Mercurial > repos > galaxyp > validate_fasta_database

comparison validate_fasta_database.xml @ 2:9c246c2e24ad draft default tip

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"planemo upload commit 76645d5795502df941e39d519ed275ac903d60c2"
author galaxyp
date Wed, 25 Aug 2021 16:30:53 +0000
parents 48c2271171f2
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1:3b18022a7613 2:9c246c2e24ad
1 <tool id="validate_fasta_database" name="Validate FASTA Database" version="0.1.4"> 1 <tool id="validate_fasta_database" name="Validate FASTA Database" version="0.1.5">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="1.0">validate-fasta-database</requirement> 3 <requirement type="package" version="1.0">validate-fasta-database</requirement>
4 </requirements> 4 </requirements>
5 <stdio> 5 <stdio>
6 <exit_code range="1" level="fatal" description="Invalid FASTA headers detected, was asked to fail"/> 6 <exit_code range="1" level="fatal" description="Invalid FASTA headers detected, was asked to fail"/>
17 '$minimumLength' 17 '$minimumLength'
18 ]]></command> 18 ]]></command>
19 <inputs> 19 <inputs>
20 <param type="data" name="inFasta" format="fasta" label="Select input FASTA dataset"/> 20 <param type="data" name="inFasta" format="fasta" label="Select input FASTA dataset"/>
21 <param type="boolean" name="crashIfInvalid" 21 <param type="boolean" name="crashIfInvalid"
22 label="Fail job if invalid FASTA headers detected?" 22 truevalue="true" falsevalue="false" checked="false"
23 value="false"/> 23 label="Fail job if invalid FASTA headers detected?"/>
24 <param type="boolean" name="checkIsProtein" 24 <param type="boolean" name="checkIsProtein"
25 truevalue="true" falsevalue="false" checked="true"
25 label="Ensure that sequence is a valid amino acid sequence?" 26 label="Ensure that sequence is a valid amino acid sequence?"
26 help="Checks that sequence only contains the 20 essential amino 27 help="Checks that sequence only contains the 20 essential amino acids (and optional non-standard AAs), and checks that is not DNA or RNA"/>
27 acids (and optional non-standard AAs), and checks that is not DNA or RNA"
28 value="true"/>
29 <param type="text" name="customLetters" value="" 28 <param type="text" name="customLetters" value=""
30 label="Optional: add one letter codes for any non-standard amino acids that you are using. " 29 label="Optional: add one letter codes for any non-standard amino acids that you are using. "
31 help="Anything that is not an upper case letter [A-Z] will be ignored."/> 30 help="Anything that is not an upper case letter [A-Z] will be ignored."/>
32 <param type="boolean" name="checkHasAccession" 31 <param type="boolean" name="checkHasAccession"
33 label="Only pass sequences with accession numbers?" 32 truevalue="true" falsevalue="false" checked="false"
34 value="false"/> 33 label="Only pass sequences with accession numbers?"/>
35 <param type="integer" name="minimumLength" 34 <param type="integer" name="minimumLength"
36 label="Minimum length for sequences to pass" 35 label="Minimum length for sequences to pass"
37 value="0"/> 36 value="0"/>
38 </inputs> 37 </inputs>
39 <outputs> 38 <outputs>
42 </outputs> 41 </outputs>
43 <tests> 42 <tests>
44 <!-- test general filtering --> 43 <!-- test general filtering -->
45 <test> 44 <test>
46 <param name="inFasta" value="fastaFilteringTest_IN.fasta"/> 45 <param name="inFasta" value="fastaFilteringTest_IN.fasta"/>
46 <param name="checkIsProtein" value="false"/>
47 <output name="goodFastaOut" file="fastaFilteringTest_OUT1.fasta" /> 47 <output name="goodFastaOut" file="fastaFilteringTest_OUT1.fasta" />
48 <output name="badFastaOut" file="fastaFilteringTest_OUT2.fasta" /> 48 <output name="badFastaOut" file="fastaFilteringTest_OUT2.fasta" />
49 </test> 49 </test>
50 50
51 <!--test filtering out genetic sequences and bad protein sequences--> 51 <!--test filtering out genetic sequences and bad protein sequences-->