Mercurial > repos > galaxyp > pepquery
comparison pepquery.xml @ 1:9b5989900a87 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 542fee4158c3dbd0c5ad8cd7e97b77f55982e0bf"
| author | galaxyp |
|---|---|
| date | Fri, 17 Jul 2020 21:05:11 +0000 |
| parents | 851dcf14ee3a |
| children | 36716331fb7a |
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| 0:851dcf14ee3a | 1:9b5989900a87 |
|---|---|
| 39 #else | 39 #else |
| 40 -anno '$req_inputs.input_type.anno' | 40 -anno '$req_inputs.input_type.anno' |
| 41 #end if | 41 #end if |
| 42 #end if | 42 #end if |
| 43 #end if | 43 #end if |
| 44 -indexType $req_inputs.indexType | |
| 44 #if $modifications.fixed_mod | 45 #if $modifications.fixed_mod |
| 45 -fixMod '$modifications.fixed_mod' | 46 -fixMod '$modifications.fixed_mod' |
| 46 #end if | 47 #end if |
| 47 #if $modifications.var_mod | 48 #if $modifications.var_mod |
| 48 -varMod '$modifications.var_mod' | 49 -varMod '$modifications.var_mod' |
| 142 </when> | 143 </when> |
| 143 --> | 144 --> |
| 144 </conditional> | 145 </conditional> |
| 145 <param name="db_file" type="data" format="fasta" label="Protein Reference Database File" argument="-db" help="an input sequence that matches a reference will be ignored." /> | 146 <param name="db_file" type="data" format="fasta" label="Protein Reference Database File" argument="-db" help="an input sequence that matches a reference will be ignored." /> |
| 146 <param name="spectrum_file" type="data" format="mgf" label="Spectrum File" argument="-ms" help="Spectrum file used for identification, mgf format" /> | 147 <param name="spectrum_file" type="data" format="mgf" label="Spectrum File" argument="-ms" help="Spectrum file used for identification, mgf format" /> |
| 148 <param name="indexType" type="select" label="Report Spectrum Scan as" argument="-indexType" help="" > | |
| 149 <option value="1" selected="true">index (1-based) in MGF</option> | |
| 150 <option value="2">spectrum title in MGF</option> | |
| 151 </param> | |
| 147 </section> | 152 </section> |
| 148 <section name="modifications" title="Modifications" expanded="false"> | 153 <section name="modifications" title="Modifications" expanded="false"> |
| 149 <param name="fixed_mod" type="select" label="Fixed modification(s)" multiple="true" argument="-fixMod" help="Fixed modification"> | 154 <param name="fixed_mod" type="select" label="Fixed modification(s)" multiple="true" argument="-fixMod" help="Fixed modification"> |
| 150 <option value="6" selected="true">Carbamidomethylation of C (57.02146372057) modaa</option> | 155 <option value="6" selected="true">Carbamidomethylation of C (57.02146372057) modaa</option> |
| 151 <option value="117">Oxidation of M (15.99491461956) modaa</option> | 156 <option value="117">Oxidation of M (15.99491461956) modaa</option> |