annotate fasplit.xml @ 3:d3f58a0dc09d draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit commit 303002db06287fb25306020c4391626842f52162
author iuc
date Sun, 22 Sep 2024 07:26:24 +0000
parents bf04bd405d5b
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
d3f58a0dc09d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit commit 303002db06287fb25306020c4391626842f52162
iuc
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1 <tool id="fasplit" name="faSplit" version="@TOOL_VERSION@" profile="22.05">
0
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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2 <description>Split a FASTA file</description>
3
d3f58a0dc09d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit commit 303002db06287fb25306020c4391626842f52162
iuc
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3 <macros>
d3f58a0dc09d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit commit 303002db06287fb25306020c4391626842f52162
iuc
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4 <token name="@TOOL_VERSION@">469</token>
d3f58a0dc09d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit commit 303002db06287fb25306020c4391626842f52162
iuc
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5 </macros>
2
bf04bd405d5b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit e021ee7a5b682d6f513ca053138acf9bb5d2b4b2"
iuc
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6 <xrefs>
bf04bd405d5b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit e021ee7a5b682d6f513ca053138acf9bb5d2b4b2"
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7 <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref>
bf04bd405d5b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit e021ee7a5b682d6f513ca053138acf9bb5d2b4b2"
iuc
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8 </xrefs>
0
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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9 <requirements>
2
bf04bd405d5b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit e021ee7a5b682d6f513ca053138acf9bb5d2b4b2"
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10 <requirement type="package" version="@TOOL_VERSION@">ucsc-fasplit</requirement>
0
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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11 </requirements>
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
iuc
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12 <command detect_errors="exit_code"><![CDATA[
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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13 mkdir out &&
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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14 faSplit
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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15 $O.split_type
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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16 '$input'
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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17 #if $O.split_type != 'byname'
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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18 $O.count
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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19 #end if
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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20 out/
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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21 ]]></command>
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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22 <inputs>
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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23 <param name="input" type="data" format="fasta" label="FASTA file" />
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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24 <conditional name="O">
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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25 <param name="split_type" type="select" label="Split by:">
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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26 <option value="sequence" selected="true">Number of files (for multi sequence FASTA)</option>
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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27 <option value="base">Number of files (for single sequence FASTA)</option>
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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28 <option value="size">Number of base (for single sequence FASTA)</option>
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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29 <option value="byname">By name</option>
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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30 </param>
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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31 <when value="sequence">
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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32 <param name="count" type="integer" value="10" label="Number of chunks" />
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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33 </when>
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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34 <when value="base">
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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35 <param name="count" type="integer" value="10" label="Number of chunks" />
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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36 </when>
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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37 <when value="size">
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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38 <param name="count" type="integer" value="100" label="Size of chunks (bp)" />
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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39 </when>
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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40 <when value="byname" />
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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41 </conditional>
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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42 </inputs>
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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43 <outputs>
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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44 <collection name="output_list" type="list" label="${tool.name} on ${on_string}">
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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45 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.fa" ext="fasta" directory="out"/>
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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46 </collection>
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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47 </outputs>
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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48
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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49 <tests>
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50 <test>
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51 <param name="input" ftype="fasta" value="CDS.fa" />
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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52 <param name="split_type" value="sequence" />
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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53 <param name="count" value="5" />
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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54 <output_collection name="output_list" type="list">
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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55 <element name="0" file="0.fa" />
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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56 <element name="1" file="1.fa" />
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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57 <element name="2" file="2.fa" />
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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58 <element name="3" file="3.fa" />
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59 <element name="4" file="4.fa" />
3
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60 </output_collection>
0
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61 </test>
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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62 <test>
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63 <param name="input" ftype="fasta" value="CDS.fa"/>
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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64 <param name="split_type" value="byname"/>
dc36d50254d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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65 <output_collection name="output_list" type="list">
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66 <element name="ENSCAFT00000022939_canisfamiliaris" file="ENSCAFT00000022939_canisfamiliaris.fa" />
3
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67 <element name="ENSCAFT00000022963_canisfamiliaris" file="ENSCAFT00000022963_canisfamiliaris.fa" />
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68 <element name="ENSCAFT00000025950_canisfamiliaris" file="ENSCAFT00000025950_canisfamiliaris.fa" />
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69 <element name="ENSMUST00000026013_musmusculus" file="ENSMUST00000026013_musmusculus.fa" />
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70 <element name="ENSMUST00000040820_musmusculus" file="ENSMUST00000040820_musmusculus.fa" />
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71 <element name="ENSMUST00000041588_musmusculus" file="ENSMUST00000041588_musmusculus.fa" />
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72 <element name="ENSMUST00000091291_musmusculus" file="ENSMUST00000091291_musmusculus.fa" />
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73 <element name="ENSMUST00000100505_musmusculus" file="ENSMUST00000100505_musmusculus.fa" />
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74 <element name="ENSMUST00000110806_musmusculus" file="ENSMUST00000110806_musmusculus.fa" />
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75 <element name="ENSMUST00000153440_musmusculus" file="ENSMUST00000153440_musmusculus.fa" />
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76 <element name="ENSMUST00000163344_musmusculus" file="ENSMUST00000163344_musmusculus.fa" />
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77 <element name="ENSMUST00000168613_musmusculus" file="ENSMUST00000168613_musmusculus.fa" />
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78 <element name="ENSMUST00000173143_musmusculus" file="ENSMUST00000173143_musmusculus.fa" />
0
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79 <element name="ENSMUST00000207100_musmusculus" file="ENSMUST00000207100_musmusculus.fa" />
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80 <element name="ENSMUST00000208839_musmusculus" file="ENSMUST00000208839_musmusculus.fa" />
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81 <element name="ENSPTRT00000019089_pantroglodytes" file="ENSPTRT00000019089_pantroglodytes.fa" />
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82 <element name="ENSPTRT00000034846_pantroglodytes" file="ENSPTRT00000034846_pantroglodytes.fa" />
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83 <element name="ENSPTRT00000040520_pantroglodytes" file="ENSPTRT00000040520_pantroglodytes.fa" />
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84 <element name="ENSPTRT00000040521_pantroglodytes" file="ENSPTRT00000040521_pantroglodytes.fa" />
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85 <element name="ENSRNOT00000041155_rattusnorvegicus" file="ENSRNOT00000041155_rattusnorvegicus.fa" />
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86 <element name="ENSRNOT00000044009_rattusnorvegicus" file="ENSRNOT00000044009_rattusnorvegicus.fa" />
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87 <element name="ENSRNOT00000064726_rattusnorvegicus" file="ENSRNOT00000064726_rattusnorvegicus.fa" />
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88 <element name="ENSRNOT00000066674_rattusnorvegicus" file="ENSRNOT00000066674_rattusnorvegicus.fa" />
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89 <element name="ENSRNOT00000067448_rattusnorvegicus" file="ENSRNOT00000067448_rattusnorvegicus.fa" />
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90 <element name="ENSSSCT00000008295_susscrofa" file="ENSSSCT00000008295_susscrofa.fa" />
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91 <element name="ENSSSCT00000013404_susscrofa" file="ENSSSCT00000013404_susscrofa.fa" />
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92 <element name="ENSSSCT00000014817_susscrofa" file="ENSSSCT00000014817_susscrofa.fa" />
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93 <element name="ENSSSCT00000023183_susscrofa" file="ENSSSCT00000023183_susscrofa.fa" />
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94 <element name="ENSSSCT00000032764_susscrofa" file="ENSSSCT00000032764_susscrofa.fa" />
0
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95 <element name="ENSSSCT00000033745_susscrofa" file="ENSSSCT00000033745_susscrofa.fa" />
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96 <element name="ENSSSCT00000035258_susscrofa" file="ENSSSCT00000035258_susscrofa.fa" />
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97 <element name="ENST00000302850_homosapiens" file="ENST00000302850_homosapiens.fa" />
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98 <element name="ENST00000338702_homosapiens" file="ENST00000338702_homosapiens.fa" />
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99 <element name="ENST00000340611_homosapiens" file="ENST00000340611_homosapiens.fa" />
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100 <element name="ENST00000341500_homosapiens" file="ENST00000341500_homosapiens.fa" />
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101 <element name="ENST00000378069_homosapiens" file="ENST00000378069_homosapiens.fa" />
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102 <element name="ENST00000421712_homosapiens" file="ENST00000421712_homosapiens.fa" />
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103 <element name="ENST00000542639_homosapiens" file="ENST00000542639_homosapiens.fa" />
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104 <element name="ENST00000600492_homosapiens" file="ENST00000600492_homosapiens.fa" />
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105 </output_collection>
0
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106 </test>
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107 </tests>
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108 <help><![CDATA[
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109 **What it does**
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110
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111 `faSplit`_ is a tool to split a single FASTA file into several files.
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112
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113 For implementation details see faSplit's `source code`_.
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114
0
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115 .. _faSplit: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt
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116 .. _source code: https://github.com/ucscGenomeBrowser/kent/blob/master/src/utils/faSplit/faSplit.c
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117 ]]></help>
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118 <citations>
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119 <citation type="doi">10.1093/bib/bbs038</citation>
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120 </citations>
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121 </tool>