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comparison check_id_map.xml @ 0:0d8e091eb3e1 draft

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author davide-albanese
date Fri, 08 Mar 2013 10:35:27 -0500
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1 <?xml version="1.0" ?>
2 <tool id="check_id_map" name="Check ID Map" version="1.6.0">
3 <description>
4 Checks user's metadata mapping file for required data, valid
5 format
6 </description>
7 <requirements>
8 <requirement type="package">qiime</requirement>
9 </requirements>
10 <command>check_id_map.py
11
12 -m $mapping_fp
13
14 #if str($char_replace):
15 -c $char_replace
16 #end if
17
18 #if $not_barcoded:
19 -b
20 #end if
21
22 #if $variable_len_barcodes:
23 -B
24 #end if
25
26 #if $disable_primer_check:
27 -p
28 #end if
29
30 #if str($added_demultiplex_field):
31 -j $added_demultiplex_field
32 #end if
33 ;
34 rm `basename $mapping_fp .txt`'.html'
35 ;
36 rm overlib.js
37 ;
38 mv `basename $mapping_fp .txt`'.log' $out_log
39 ;
40 mv `basename $mapping_fp .txt`'_corrected.txt' $out_txt
41 </command>
42 <inputs>
43 <param name="mapping_fp" label="Metadata mapping file" optional="False" type="data" format="tabular"/>
44
45 <param name="char_replace" value="_" label="Character used to replace invalid characters found in the mapping file. Must be a valid character (alphanumeric, period, or underscore)" optional="False" type="text"/>
46
47 <param name="not_barcoded" label="Set if barcodes are not present. BarcodeSequence header still required" selected="False" type="boolean"/>
48
49 <param name="variable_len_barcodes" label="Set if variable length barcodes are present to suppress warnings about barcodes of unequal length" selected="False" type="boolean"/>
50
51 <param name="disable_primer_check" label="Set to disable checks for primers. LinkerPrimerSequence header still required" selected="False" type="boolean"/>
52
53 <param name="added_demultiplex_field" label="Use to add a field to use in the mapping file as additional demultiplexing (can be used with or without barcodes). All combinations of barcodes/primers and the these fields must be unique. The fields must contain values that can be parsed from the fasta labels such as 'plate=R_2008_12_09'. In this case, 'plate' would be the column header and 'R_2008_12_09' would be the field data (minus quotes) in the mapping file. To use the run prefix from the fasta label, such as '>FLP3FBN01ELBSX', where 'FLP3FBN01' is generated from the run ID, use '-j run_prefix' and set the run prefix to be used as the data under the column header 'run_prefix'" optional="False" type="text" value=""/>
54 </inputs>
55 <outputs>
56 <data format="txt" name="out_log" label="${tool.name} on ${mapping_fp.name}"/>
57 <data format="tabular" name="out_txt" label="Corrected ${mapping_fp.name}"/>
58 </outputs>
59 <help>
60
61 Specifically, we check that:
62
63 1. The BarcodeSequence, LinkerPrimerSequences, and ReversePrimer fields
64 have valid IUPAC DNA characters, and BarcodeSequence characters
65 are non-degenerate (error)
66
67 2. The SampleID, BarcodeSequence, LinkerPrimerSequence, and Description
68 headers are present (error)
69
70 3. There are not duplicate header fields (error)
71
72 4. There are not duplicate barcodes (error)
73
74 5. Barcodes are of the same length. Suppressed when
75 variable_len_barcode flag is passed (warning)
76
77 6. The headers do not contain invalid characters (alphanumeric and
78 underscore only) (warning)
79
80 7. The data fields do not contain invalid characters (alphanumeric,
81 underscore, space, and +-%./:,; characters) (warning)
82
83 8. SampleID fields are MIENS compliant (only alphanumeric
84 and . characters). (warning)
85
86 9. There are no duplicates when the primer and variable length
87 barcodes are appended (error)
88
89 10. There are no duplicates when barcodes and added demultiplex
90 fields (-j option) are combined (error)
91
92 11. Data fields are not found beyond the Description column (warning)
93
94 Details about the metadata mapping file format can be found here:
95 http://www.qiime.org/documentation/file_formats.html#metadata-mapping-files
96
97 Errors and warnings are saved to a log file. Errors can be caused
98 by problems with the headers, invalid characters in barcodes or
99 primers, or by duplications in SampleIDs or barcodes.
100
101 Warnings can arise from invalid characters and variable length
102 barcodes that are not specified with the --variable_len_barcode.
103 Warnings will contain a reference to the cell (row,column) that
104 the warning arose from.
105
106 In addition to the log file, a 'corrected_mapping' file will be
107 created. Any invalid characters will be replaced with '.'
108 characters in the SampleID fields (to enforce MIENS compliance)
109 and text in other data fields will be replaced with the character
110 specified by the -c parameter, which is an underscore '_' by
111 default.
112
113 If pooled primers are used, separate with a comma. For instance,
114 a pooled set of three 27f primers (used to increase taxonomic
115 coverage) could be specified in the LinkerPrimerSequence fields as
116 such:
117 AGGGTTCGATTCTGGCTCAG,AGAGTTTGATCCTGGCTTAG,AGAATTTGATCTTGGTTCAG
118 </help>
119 </tool>