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1 <?xml version="1.0"?>
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2 <tool id="edu.tamu.cpt.fasta.remove_desc" name="Remove Description" version="19.1.0.0">
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3 <description>from fasta file</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 <import>cpt-macros.xml</import>
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7 </macros>
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8 <expand macro="requirements"/>
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9 <command detect_errors="aggressive">
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10 $__tool_directory__/fasta_remove_id.py
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11 @SEQUENCE@
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12 > $out
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13 </command>
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14 <inputs>
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15 <expand macro="input/fasta" />
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16 </inputs>
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17 <outputs>
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18 <data format="fasta" name="out" />
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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="sequences" value="T7_RemIDIn.fasta"/>
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23 <output name="out" file="T7_RemIDOut.fasta" />
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24 </test>
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25 </tests>
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26 <help>
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27 **What it does**
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28
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29 From an input FASTA file, removes the "description" field (all characters after
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30 the first space in the top line until a return) after the FASTA ID (from the >
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31 to the first space).
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32
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33 This is a permanent removal of the description. It is useful for tools that
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34 behave in unexpected ways if it is present, e.g. Glimmer/GeneMarkS.
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35
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36 **Example Input/Output**
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37
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38 For an input FASTA file::
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39
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40 >1|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 288 bp
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41 acttacgcggagagatgagaccaacgctcgcctaggggcacgcttgtaattgacttatct
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42 >2|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 232 bp
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43 gttggggacccacctatcagggagtgtagtagtataagactgtccaataccccccaacat
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44
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45 The resulting FASTA will contain only IDs without a description::
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46
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47 >1|random
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48 acttacgcggagagatgagaccaacgctcgcctaggggcacgcttgtaattgacttatct
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49 >2|random
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50 gttggggacccacctatcagggagtgtagtagtataagactgtccaataccccccaacat
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51 </help>
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52 <expand macro="citations" />
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53 </tool>
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