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/tools/filters/gff/gff_filter_by_feature_count.xml

https://bitbucket.org/cistrome/cistrome-harvard/
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 1<tool id="gff_filter_by_feature_count" name="Filter GFF data by feature count" version="0.1">
 2  <description>using simple expressions</description>
 3  <command interpreter="python">
 4    gff_filter_by_feature_count.py $input_file1 $out_file1 "$feature_name" "$cond"
 5  </command>
 6  <inputs>
 7    <param format="gff" name="input_file1" type="data" label="Filter"/>
 8    <param name="feature_name" type="select" label="Using feature name">
 9        <options from_dataset="input_file1">
10            <column name="name" index="2"/>
11            <column name="value" index="2"/>
12            <filter type="unique_value" name="unique" column="2"/>
13        </options>
14    </param>
15    <param name="cond" size="40" type="text" value=">0" label="With following condition">
16      <validator type="empty_field" message="Enter a valid filtering condition, see syntax and examples below."/>
17    </param>
18  </inputs>
19  <outputs>
20    <data format="input" name="out_file1" metadata_source="input_file1"/>
21  </outputs>
22  <tests>
23      <!-- Test GTF filtering. -->
24      <test>
25          <param name="input_file1" value="gops_subtract_in1.gff"/>
26          <param name="feature_name" value="exon"/>
27          <param name="cond" value=">1"/>
28          <output name="out_file1" file="gff_filter_by_feature_count_out1.gff"/>
29      </test>
30      <!-- Test GFF3 filtering. -->
31      <test>
32          <param name="input_file1" value="5.gff3"/>
33          <param name="feature_name" value="HSP"/>
34          <param name="cond" value=">=5"/>
35          <output name="out_file1" file="gff_filter_by_feature_count_out2.gff"/>
36      </test>
37  </tests>
38
39  <help>
40
41
42.. class:: infomark
43
44Valid comparison operators are: &gt; &lt; &gt;=, &lt;=, !=, and ==
45
46-----
47
48**Syntax**
49
50The filter tool allows you to restrict the dataset based on transcripts' feature counts.
51
52</help>
53</tool>