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1 <tool id="fimo_gff_to_gff" name="Fimo Gff to Gff" version="1.0.0">
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2 <description></description>
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3 <requirements>
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4 <requirement type="package" version="5.18.1">perl</requirement>
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5 </requirements>
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6 <command>
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7 <![CDATA[
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8 mkdir -p output &&
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9 perl $__tool_directory__/fimo_gff_to_gff.pl "$input" output
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10 ]]>
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11 </command>
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12 <inputs>
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13 <param name="input" type="data" format="tabular" label="FIMO (almost) Gff input" />
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14 </inputs>
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15 <outputs>
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16 <collection name="motifs" type="list" label="Motifs: ${tool.name} on ${on_string}">
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17 <discover_datasets pattern="(?P<designation>.*)" directory="output" ext="gff" visible="false" />
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18 </collection>
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19 </outputs>
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20 <tests>
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21 <test>
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22 <param name="input" value="input.tabular" ftype="tabular" />
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23 <output_collection name="motifs" type="list">
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24 <element name="MOTIF1" file="motif1.gff" ftype="gff"/>
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25 </output_collection>
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26 </test>
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27 </tests>
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28 <help>
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29
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30 .. class:: warningmark
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31
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32 This tool requires 1-based input data, 0-based data will produce incorrect results.
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33
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34 .. class:: warningmark
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35
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36 This tool requires FASTA headers that use the default bedtools getfasta header format of
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37 **chrom:start-stop(strand)** or **chrom:start-stop** in which case strand is set as '+'
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38 per the bedtools standard.
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39
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40 **What it does**
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41
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42 Converts FIMO tabular (almost GFF) files to true genomic coordinates in valid GFF format. A
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43 collection of datasets is produced consisting of one dataset per motif discovered in the input.
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44
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45 </help>
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46 <citations>
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47 <citation type="bibtex">
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48 @unpublished{None,
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49 author = {Lai, William},
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50 title = {None},
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51 year = {None},
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52 eprint = {None},
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53 url = {http://www.huck.psu.edu/content/research/independent-centers-excellence/center-for-eukaryotic-gene-regulation}
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54 }</citation>
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55 </citations>
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56 </tool>
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