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comparison peptide_indexer.xml @ 4:1183846e70a1 draft

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author galaxyp
date Wed, 19 Jun 2013 13:15:44 -0400
parents cf0d72c7b482
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3:8fa16707e162 4:1183846e70a1
14 <configfile name="config">[simple_options] 14 <configfile name="config">[simple_options]
15 in=$input1 15 in=$input1
16 fasta=$database 16 fasta=$database
17 out=$output 17 out=$output
18 decoy_string=$decoy_string 18 decoy_string=$decoy_string
19 #if $decoy_string_position == "prefix" 19 prefix=$prefix
20 prefix=true
21 #end if
22 $extact_search 20 $extact_search
23 $write_protein_sequence 21 $write_protein_sequence
24 $keep_unreferenced_proteins 22 $keep_unreferenced_proteins
25 aaa_max=$aaa_max 23 aaa_max=$aaa_max
26 </configfile> 24 </configfile>
27 </configfiles> 25 </configfiles>
28 <inputs> 26 <inputs>
29 <param name="input1" label="Identification Input" type="data" format="idxml" /> 27 <param name="input1" label="Identification Input" type="data" format="idxml" />
30 <param name="database" label="Database" type="data" format="fasta" /> 28 <param name="database" label="Database" type="data" format="fasta" />
31 <param name="decoy_string" type="text" value="_rev" label="Decoy string"/> 29 <param name="decoy_string" type="text" value="_rev" label="Decoy string"/>
32 <param name="decoy_string_position" type="select" label="Decoy Position"> 30 <param name="prefix" type="select" label="Decoy Position">
33 <option value="suffix" selected="true">Suffix</option> 31 <option value="false" selected="true">Suffix</option>
34 <option value="prefix">Prefix</option> 32 <option value="true">Prefix</option>
35 </param> 33 </param>
36 <param name="extact_search" label="Exact Search" type="boolean" truevalue="" falsevalue="full_tolerant_search=true" checked="true" /> 34 <param name="extact_search" label="Exact Search" type="boolean" truevalue="" falsevalue="full_tolerant_search=true" checked="true" />
37 <param name="write_protein_sequence" type="boolean" truevalue="write_protein_sequence=true" falsevalue="" checked="false" label="Store Protein Sequences" /> 35 <param name="write_protein_sequence" type="boolean" truevalue="write_protein_sequence=true" falsevalue="" checked="false" label="Store Protein Sequences" />
38 <param name="keep_unreferenced_proteins" label="Keep Unreferenced Proteins" truevalue="keep_unreferenced_proteins=true" falsevalue="" type="boolean" /> 36 <param name="keep_unreferenced_proteins" label="Keep Unreferenced Proteins" truevalue="keep_unreferenced_proteins=true" falsevalue="" type="boolean" />
39 <param name="aaa_max" type="integer" value="4" label="Maximum Number of Ambiguous Amino Acids" help=" Maximal number of ambiguous amino acids (AAA) allowed when matching to a protein DB with AAA's. AAA's are 'B', 'Z', and 'X'" /> 37 <param name="aaa_max" type="integer" value="4" label="Maximum Number of Ambiguous Amino Acids" help=" Maximal number of ambiguous amino acids (AAA) allowed when matching to a protein DB with AAA's. AAA's are 'B', 'Z', and 'X'" />