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annotate fastx_renamer.xml @ 3:d8baeed2ce62 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit 3953b65f6b1c0336e9cadbe0792a5d3b14b5643a
author iuc
date Wed, 22 Aug 2018 11:03:24 -0400
parents 2b324adf4e58
children 51b360968c30
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2b324adf4e58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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1 <tool id="cshl_fastx_renamer" name="Rename sequences" version="@VERSION@+galaxy0" >
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2 <description></description>
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iuc
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3 <macros>
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iuc
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4 <import>macros.xml</import>
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iuc
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5 </macros>
2b324adf4e58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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6 <expand macro="requirements" />
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iuc
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7 <command detect_errors="exit_code"><![CDATA[
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8 @CATS@ fastx_renamer
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iuc
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9 -n $TYPE
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10 -o '$output'
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11 -v
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12 @FQQUAL@
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d8baeed2ce62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit 3953b65f6b1c0336e9cadbe0792a5d3b14b5643a
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13 @GZIP@
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14 ]]></command>
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16 <inputs>
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17 <expand macro="fastx_input" />
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18
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19 <param name="TYPE" type="select" label="Rename sequence identifiers to">
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20 <option value="SEQ">Nucleotides sequence</option>
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21 <option value="COUNT">Numeric Counter</option>
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22 </param>
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23 </inputs>
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25 <outputs>
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26 <data name="output" format_source="input" metadata_source="input" />
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27 </outputs>
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28 <tests>
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iuc
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29 <test>
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iuc
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30 <param name="input" value="fastx_renamer-in1.fastq" />
2b324adf4e58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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31 <param name="TYPE" value="SEQ" />
2b324adf4e58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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32 <output name="output" file="fastx_renamer-out1.fastq" />
2b324adf4e58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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33 </test>
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34 </tests>
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35 <help><![CDATA[
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36 **What it does**
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37
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38 This tool renames the sequence identifiers in a FASTQ/A file.
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39
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40 .. class:: infomark
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41
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42 Use this tool at the beginning of your workflow, as a way to keep the original sequence (before trimming, clipping, barcode-removal, etc).
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43
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44 --------
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45
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46 **Example**
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47
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48 The following Solexa-FASTQ file::
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49
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50 @CSHL_4_FC042GAMMII_2_1_517_596
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51 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
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52 +CSHL_4_FC042GAMMII_2_1_517_596
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53 40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40
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54
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55 Renamed to **nucleotides sequence**::
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56
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57 @GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
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58 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
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59 +GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
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60 40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40
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61
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62 Renamed to **numeric counter**::
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63
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64 @1
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65 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
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66 +1
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67 40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40
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68
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69 ------
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70
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71 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
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72
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73 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
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74 ]]></help>
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75 <expand macro="citations" />
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76 </tool>