Mercurial > repos > galaxyp > validate_fasta_database

comparison validate_fasta_database.xml @ 2:5f6657ae8e81 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 76645d5795502df941e39d519ed275ac903d60c2"
author galaxyp
date Wed, 25 Aug 2021 16:30:26 +0000
parents 8eb277262715
children
comparison
equal deleted inserted replaced
1:5f85bf247f99 2:5f6657ae8e81
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-->