<commit_before><tool id="concat_channels" name="Concat Channels" version="0.1">
    <description>Concatenate images</description>
    <requirements>
        <requirement type="package" version="0.12.3" >scikit-image</requirement>
    </requirements>
    <command>
        <![CDATA[
        python '$__tool_directory__/concat_channels.py' 
        #for $input in $inputs
            '$input' 
        #end for
        -o '$output' --axis '$axis'
        ]]>
    </command>
    <inputs>
        <param name="inputs" type="data" multiple="true" format="tiff,png,jpg,bmp" label="Binary Image File"/>
        <param name="axis" type="select" label="Concatenation Axis">
            <option value="0">0</option>
            <option value="2">2</option>
        </param>
    </inputs>
    <outputs>
        <data format="tiff" name="output"/>
    </outputs>
    <tests>
        <test>
            <param name="inputs" value="sample1.png,sample2.png" />
            <output name="output" value="out.tiff" ftype="tiff" />
        </test>
    </tests>
    <help>This tool concatenates images.</help>
    <citations>
        <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
    </citations>
</tool><commit_msg>change "inputs"<commit_after><tool id="concat_channels" name="Concat Channels" version="0.1">
    <description>Concatenate images</description>
    <requirements>
        <requirement type="package" version="0.12.3" >scikit-image</requirement>
    </requirements>
    <command><!--input line seems to be the problem (probably "sample1.png,sample2.png" is processed as if it were only one input according to the error; not sure how to address this problem though)-->
        <![CDATA[
        python '$__tool_directory__/concat_channels.py' 
        #for $input in '$inputs' 
            '$input' 
        #end for
        -o '$output' --axis '$axis'
        ]]>
    </command>
    <inputs>
        <param name="inputs" type="data" multiple="true" format="tiff,png,jpg,bmp" label="Binary Image Files" help="one or multiple binary image fiels"/>
        <param name="axis" type="select" label="Concatenation Axis">
            <option value="0">0</option>
            <option value="2">2</option>
        </param>
    </inputs>
    <outputs>
        <data format="tiff" name="output"/>
    </outputs>
    <tests>
        <test>
            <param name="inputs" value="sample1.png, sample2.png" />
            <output name="output" value="out.tiff" ftype="tiff" />
        </test>
    </tests>
    <help>This tool concatenates images.</help>
    <citations>
        <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
    </citations>
</tool>
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