Commit c000c228 authored by McDonnell, Marshall's avatar McDonnell, Marshall
Browse files

Merge branch 'hotfix-imaginex-peak-finding-input-files' into 'dev' 

Fixes imaginex peak finding input files name

See merge request ndip/galaxy-tools!170
parents a911f2e4 c0404c76

tools/neutrons/imaginex_peak_finding.xml

+10 −15
Original line number Diff line number Diff line
@@ -4,27 +4,25 @@ 
        <container type="docker">code.ornl.gov:4567/dnp-computational-project/data-reduction-ndip-tools/peak-finding/v0.1.0</container>

    </requirements>

    <command detect_errors="exit_code"><![CDATA[

        mkdir in &&

        mkdir out &&



        ##Move files to execution directory

        #for $data in $dataFiles

            #set $dataFile = str($data["dataFile"])

            echo $dataFile >> ./input_filenames.txt &&

        #for $data in $data_files

            cp $data in/$data.element_identifier &&

        #end for



        touch $output &&

        peak_finding 

            --input-file ./input_filenames.txt

            --data-directory in/

            --scan-average $scan_average

            --file-type $file_type

            --peak-threshold $peak_threshold

            --save-directory /portal &&

        mv /portal/peak_list.npy $output

            --save-directory out/ &&

        mv out/peak_list.npy $output



    ]]></command>

    <inputs>

    	<repeat name="dataFiles" title="Data Files">

	    	<param name="dataFile" type="data" format="txt" label="Data File">

		    </param>

	    </repeat>

        <param format="txt" multiple="true" name="data_files" type="data" label="Data Files" />

        <param name="instrument" type="select" label="Select instrument name:" optional="false">

            <option value="DEMAND" selected="true">DEMAND</option>

        </param>
@@ -45,10 +43,7 @@ 
    </help>

    <tests>

        <test>

            <param name="dataFiles_0|dataFile" value="HB3A_exp770_scan0008_0001.jpg" />

            <param name="dataFiles_1|dataFile" value="HB3A_exp770_scan0008_0002.jpg" />

            <param name="dataFiles_2|dataFile" value="HB3A_exp770_scan0009_0001.jpg" />

            <param name="dataFiles_3|dataFile" value="HB3A_exp770_scan0009_0002.jpg" />

            <param name="data_files" value="HB3A_exp770_scan0008_0001.jpg,HB3A_exp770_scan0008_0002.jpg,HB3A_exp770_scan0009_0001.jpg,HB3A_exp770_scan0009_0002.jpg" />

            <param name="scan_average" value="yes"/>

            <param name="file_type" value="jpg"/>

            <param name="peak_threshold" value="0.0035"/>