Mercurial > repos > lparsons > fastx_barcode_splitter_enhanced

annotate fastx_barcode_splitter.xml @ 4:0fb7e9130a70 draft default tip

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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit 460463a5406419fe8e113467bdb8bd093d21e7c5
author lparsons
date Mon, 02 May 2016 17:04:32 -0400
parents e7b7cdc1834d
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0fb7e9130a70 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit 460463a5406419fe8e113467bdb8bd093d21e7c5
lparsons
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1 <tool id="cshl_princeton_fastx_barcode_splitter" version="1.2" name="Barcode Splitter">
0fb7e9130a70 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit 460463a5406419fe8e113467bdb8bd093d21e7c5
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2 <description></description>
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3 <command interpreter="bash" detect_errors="aggressive"><![CDATA[
2
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lparsons
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4 fastx_barcode_splitter_galaxy_wrapper.sh $BARCODE $input "split/" $input.extension --mismatches $mismatches --partial $partial
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5 #if $refBarcodeLocation.barcodeLocation == "idxfile":
b7b3d008e2d3 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit e6a486662201362134119c0ddc7151b8dd181ebd
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6 --idxfile $refBarcodeLocation.idxfile
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7 #else:
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8 $refBarcodeLocation.EOL
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9 #end if
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10 > $summary
1
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11 ]]>
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12 </command>
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84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history.
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13
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14 <inputs>
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lparsons
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15 <param format="txt" name="BARCODE" type="data" label="Barcodes to use" />
0fb7e9130a70 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit 460463a5406419fe8e113467bdb8bd093d21e7c5
lparsons
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16 <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to split" />
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lparsons
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18 <conditional name="refBarcodeLocation">
0fb7e9130a70 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit 460463a5406419fe8e113467bdb8bd093d21e7c5
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19 <param name="barcodeLocation" type="select" label="Barcodes found at">
0fb7e9130a70 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit 460463a5406419fe8e113467bdb8bd093d21e7c5
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20 <option value="bol">Start of sequence (5' end)</option>
0fb7e9130a70 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit 460463a5406419fe8e113467bdb8bd093d21e7c5
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21 <option value="eol">End of sequence (3' end)</option>
0fb7e9130a70 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit 460463a5406419fe8e113467bdb8bd093d21e7c5
lparsons
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22 <option value="idxfile">Separate index file</option>
0fb7e9130a70 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit 460463a5406419fe8e113467bdb8bd093d21e7c5
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23 </param>
0fb7e9130a70 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit 460463a5406419fe8e113467bdb8bd093d21e7c5
lparsons
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24 <when value="bol">
0fb7e9130a70 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit 460463a5406419fe8e113467bdb8bd093d21e7c5
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25 <param name="EOL" type="hidden" value="--bol" />
0fb7e9130a70 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit 460463a5406419fe8e113467bdb8bd093d21e7c5
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26 </when>
0fb7e9130a70 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit 460463a5406419fe8e113467bdb8bd093d21e7c5
lparsons
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27 <when value="eol">
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lparsons
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28 <param name="EOL" type="hidden" value="--eol" />
0fb7e9130a70 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit 460463a5406419fe8e113467bdb8bd093d21e7c5
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29 </when>
0fb7e9130a70 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit 460463a5406419fe8e113467bdb8bd093d21e7c5
lparsons
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30 <when value="idxfile">
0fb7e9130a70 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit 460463a5406419fe8e113467bdb8bd093d21e7c5
lparsons
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31 <param name="idxfile" type="data" format="fasta,fastq,fastqsanger" label="Select index read file" />
0fb7e9130a70 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit 460463a5406419fe8e113467bdb8bd093d21e7c5
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32 </when>
0fb7e9130a70 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit 460463a5406419fe8e113467bdb8bd093d21e7c5
lparsons
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33 </conditional>
0
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history.
lparsons
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34
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35 <param name="mismatches" type="integer" size="3" value="0" label="Number of allowed mismatches" />
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37 <param name="partial" type="integer" size="3" value="0" label="Number of allowed barcodes nucleotide deletions" />
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38
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39 </inputs>
1
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41 <outputs>
0fb7e9130a70 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit 460463a5406419fe8e113467bdb8bd093d21e7c5
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42 <data format="tabular" name="summary" label="${tool.name} on ${on_string}: Summary" />
0fb7e9130a70 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit 460463a5406419fe8e113467bdb8bd093d21e7c5
lparsons
parents: 3
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43 <collection name="split_output" type="list" format_source="input" label="${tool.name} on ${on_string}">
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44 <discover_datasets pattern="__designation_and_ext__" directory="split" visible="false" label="${designation}"/>
0fb7e9130a70 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit 460463a5406419fe8e113467bdb8bd093d21e7c5
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45 </collection>
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46 </outputs>
1
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47
4
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48 <tests>
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49 <test>
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50 <!-- Split a FASTQ file -->
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lparsons
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51 <param name="BARCODE" value="fastx_barcode_splitter1.txt" />
0fb7e9130a70 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit 460463a5406419fe8e113467bdb8bd093d21e7c5
lparsons
parents: 3
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52 <param name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" />
0fb7e9130a70 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit 460463a5406419fe8e113467bdb8bd093d21e7c5
lparsons
parents: 3
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53 <param name="barcodeLocation" value="bol" />
0fb7e9130a70 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit 460463a5406419fe8e113467bdb8bd093d21e7c5
lparsons
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54 <param name="mismatches" value="2" />
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55 <param name="partial" value="0" />
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lparsons
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56 <output name="summary" file="fastx_barcode_splitter1.out" />
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57 <collection name="output" type="list">
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58 <discovered_dataset designation="BC1" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC1.out" />
0fb7e9130a70 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit 460463a5406419fe8e113467bdb8bd093d21e7c5
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59 <discovered_dataset designation="BC2" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC2.out" />
0fb7e9130a70 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit 460463a5406419fe8e113467bdb8bd093d21e7c5
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60 <discovered_dataset designation="BC3" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC3.out" />
0fb7e9130a70 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit 460463a5406419fe8e113467bdb8bd093d21e7c5
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61 <discovered_dataset designation="BC4" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC4.out" />
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62 <discovered_dataset designation="unmatched" ftype="fastqsolexa" file="fastx_barcode_splitter1_unmatched.out" />
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63 </collection>
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64 </test>
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65
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66 <test>
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67 <!-- Split a FASTQ file, using separate index read -->
0fb7e9130a70 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit 460463a5406419fe8e113467bdb8bd093d21e7c5
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68 <param name="BARCODE" value="fastx_barcode_splitter1.txt" />
0fb7e9130a70 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit 460463a5406419fe8e113467bdb8bd093d21e7c5
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69 <param name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" />
0fb7e9130a70 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit 460463a5406419fe8e113467bdb8bd093d21e7c5
lparsons
parents: 3
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70 <param name="idxfile" value="fastx_barcode_splitter_index.fastq" ftype="fastqsolexa" />
0fb7e9130a70 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit 460463a5406419fe8e113467bdb8bd093d21e7c5
lparsons
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71 <param name="barcodeLocation" value="idxfile" />
0fb7e9130a70 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit 460463a5406419fe8e113467bdb8bd093d21e7c5
lparsons
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72 <param name="mismatches" value="2" />
0fb7e9130a70 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit 460463a5406419fe8e113467bdb8bd093d21e7c5
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73 <param name="partial" value="0" />
0fb7e9130a70 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit 460463a5406419fe8e113467bdb8bd093d21e7c5
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74 <output name="output" file="fastx_barcode_splitter1.out" />
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75 <collection name="split_output" type="list">
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76 <discovered_dataset designation="BC1" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC1.out" />
0fb7e9130a70 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit 460463a5406419fe8e113467bdb8bd093d21e7c5
lparsons
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77 <discovered_dataset designation="BC2" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC2.out" />
0fb7e9130a70 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit 460463a5406419fe8e113467bdb8bd093d21e7c5
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78 <discovered_dataset designation="BC3" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC3.out" />
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79 <discovered_dataset designation="BC4" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC4.out" />
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80 <discovered_dataset designation="unmatched" ftype="fastqsolexa" file="fastx_barcode_splitter1_unmatched.out" />
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81 </collection>
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82 </test>
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83 </tests>
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84
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85 <help><![CDATA[
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86 **What it does**
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87
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88 This tool splits a FASTQ or FASTA file into several files, using barcodes as the split criteria.
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89
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90 --------
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91
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92 **Barcode file Format**
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93
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94 Barcode files are simple text files.
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95 Each line should contain an identifier (descriptive name for the barcode), and the barcode itself (A/C/G/T), separated by a TAB character.
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96 Example::
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97
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98 #This line is a comment (starts with a 'number' sign)
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99 BC1 GATCT
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100 BC2 ATCGT
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101 BC3 GTGAT
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102 BC4 TGTCT
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103
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104 For each barcode, a new FASTQ file will be created (with the barcode's identifier as part of the file name).
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105 Sequences matching the barcode will be stored in the appropriate file.
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106
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107 One additional FASTQ file will be created (the 'unmatched' file), where sequences not matching any barcode will be stored.
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108
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109 The output of this tool is a summary tabel displaying the split counts for each barcode identifier.
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110 In addition, each fastq file produced will be loaded into the galaxy history as part of a collection list.
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111 ]]>
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112 </help>
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113
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114 <!-- FASTX-barcode-splitter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
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115 <citations>
2
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116 <citation type="bibtex">
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117 @misc{gordon_fastx-toolkit_????,
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118 title = {{FASTX}-{Toolkit}},
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119 url = {http://hannonlab.cshl.edu/fastx_toolkit/index.html},
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120 author = {Gordon, Assaf}
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121 }
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122 </citation>
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123 </citations>
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124
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125 </tool>