<tool id="annotation_collector" name="Collect Annotation counts" version="0.9.0">
    <description> from matched fasta files</description>
    <command interpreter="python">
        annotation_collector.py
        $out_file
        $input1 $label1
        #for $q in $queries
            ${q.input2} ${q.label2}
        #end for
        $title
    </command>
    <inputs>
        <param label="Annotation Title" name="title" type="text" />
        <param label="fasta file to annotate" name="input1" type="data" />
        <param label="category label" name="label1" type="text" />
        <repeat name="queries" title="Additional fasta file and label">
            <param label="Select" name="input2" type="data" />
            <param label="Label" name="label2" type="text" />
        </repeat>
    </inputs>
    <outputs>
        <data format="tabular" label="Annotations" metadata_source="input1" name="out_file" />
    </outputs>
    <help>

.. class:: warningmark

**WARNING:** Be careful not to agregate datasets of different kinds (e.g., datasets must be matched fasta files). This tool does not check if the datasets being annotated are in the same format. 

-----

**What it does**

Generates Annotation Table from fasta files

   </help>
</tool>

<tool id="annotation_collector" name="Collect Annotation counts" version="0.9.0">
    <description> from matched fasta files</description>
    <command interpreter="python">
        annotation_collector.py
        $out_file
        $input1 $label1
        #for $q in $queries
            ${q.input2} ${q.label2}
        #end for
        $title
    </command>
    <inputs>
        <param label="Annotation Title" name="title" type="text" />
        <param label="fasta file to annotate" name="input1" type="data" />
        <param label="category label" name="label1" type="text" />
        <repeat name="queries" title="Additional fasta file and label">
            <param label="Select" name="input2" type="data" />
            <param label="Label" name="label2" type="text" />
        </repeat>
    </inputs>
    <outputs>
        <data format="tabular" label="Annotations" metadata_source="input1" name="out_file" />
    </outputs>
    <help>

.. class:: warningmark

**WARNING:** Be careful not to agregate datasets of different kinds (e.g., datasets must be matched fasta files). This tool does not check if the datasets being annotated are in the same format. 

-----

**What it does**

Generates Annotation Table from fasta files

Collect Annotation counts from matched fasta files.
Counts number of lines in fasta files and outputs a
tabular file with Label in the first column, number of fasta
sequences in second column. Percent of counts is in the third
column with the number of fasta entries in the first file
set to 100%, and the remaining lines expressed as fractions.

   </help>
</tool>

Add some more text in the help section.
Add some more text in the help section.
