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comparison masscomb_fasta_validator.xml @ 0:d6001e8d7441

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author pieter.lukasse@wur.nl
date Wed, 08 Jan 2014 11:34:51 +0100
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1 <tool name="Fasta Validator" id="masscomb_fastavalidator" version="1.0.1">
2 <description>Basic FASTA file validation</description>
3 <!--
4 For remote debugging start you listener on port 8000 and use the following as command interpreter:
5 java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000
6 -->
7 <command interpreter="java -jar">
8 MassComb.jar
9 -action FASTAVALIDATOR
10 -fastaFile $inputFile
11 -outputFile $outputFile
12 -expressions "$expressions"
13 -maxLengthSequenceLine $maxLengthSequenceLine
14 </command>
15 <inputs>
16 <param name="inputFile" type="data" format="" label="Fasta file to validate"/>
17
18 <param name="expressions" type="select" display="checkboxes" multiple="true" label="Error patterns to search for in each line" help="">
19 <option value="description=White space in SEQUENCE;regex=^[a-zA-Z]+SLASHs[a-zA-Z]">White space in SEQUENCE (^[a-zA-Z]+\s[a-zA-Z])</option>
20 <option value="description=Numbers in SEQUENCE;regex=^[0-9]PIPE^[a-zA-Z]+.*[0-9]">Numbers in SEQUENCE (^[0-9]|^[a-zA-Z]+.*[0-9])</option>
21 <option value="description=Line starting with white space followed by alpha numeric characters;regex=^SLASHs[a-zA-Z0-9]+">Line starting with white space followed by alpha numeric characters (^\s[a-zA-Z0-9]+)</option>
22 <option value="description=Line ending with white space;regex=.*SLASHsDOLLAR">Line ending with white space (.*\s$)</option>
23 <option value="description=Sequence lines with non-Amino Acid characters;regex=(^[SLASHwAMPAMP[^ARNDCEQGHILKMFPSTWYV]])PIPE(^[ARNDCEQGHILKMFPSTWYV]+[SLASHwAMPAMP[^ARNDCEQGHILKMFPSTWYV]]+)">Sequence lines with non-Amino Acid characters ((^[\w&amp;&amp;[^ARNDCEQGHILKMFPSTWYV]])|(^[ARNDCEQGHILKMFPSTWYV]+[\w&amp;&amp;[^ARNDCEQGHILKMFPSTWYV]]+))</option>
24 <option value="description=Hyphen in accession numbers;regex=^SLASHS*-">Hyphen in accession numbers (^\S*-)</option>
25 <option value="description=Lines with stretches of X;regex=XX+">Lines with stretches of X (XX+)</option>
26 </param>
27
28 <param name="maxLengthSequenceLine" type="integer" size="10" value="0" label="Max length sequence line "
29 help="(Optional) the maximum line width in the protein sequence part. Leave to 0 (zero) for no restrictions "/>
30
31 </inputs>
32 <outputs>
33 <data format="txt" name="outputFile" />
34 </outputs>
35 <tests>
36 <test>
37 </test>
38 </tests>
39 <help>
40
41 </help>
42 </tool>