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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit fd099d17eceaa319fbfe429f4725328d88b18c9f
author iuc
date Thu, 10 Aug 2023 06:51:47 +0000
parents 7bda0f25191f
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1e76bd67fb73 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit fd099d17eceaa319fbfe429f4725328d88b18c9f
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1 <tool id="cshl_fastx_collapser" version="1.0.1+galaxy@VERSION_SUFFIX@" profile="22.05" name="Collapse">
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2 <description>sequences</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 @CATS@ fastx_collapser -v
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9 -o '$output'
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10 @FQQUAL@
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11 ]]></command>
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12
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13 <inputs>
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14 <expand macro="fastx_input" />
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15 </inputs>
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16 <outputs>
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17 <data name="output" format="fasta" metadata_source="input" />
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18 </outputs>
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19 <tests>
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20 <test>
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21 <param name="input" value="fasta_collapser1.fasta" />
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22 <!-- The output is sorted differently depending on architecture,
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23 so the sort attribute is needed here -->
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24 <output name="output" file="fasta_collapser1.out" sort="true" />
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25 </test>
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26 </tests>
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27 <help><![CDATA[
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28 **What it does**
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29
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30 This tool collapses identical sequences in a FASTA file into a single sequence.
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31
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32 --------
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33
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34 **Example**
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35
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36 Example Input File (Sequence "ATAT" appears multiple times)::
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37
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38 >CSHL_2_FC0042AGLLOO_1_1_605_414
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39 TGCG
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40 >CSHL_2_FC0042AGLLOO_1_1_537_759
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41 ATAT
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42 >CSHL_2_FC0042AGLLOO_1_1_774_520
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43 TGGC
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44 >CSHL_2_FC0042AGLLOO_1_1_742_502
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45 ATAT
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46 >CSHL_2_FC0042AGLLOO_1_1_781_514
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47 TGAG
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48 >CSHL_2_FC0042AGLLOO_1_1_757_487
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49 TTCA
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50 >CSHL_2_FC0042AGLLOO_1_1_903_769
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51 ATAT
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52 >CSHL_2_FC0042AGLLOO_1_1_724_499
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53 ATAT
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54
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55 Example Output file::
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56
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57 >1-1
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58 TGCG
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59 >2-4
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60 ATAT
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61 >3-1
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62 TGGC
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63 >4-1
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64 TGAG
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65 >5-1
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66 TTCA
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67
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68 .. class:: infomark
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69
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70 Original Sequence Names / Lane descriptions (e.g. "CSHL_2_FC0042AGLLOO_1_1_742_502") are discarded.
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71
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72 The output sequence name is composed of two numbers: the first is the sequence's number, the second is the multiplicity value.
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73
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74 The following output::
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75
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76 >2-4
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77 ATAT
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78
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79 means that the sequence "ATAT" is the second sequence in the file, and it appeared 4 times in the input FASTA file.
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80
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81 ------
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82
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83 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
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84
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85 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
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86 ]]></help>
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87 <expand macro="citations" />
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88 </tool>