples $samples | |
| 16 -out_fp $output1 | |
| 17 ]]></command> | |
| 18 <inputs> | |
| 19 <param type="data" name="input1" format="fasta" /> | |
| 20 <param type="data" name="input2" format="sam" /> | |
| 21 <param name="min" type="integer" label="Starting sample level" | |
| 22 value="1" min="1" max="100" help="(-min)" /> | |
| 23 <param name="max" type="integer" label="Ending sample level" | |
| 24 value="1" min="1" max="100" help="(-max)" /> | |
| 25 <param name="threshold" type="integer" label="Gene threshold" | |
| 26 value="1" min="1" max="100" help="(-t)" /> | |
| 27 <param name="skip" type="integer" label="Amount of levels to skip" | |
| 28 value="1" min="1" max="100" help="(-skip)" /> | |
| 29 <param name="samples" type="integer" label="Amount of samples per level" | |
| 30 value="1" min="1" max="100" help="(-samples)" /> | |
| 31 </inputs> | |
| 32 <outputs> | |
| 33 <data name="output1" format="tabular" /> | |
| 34 </outputs> | |
| 35 <tests> | |
| 36 <test> | |
| 37 <param name="input1" value="ref.fa"/> | |
| 38 <param name="input2" value="test.sam"/> | |
| 39 <output name="outfil1" file="out.txt"/> | |
| 40 </test> | |
| 41 </tests> | |
| 42 <help><![CDATA[ | |
| 43 | |
| 44 Program: Coverage Sampler | |
| 45 Contact: Chris Dean <cdean11@rams.colostate.edu | |
| 46 | |
| 47 Usage: csa [options] | |
| 48 | |
| 49 Options: | |
| 50 | |
| 51 -amr_fp amr database path | |
| 52 -sam_fp sam file path | |
| 53 -min starting level | |
| 54 -max ending level | |
| 55 -skip amount of levels to skip | |
| 56 -t gene fraction threshold | |
| 57 -samples amount of samples per level | |
| 58 -d directory parsing | |
| 59 -bam bam file parsing | |
| 60 -out_fp output file path | |
| 61 | |
| 62 | |
| 63 ]]></help> | |
| 64 </tool> |