comparison cwpair2.xml @ 5:71188f3f4b76 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit cb490a0eee9efc2cd6c98d5bb714b75b5894c56c

4:d843468aeb8f

    <description>find matched pairs and unmatched orphans</description>
    <macros>
        <import>cwpair2_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="aggressive">
        <![CDATA[
            python $__tool_directory__/cwpair2.py
            #for $i in $input:
                 --input "${i}" "${i.hid}"
            #end for
            --up_distance $up_distance
            --down_distance $down_distance
            --method $method
            --binsize $binsize
            --threshold_format $threshold_format_cond.threshold_format
            #if str($threshold_format_cond.threshold_format) == "absolute_threshold":
                --absolute_threshold $threshold_format_cond.absolute_threshold
            #elif str($threshold_format_cond.threshold_format) == "relative_threshold":
                --relative_threshold $threshold_format_cond.relative_threshold
            #end if
            --output_files $output_files
            --statistics_output "$statistics_output"
        ]]>
    </command>
    <inputs>
        <param  name="input" type="data" format="gff" multiple="True" label="Find matched pairs on" />
        <param name="up_distance" type="integer" value="50" min="0" label="Distance upstream from a peak to allow a pair" help="The maximum distance upstream or 5’ to the primary peak"/>
        <param name="down_distance" type="integer" value="100" min="0" label="Distance downstream from a peak to allow a pair" help="The maximum distance downstream or 3’ to the primary peak"/>
        <param name="method" type="select" label="Method of finding a match">
            <option value="mode" selected="True">Mode</option>
            <option value="closest">Closest</option>
            <option value="largest">Largest</option>
            <option value="all">All</option>
        </param>
        <param name="binsize" type="integer" value="1" min="0" label="Width of bins for frequency plots and mode calculation" help="Value 1 implies no bins" />

 * **closest/largest/mode C** - pdf file that provides the frequency distribution of peak pair distances.
 * **closest/largest/mode P** - pdf file that provides the preview plots graph (the initial iteration of the process for finding the mode).
 * **closest/largest/mode F** - pdf file that provides the final plots graph.
 * **Statistics Table** - provides the number of peaks in pairs (dividing this by 2 provides the number of peak-pairs).

    </help>
    <expand macro="citations" />
</tool>

5:71188f3f4b76

    <description>find matched pairs and unmatched orphans</description>
    <macros>
        <import>cwpair2_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="aggressive"><![CDATA[
python '$__tool_directory__/cwpair2.py'
#for $i in $input:
    --input '${i}' '${i.hid}'
#end for
--up_distance $up_distance
--down_distance $down_distance
--method $method
--binsize $binsize
--threshold_format $threshold_format_cond.threshold_format
#if str($threshold_format_cond.threshold_format) == "absolute_threshold":
    --absolute_threshold $threshold_format_cond.absolute_threshold
#elif str($threshold_format_cond.threshold_format) == "relative_threshold":
    --relative_threshold $threshold_format_cond.relative_threshold
#end if
--output_files $output_files
--statistics_output '$statistics_output'
    ]]></command>
    <inputs>
        <param  name="input" type="data" format="gff" multiple="true" label="Find matched pairs on" />
        <param name="up_distance" type="integer" value="50" min="0" label="Distance upstream from a peak to allow a pair" help="The maximum distance upstream or 5’ to the primary peak"/>
        <param name="down_distance" type="integer" value="100" min="0" label="Distance downstream from a peak to allow a pair" help="The maximum distance downstream or 3’ to the primary peak"/>
        <param name="method" type="select" label="Method of finding a match">
            <option value="mode" selected="true">Mode</option>
            <option value="closest">Closest</option>
            <option value="largest">Largest</option>
            <option value="all">All</option>
        </param>
        <param name="binsize" type="integer" value="1" min="0" label="Width of bins for frequency plots and mode calculation" help="Value 1 implies no bins" />

 * **closest/largest/mode C** - pdf file that provides the frequency distribution of peak pair distances.
 * **closest/largest/mode P** - pdf file that provides the preview plots graph (the initial iteration of the process for finding the mode).
 * **closest/largest/mode F** - pdf file that provides the final plots graph.
 * **Statistics Table** - provides the number of peaks in pairs (dividing this by 2 provides the number of peak-pairs).
    </help>
    <expand macro="citations" />
</tool>