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