Mercurial > repos > davide-albanese > qiime_1_6_0

annotate check_id_map.xml @ 4:51eb500d6526 draft

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check_id_map minor fix
author Davide Albanese <davide.albanese@gmail.com>
date Sat, 09 Mar 2013 22:27:31 +0100
parents 3e5da170ffdd
children 60b88c61566f
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1 <!-- Author: Davide Albanese - Fondazione Edmud Mach, 2013 -->
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2
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3 <tool id="check_id_map" name="Check ID Map" version="1.6.0-2">
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4 <description>
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5 Checks user's metadata mapping file for required data, valid
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6 format
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7 </description>
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8 <requirements>
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9 <requirement type="binary">check_id_map.py</requirement>
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10 </requirements>
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11 <command>
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12 check_id_map.py
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13
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14 -m $mapping_fp
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15
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16 #if str($char_replace):
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17 -c $char_replace
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18 #end if
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19
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20 #if $not_barcoded:
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21 -b
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22 #end if
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23
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24 #if $variable_len_barcodes:
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25 -B
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26 #end if
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27
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28 #if $disable_primer_check:
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29 -p
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30 #end if
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31
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32 #if str($added_demultiplex_field):
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33 -j $added_demultiplex_field
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34 #end if
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35 ;
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36 rm `basename $mapping_fp .txt`'.html'
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37 ;
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38 rm overlib.js
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39 ;
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40 mv `basename $mapping_fp .txt`'.log' $out_log
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41 ;
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42 mv `basename $mapping_fp .txt`'_corrected.txt' $out_txt
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43 </command>
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44 <inputs>
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45 <param name="mapping_fp" label="Metadata mapping file" optional="False" type="data" format="tabular"/>
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46
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47 <param name="char_replace" value="_" label="Character used to replace invalid characters found in the mapping file. Must be a valid character (alphanumeric, period, or underscore)" optional="False" type="text"/>
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48
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49 <param name="not_barcoded" label="Set if barcodes are not present. BarcodeSequence header still required" selected="False" type="boolean"/>
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50
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51 <param name="variable_len_barcodes" label="Set if variable length barcodes are present to suppress warnings about barcodes of unequal length" selected="False" type="boolean"/>
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52
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53 <param name="disable_primer_check" label="Set to disable checks for primers. LinkerPrimerSequence header still required" selected="False" type="boolean"/>
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54
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55 <param name="added_demultiplex_field" label="Use to add a field to use in the mapping file as additional demultiplexing (can be used with or without barcodes). All combinations of barcodes/primers and the these fields must be unique. The fields must contain values that can be parsed from the fasta labels such as 'plate=R_2008_12_09'. In this case, 'plate' would be the column header and 'R_2008_12_09' would be the field data (minus quotes) in the mapping file. To use the run prefix from the fasta label, such as '>FLP3FBN01ELBSX', where 'FLP3FBN01' is generated from the run ID, use '-j run_prefix' and set the run prefix to be used as the data under the column header 'run_prefix'" optional="False" type="text" value=""/>
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56 </inputs>
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57 <outputs>
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58 <data format="txt" name="out_log" label="${tool.name} on ${mapping_fp.name}"/>
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59 <data format="tabular" name="out_txt" label="Corrected ${mapping_fp.name}"/>
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60 </outputs>
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61 <help>
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62 Check ID Map checks::
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63
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64 1. The BarcodeSequence, LinkerPrimerSequences, and ReversePrimer fields
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65 have valid IUPAC DNA characters, and BarcodeSequence characters
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66 are non-degenerate (error)
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67
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68 2. The SampleID, BarcodeSequence, LinkerPrimerSequence, and Description
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69 headers are present (error)
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70
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71 3. There are not duplicate header fields (error)
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72
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73 4. There are not duplicate barcodes (error)
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75 5. Barcodes are of the same length. Suppressed when
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76 variable_len_barcode flag is passed (warning)
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78 6. The headers do not contain invalid characters (alphanumeric and
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79 underscore only) (warning)
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81 7. The data fields do not contain invalid characters (alphanumeric,
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82 underscore, space, and +-%./:,; characters) (warning)
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83
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84 8. SampleID fields are MIENS compliant (only alphanumeric
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85 and . characters). (warning)
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87 9. There are no duplicates when the primer and variable length
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88 barcodes are appended (error)
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90 10. There are no duplicates when barcodes and added demultiplex
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91 fields (-j option) are combined (error)
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93 11. Data fields are not found beyond the Description column (warning)
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94
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95 Details about the metadata mapping file format can be found here:
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96 http://www.qiime.org/documentation/file_formats.html#metadata-mapping-files
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97
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98 Errors and warnings are saved to a log file. Errors can be caused
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99 by problems with the headers, invalid characters in barcodes or
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100 primers, or by duplications in SampleIDs or barcodes.
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101
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102 Warnings can arise from invalid characters and variable length
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103 barcodes that are not specified with the --variable_len_barcode.
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104 Warnings will contain a reference to the cell (row,column) that
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105 the warning arose from.
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106
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107 In addition to the log file, a 'corrected_mapping' file will be
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108 created. Any invalid characters will be replaced with '.'
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109 characters in the SampleID fields (to enforce MIENS compliance)
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110 and text in other data fields will be replaced with the character
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111 specified by the -c parameter, which is an underscore '_' by
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112 default.
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113
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114 If pooled primers are used, separate with a comma. For instance,
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115 a pooled set of three 27f primers (used to increase taxonomic
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116 coverage) could be specified in the LinkerPrimerSequence fields as
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117 such:
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118 AGGGTTCGATTCTGGCTCAG,AGAGTTTGATCCTGGCTTAG,AGAATTTGATCTTGGTTCAG
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119 </help>
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120 </tool>