<tool id="get_sequences" name="Get_Sequences" version="1.0">
<description>Create a file of selected sequences</description>
<command interpreter="perl">get_seqs.pl
$cosorted
$paired
$ignorecase
-db $infile
-table $input_table
-col $id_column
-selected $selected
-unselected $unselected
#for $i in $filters
"${i.condition}:${i.column}:{i.value}"
#end for
</command>
<inputs>
    <param name="infile" type="data" format="fasta,fastq,fastqsanger,fastqillumina,fastqsolexa" label="Sequence Database"/>
    <param name="input_table" type="data" format="tabular" label="File containing target IDs"/>
    <param name='id_column' type='data_column' data_ref='input_table' label='Column containing sequence IDs'/>
    <param name="cosorted" type="boolean" checked="true" truevalue='--cosorted' falsevalue='' label='Sequences appear in same order in both files' />
    <param name="paired" type="boolean" checked="true" truevalue="--paired" falsevalue="" label="Select both paired reads if one read matches" help="Requires Illumina-style read IDs (e.g. */1, */2)" />
    <param name='ignorecase' type='boolean' checked='false' truevalue='--ignorecase' falsevalue='' label='Ignore case differences between table and database IDs' />
    <param name='outselect' type='select' display='radio'>
        <option value='selected'>output selected sequences file only</option>
        <option value='unselected'>output other sequences file only</option>
        <option value='both'>generate both outfiles</option>
    </param>
    <repeat name='filters' title='Filter'>
        <param name='condition' type='select' display='radio' label='Condition'>
            <option value='s_eq'>text equals</option>
            <option value='s_ne'>text not equals</option>
            <option value='s_contains'>text contains</option>
            <option value='s_notcontains'>text does not contain</option>
            <option value='s_startswith'>text starts with</option>
            <option value='s_notstartswith'>text does not start with</option>
            <option value='s_endswith'>text ends with</option>
            <option value='s_notendswith'>text does not end with</option>
            <option value='n_eq'>number equals (==)</option>
            <option value='n_ne'>number not equals (!=)</option>
            <option value='n_gt'>number greater than (&gt;)</option>
            <option value='n_lt'>number less than (&lt;)</option>
        </param>
        <param name='column' type='data_column' data_ref='input_table' label='On column'/>
        <param name='value' type='text' label='Value'/>
    </repeat>
</inputs>
<outputs>
    <data name="selected" format="input" label="${tool.name} on $on_string: Selected sequences">
        <filter>outselect == "selected" or outselect == "both"</filter>
    </data>
    <data name="unselected" format="input" label="${tool.name} on $on_string: Unselected sequences">
        <filter>outselect == "unselected" or outselect == "both"</filter>
    </data>
</outputs>
<help>
**What it does**

Produces a file of selected sequences.

If the files are cosorted, a much faster algorithm is used.  If it fails, it assumes the files were not cosorted and automatically tries again using the slower algorithm which does not require cosorted files.

One or more filters may be included to evaluate text or numeric data.

------

**Inputs**

FASTA file of sequence database, text file of target IDs.

------

**Outputs**

FASTA file. User may select to either output the selected sequences, the other sequences, or both files. 

-------

**Additional Information**

Please direct questions or comments to ucsb_phylogenetics@lifesci.ucsb.edu or, if you can, enter them on the osiris_phylogenetics site at bitbucket.org

-------

**Citations**

This tool is part of the Osiris Phylogenetics Tool Package for Galaxy. If you make extensive use of this tool in a publication, please consider citing the following.

Current Osiris Citation is here

http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
</help>
</tool>