output-prefixes Without a known single file ending/extension

[temehi]

We have Nodes/indexers (in SeqAn) that doesn't output a single known file_type. The GenericKnimeNodes has a way to deal with output-prefixes but yet it expects a common ending/extension for all the resulting files. If one doesn't provide an extension the configuration dialoag produces the error "Configure failed (ArrayIndexOutOfBoundsException): 0"

A particular example is "Community Nodes->SeqAn->Read Mapping->YaraIndexer" Bellow I have dumped the ctd of the node from which it's being generated.

<?xml version="1.0" encoding="UTF-8"?>
<tool name="YaraIndexer" version="0.9.3 [e872daf]" docurl="http://www.seqan.de" category="Read Mapping" >
    <executableName>yara_indexer</executableName>
    <description>Yara Indexer</description>
    <manual>Yara - Yet Another Read Aligner.
See http://www.seqan.de/projects/yara for more information.
(c) Copyright 2011-2014 by Enrico Siragusa.
(c) Copyright 2013 by NVIDIA Corporation.
</manual>
    <cli>
        <clielement optionIdentifier="--write-ctd-file-ext" isList="false">
            <mapping referenceName="yara_indexer.write-ctd-file-ext" />
        </clielement>
        <clielement optionIdentifier="--arg-1-file-ext" isList="false">
            <mapping referenceName="yara_indexer.arg-1-file-ext" />
        </clielement>
        <clielement optionIdentifier="--verbose" isList="false">
            <mapping referenceName="yara_indexer.verbose" />
        </clielement>
        <clielement optionIdentifier="--output-prefix" isList="false">
            <mapping referenceName="yara_indexer.output-prefix" />
        </clielement>
        <clielement optionIdentifier="--tmp-dir" isList="false">
            <mapping referenceName="yara_indexer.tmp-dir" />
        </clielement>
        <!-- Following clielements are arguments. You should consider providing a help text to ease understanding. -->
        <clielement optionIdentifier="" isList="false">
            <mapping referenceName="yara_indexer.argument-0" />
        </clielement>
    </cli>
    <PARAMETERS version="1.6.2" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/Param_1_6_2.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
        <NODE name="yara_indexer" description="Yara Indexer">
            <ITEM name="write-ctd-file-ext" value="" type="string" description="Override file extension for --write-ctd" required="false" advanced="true" tags="file-ext-override,gkn-ignore" />
            <ITEM name="arg-1-file-ext" value="" type="string" description="Override file extension for argument 1" restrictions="fq,fq.bgzf,fq.gz,fq.bz2,fastq,fastq.bgzf,fastq.gz,fastq.bz2,fa,fa.bgzf,fa.gz,fa.bz2,fasta,fasta.bgzf,fasta.gz,fasta.bz2,faa,faa.bgzf,faa.gz,faa.bz2,ffn,ffn.bgzf,ffn.gz,ffn.bz2,fna,fna.bgzf,fna.gz,fna.bz2,frn,frn.bgzf,frn.gz,frn.bz2,embl,embl.bgzf,embl.gz,embl.bz2,gbk,gbk.bgzf,gbk.gz,gbk.bz2,raw,raw.bgzf,raw.gz,raw.bz2" required="false" advanced="true" tags="file-ext-override,gkn-ignore" />
            <ITEM name="verbose" value="false" type="string" description="Displays verbose output." restrictions="true,false" required="false" advanced="false" />
            <ITEM name="output-prefix" value="" type="output-prefix" description="Specify a filename prefix for the reference genome index.                                      Default: use the filename prefix of the reference genome." required="false" advanced="false" />
            <ITEM name="tmp-dir" value="" type="string" description="Specify a temporary directory where to construct the index.                                      Default: use the output directory." required="false" advanced="false" />
            <ITEM name="argument-0" value="" type="input-file" description="A reference genome file." supported_formats="*.fq,*.fq.bgzf,*.fq.gz,*.fq.bz2,*.fastq,*.fastq.bgzf,*.fastq.gz,*.fastq.bz2,*.fa,*.fa.bgzf,*.fa.gz,*.fa.bz2,*.fasta,*.fasta.bgzf,*.fasta.gz,*.fasta.bz2,*.faa,*.faa.bgzf,*.faa.gz,*.faa.bz2,*.ffn,*.ffn.bgzf,*.ffn.gz,*.ffn.bz2,*.fna,*.fna.bgzf,*.fna.gz,*.fna.bz2,*.frn,*.frn.bgzf,*.frn.gz,*.frn.bz2,*.embl,*.embl.bgzf,*.embl.gz,*.embl.bz2,*.gbk,*.gbk.bgzf,*.gbk.gz,*.gbk.bz2,*.raw,*.raw.bgzf,*.raw.gz,*.raw.bz2" required="true" advanced="false" />
        </NODE>
    </PARAMETERS>
</tool>

[jpfeuffer]

Closed via #122 and #123