Mercurial > repos > galaxyp > pepquery

comparison pepquery.xml @ 1:528bcf03e561 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 542fee4158c3dbd0c5ad8cd7e97b77f55982e0bf"
author galaxyp
date Fri, 17 Jul 2020 17:05:41 -0400
parents 32d3818fc635
children 5b5a9f59e2c7
comparison
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0:32d3818fc635 1:528bcf03e561
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>