Mercurial > repos > chrisd > coverage_sampler
comparison coverage_sampler.xml @ 1:fa1aae53a2f3 draft
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit b9f62f2ab10f5ff1c56edb895323820df36bdd0e-dirty
| author | chrisd |
|---|---|
| date | Tue, 28 Jun 2016 23:31:46 -0400 |
| parents | |
| children | ec439b0e7512 |
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| 0:72901052a829 | 1:fa1aae53a2f3 |
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| 1 <tool id="gene_fraction" name="Coverage Sampler" version="0.1.0"> | |
| 2 <description>A simple tool for calculating the amount of a gene that is covered by a sample of alignments</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="0.1">csa</requirement> | |
| 5 </requirements> | |
| 6 <stdio> | |
| 7 <exit_code range="1:" /> | |
| 8 </stdio> | |
| 9 <command><![CDATA[ | |
| 10 csa | |
| 11 -ref_fp $reference | |
| 12 -sam_fp $sam | |
| 13 -min $min | |
| 14 -max $max | |
| 15 -t $threshold | |
| 16 -skip $skip | |
| 17 -samples $samples | |
| 18 -out_fp $output | |
| 19 ]]></command> | |
| 20 <inputs> | |
| 21 <param type="data" name="reference" format="fasta" label="Reference sequence" /> | |
| 22 <param type="data" name="sam" 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 fraction threshold" | |
| 28 value="0" min="0" max="100" help="(-t)" /> | |
| 29 <param name="skip" type="integer" label="Amount of sample levels to skip" | |
| 30 value="1" min="1" max="100" help="(-skip)" /> | |
| 31 <param name="samples" type="integer" label="Iterations per sample level" | |
| 32 value="1" min="1" max="100" help="(-samples)" /> | |
| 33 </inputs> | |
| 34 <outputs> | |
| 35 <data name="output" format="tabular" /> | |
| 36 </outputs> | |
| 37 <tests> | |
| 38 <test> | |
| 39 <param name="reference" value="ref.fa"/> | |
| 40 <param name="sam" value="sampe.sam"/> | |
| 41 <param name="min" value="100"/> | |
| 42 <param name="max" value="100"/> | |
| 43 <param name="threshold" value="50"/> | |
| 44 <param name="skip" value="5"/> | |
| 45 <param name="samples" value="1"/> | |
| 46 <output name="output" file="csa_result" ftype="tabular"/> | |
| 47 </test> | |
| 48 <test> | |
| 49 <param name="reference" value="ref.fa"/> | |
| 50 <param name="sam" value="sampe.sam"/> | |
| 51 <param name="min" value="100"/> | |
| 52 <param name="max" value="100"/> | |
| 53 <param name="threshold" value="80"/> | |
| 54 <param name="skip" value="5"/> | |
| 55 <param name="samples" value="1"/> | |
| 56 <output name="output" file="csa_no_result" ftype="tabular"/> | |
| 57 </test> | |
| 58 </tests> | |
| 59 <help><![CDATA[ | |
| 60 A simple tool for calculating the amount of a gene that is covered by a sample of alignments. | |
| 61 | |
| 62 Program: Coverage Sampler | |
| 63 | |
| 64 Contact: Chris Dean <cdean11@rams.colostate.edu> | |
| 65 | |
| 66 Usage: csa [options] | |
| 67 | |
| 68 Options: | |
| 69 -ref_fp STR/FILE ref file path | |
| 70 -sam_fp STR/FILE sam file path | |
| 71 -min INT starting sample level | |
| 72 -max INT ending sample level | |
| 73 -skip INT amount of sample levels to skip | |
| 74 -t INT gene fraction threshold | |
| 75 -samples INT iterations per sample level | |
| 76 -out_fp STR/FILE output file path | |
| 77 ]]></help> | |
| 78 <citations> | |
| 79 </citations> | |
| 80 </tool> |