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1 <tool id="filter_columns" name="Filter Columns" version="1.2">
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2
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3 <description> filter file based on column values </description>
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4
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5 <command interpreter="bash">
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6 filter_columns.sh
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7 --infile $infile
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8 #for $f in $filters <!--get each var/mastervar file-->
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9 --filter ${f.column},${f.condition},${f.value}
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10 #end for
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11 --outfile_rem $outputfile_removed
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12 --outfile_ret $outputfile_retained
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13 </command>
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14
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15 <outputs>
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16 <data format="input" name="outputfile_removed" label="${sample} - Removed lines Column filter on ${on_string}" metadata_source="infile"/>
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17 <data format="input" name="outputfile_retained" label="${sample} - Retained lines Column filter on ${on_string}" metadata_source="infile"/>
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18 </outputs>
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19
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20 <inputs>
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21
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22 <param name="infile" type="data" label="Select input file" help="expects header lines to be indicated by # or > symbols. First line is always considered header line"/>
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23
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24 <repeat name="filters" title="Filter" min="1" help="Multiple filters: lines removed if match any of the filters, not all (rules are OR'd, not AND'd)">
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25 <param name="column" type="data_column" data_ref="infile" multiple="False" label="Select Column to filter on" />
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26 <param name="condition" type="select" label="Remove line if column value.." help="you will receive both file with retained lines and file with removed lines">
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27 <option value="nonempty"> non-empty </option>
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28 <option value="empty" > empty </option>
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29 <option value="equals" > equals (string or number) </option>
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30 <option value="nequals" > not equals (string or number)</option>
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31 <option value="contains"> contains (substring) </option>
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32 <option value="ncontains"> does not contain (substring) </option>
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33 <option value="gt" > greater than </option>
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34 <option value="ge" > greater than or equals </option>
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35 <option value="lt" > less than </option>
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36 <option value="le" > less than or equals </option>
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37 </param>
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38
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39
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40 <param name="value" type="text" value="" label="enter number or string unless above option was set to empty or nonempty"/>
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41 </repeat>
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42
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43 <param name="sample" type="text" value="" label="Output File Name" help="Optional."/>
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44
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45 </inputs>
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46
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47 <help>
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48
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49 **What it does**
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50 Concatenates 2 files
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51
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52 </help>
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53 </tool>
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