Mercurial > repos > artbio > repenrich
comparison edger-repenrich.xml @ 3:1c9810ba0638 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 50a80e047ef74664d616a332f93c84f27cb6b7a0
| author | artbio |
|---|---|
| date | Fri, 22 Sep 2017 03:19:23 -0400 |
| parents | 15e3e29f310e |
| children | 83b5ea7cc342 |
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| 2:15e3e29f310e | 3:1c9810ba0638 |
|---|---|
| 1 <tool id="edger-repenrich" name="edgeR-repenrich" version="1.4.2"> | 1 <tool id="edger-repenrich" name="edgeR-repenrich" version="1.4.3"> |
| 2 <description>Determines differentially expressed features from RepEnrich counts</description> | 2 <description>Determines differentially expressed features from RepEnrich counts</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="3.16.5">bioconductor-edger</requirement> | 4 <requirement type="package" version="3.16.5">bioconductor-edger</requirement> |
| 5 <requirement type="package" version="3.30.13">bioconductor-limma</requirement> | 5 <requirement type="package" version="3.30.13">bioconductor-limma</requirement> |
| 6 <requirement type="package" version="1.20.0">r-getopt</requirement> | 6 <requirement type="package" version="1.20.0">r-getopt</requirement> |
| 70 #end if | 70 #end if |
| 71 -o '$edger_out' | 71 -o '$edger_out' |
| 72 ]]> | 72 ]]> |
| 73 </command> | 73 </command> |
| 74 <inputs> | 74 <inputs> |
| 75 <param name="factorName" type="text" value="FactorName" label="Specify a factor name, e.g. genotype or age or drug_x" | 75 <param name="factorName" type="text" value="FactorName" label="Specify a factor name, e.g. genotype or age or drug_x" |
| 76 help="Only letters, numbers and underscores will be retained in this field"> | 76 help="Only letters, numbers and underscores will be retained in this field"> |
| 77 <sanitizer> | 77 <sanitizer> |
| 78 <valid initial="string.letters,string.digits"><add value="_" /></valid> | 78 <valid initial="string.letters,string.digits"><add value="_" /></valid> |
| 79 </sanitizer> | 79 </sanitizer> |
| 80 </param> | 80 </param> |
| 81 <param name="factorLevel_A" type="text" value="FactorLevel1" label="Specify a factor level, typical values could be 'wildtype' or 'control'" | 81 <param name="factorLevel_A" type="text" value="FactorLevel1" label="Specify a factor level, typical values could be 'mutant' or 'Drug_X'" |
| 82 help="Only letters, numbers and underscores will be retained in this field"> | 82 help="Only letters, numbers and underscores will be retained in this field"> |
| 83 <sanitizer> | 83 <sanitizer> |
| 84 <valid initial="string.letters,string.digits"><add value="_" /></valid> | 84 <valid initial="string.letters,string.digits"><add value="_" /></valid> |
| 85 </sanitizer> | 85 </sanitizer> |
| 86 </param> | 86 </param> |
| 87 <param name="countsFiles_A" type="data" format="tabular" multiple="true" label="Counts file(s)" help="Count files must have been generated by repenrich" /> | 87 <param name="countsFiles_A" type="data" format="tabular" multiple="true" label="Counts file(s)" help="Count files must have been generated by repenrich" /> |
| 88 <param name="alignmentFiles_A" type="data" format="tabular" multiple="true" label="Number of aligned reads file(s)" help="files of total aligned reads generated by repenrich"/> | 88 <param name="alignmentFiles_A" type="data" format="tabular" multiple="true" label="Number of aligned reads file(s)" help="files of total aligned reads generated by repenrich"/> |
| 89 <param name="factorLevel_B" type="text" value="FactorLevel2" label="Specify a factor level, typical values could be 'mutant' or 'Drug_X'" | 89 <param name="factorLevel_B" type="text" value="FactorLevel2" label="Specify a factor level, typical values could be 'wildtype' or 'control'" |
| 90 help="Only letters, numbers and underscores will be retained in this field"> | 90 help="Only letters, numbers and underscores will be retained in this field"> |
| 91 <sanitizer> | 91 <sanitizer> |
| 92 <valid initial="string.letters,string.digits"><add value="_" /></valid> | 92 <valid initial="string.letters,string.digits"><add value="_" /></valid> |
| 93 </sanitizer> | 93 </sanitizer> |
| 94 </param> | 94 </param> |