annotate masscomb_fasta_validator.xml @ 0:d6001e8d7441

Push to main toolshed
author pieter.lukasse@wur.nl
date Wed, 08 Jan 2014 11:34:51 +0100
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
1 <tool name="Fasta Validator" id="masscomb_fastavalidator" version="1.0.1">
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
2 <description>Basic FASTA file validation</description>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
3 <!--
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
4 For remote debugging start you listener on port 8000 and use the following as command interpreter:
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
5 java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
6 -->
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
7 <command interpreter="java -jar">
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
8 MassComb.jar
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
9 -action FASTAVALIDATOR
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
10 -fastaFile $inputFile
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
11 -outputFile $outputFile
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
12 -expressions "$expressions"
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
13 -maxLengthSequenceLine $maxLengthSequenceLine
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
14 </command>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
15 <inputs>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
16 <param name="inputFile" type="data" format="" label="Fasta file to validate"/>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
17
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
18 <param name="expressions" type="select" display="checkboxes" multiple="true" label="Error patterns to search for in each line" help="">
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
19 <option value="description=White space in SEQUENCE;regex=^[a-zA-Z]+SLASHs[a-zA-Z]">White space in SEQUENCE (^[a-zA-Z]+\s[a-zA-Z])</option>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
20 <option value="description=Numbers in SEQUENCE;regex=^[0-9]PIPE^[a-zA-Z]+.*[0-9]">Numbers in SEQUENCE (^[0-9]|^[a-zA-Z]+.*[0-9])</option>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
21 <option value="description=Line starting with white space followed by alpha numeric characters;regex=^SLASHs[a-zA-Z0-9]+">Line starting with white space followed by alpha numeric characters (^\s[a-zA-Z0-9]+)</option>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
22 <option value="description=Line ending with white space;regex=.*SLASHsDOLLAR">Line ending with white space (.*\s$)</option>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
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>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
24 <option value="description=Hyphen in accession numbers;regex=^SLASHS*-">Hyphen in accession numbers (^\S*-)</option>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
25 <option value="description=Lines with stretches of X;regex=XX+">Lines with stretches of X (XX+)</option>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
26 </param>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
27
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
28 <param name="maxLengthSequenceLine" type="integer" size="10" value="0" label="Max length sequence line "
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
29 help="(Optional) the maximum line width in the protein sequence part. Leave to 0 (zero) for no restrictions "/>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
30
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
31 </inputs>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
32 <outputs>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
33 <data format="txt" name="outputFile" />
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
34 </outputs>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
35 <tests>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
36 <test>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
37 </test>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
38 </tests>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
39 <help>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
40
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
41 </help>
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
42 </tool>