1 | <tool id="gff_filter_by_feature_count" name="Filter GFF file by feature count" version="0.1">
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2 | <description>using simple expressions</description>
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3 | <command interpreter="python">
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4 | gff_filter_by_feature_count.py $input_file1 $out_file1 "$feature_name" "$cond"
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5 | </command>
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6 | <inputs>
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7 | <param format="gff" name="input_file1" type="data" label="Filter"/>
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8 | <param name="feature_name" type="select" label="Using feature name">
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9 | <options from_dataset="input_file1">
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10 | <column name="name" index="2"/>
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11 | <column name="value" index="2"/>
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12 | <filter type="unique_value" name="unique" column="2"/>
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13 | </options>
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14 | </param>
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15 | <param name="cond" size="40" type="text" value=">0" label="With following condition">
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16 | <validator type="empty_field" message="Enter a valid filtering condition, see syntax and examples below."/>
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17 | </param>
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18 | </inputs>
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19 | <outputs>
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20 | <data format="input" name="out_file1" metadata_source="input_file1"/>
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21 | </outputs>
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22 | <tests>
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23 | <test>
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24 | <param name="input_file1" value="gops_subtract_in1.gff"/>
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25 | <param name="feature_name" value="exon"/>
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26 | <param name="cond" value=">1"/>
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27 | <output name="out_file1" file="gff_filter_by_feature_count_out1.gff"/>
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28 | </test>
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29 | </tests>
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30 |
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31 | <help>
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32 |
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33 |
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34 | .. class:: infomark
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35 |
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36 | Valid comparison operators are: > < >=, <=, !=, and ==
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37 |
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38 | -----
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39 |
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40 | **Syntax**
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41 |
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42 | The filter tool allows you to restrict the dataset based on transcripts' feature counts.
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43 |
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44 | </help>
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45 | </tool>
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