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comparison check_id_map.xml @ 7:fb797308e552 draft default tip

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author davide-albanese
date Sat, 09 Mar 2013 17:01:28 -0500
parents 27a2d07f4d53
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6:27a2d07f4d53 7:fb797308e552
1 <!-- Author: Davide Albanese - Fondazione Edmud Mach, 2013 -->
2
3 <tool id="check_id_map" name="Check ID Map" version="1.6.0-3">
4 <description>
5 Checks user's metadata mapping file for required data, valid
6 format
7 </description>
8 <requirements>
9 <requirement type="binary">check_id_map.py</requirement>
10 </requirements>
11 <command>
12 check_id_map.py
13
14 -m $mapping_fp
15
16 #if str($char_replace):
17 -c $char_replace
18 #end if
19
20 #if $not_barcoded:
21 -b
22 #end if
23
24 #if $variable_len_barcodes:
25 -B
26 #end if
27
28 #if $disable_primer_check:
29 -p
30 #end if
31
32 #if str($added_demultiplex_field):
33 -j $added_demultiplex_field
34 #end if
35 ;
36 rm `basename $mapping_fp .txt`'.html'
37 ;
38 rm overlib.js
39 ;
40 mv `basename $mapping_fp .txt`'.log' $out_log
41 ;
42 mv `basename $mapping_fp .txt`'_corrected.txt' $out_txt
43 </command>
44 <inputs>
45 <param name="mapping_fp" label="Metadata mapping file" optional="False" type="data" format="tabular"/>
46
47 <param name="char_replace" value="_" label="Character used to replace invalid characters found in the mapping file. Must be a valid character (alphanumeric, period, or underscore)" optional="False" type="text"/>
48
49 <param name="not_barcoded" label="Set if barcodes are not present. BarcodeSequence header still required" selected="False" type="boolean"/>
50
51 <param name="variable_len_barcodes" label="Set if variable length barcodes are present to suppress warnings about barcodes of unequal length" selected="False" type="boolean"/>
52
53 <param name="disable_primer_check" label="Set to disable checks for primers. LinkerPrimerSequence header still required" selected="False" type="boolean"/>
54
55 <param name="added_demultiplex_field" label="Use to add a field to use in the mapping file as additional demultiplexing (can be used with or without barcodes). All combinations of barcodes/primers and the these fields must be unique. The fields must contain values that can be parsed from the fasta labels such as 'plate=R_2008_12_09'. In this case, 'plate' would be the column header and 'R_2008_12_09' would be the field data (minus quotes) in the mapping file. To use the run prefix from the fasta label, such as '>FLP3FBN01ELBSX', where 'FLP3FBN01' is generated from the run ID, use '-j run_prefix' and set the run prefix to be used as the data under the column header 'run_prefix'" optional="False" type="text" value=""/>
56 </inputs>
57 <outputs>
58 <data format="txt" name="out_log" label="${tool.name} on ${mapping_fp.name}"/>
59 <data format="tabular" name="out_txt" label="Corrected ${mapping_fp.name}"/>
60 </outputs>
61 <help>
62 Check ID Map checks:
63
64 1. The BarcodeSequence, LinkerPrimerSequences, and ReversePrimer fields
65 have valid IUPAC DNA characters, and BarcodeSequence characters
66 are non-degenerate (error)
67
68 2. The SampleID, BarcodeSequence, LinkerPrimerSequence, and Description
69 headers are present (error)
70
71 3. There are not duplicate header fields (error)
72
73 4. There are not duplicate barcodes (error)
74
75 5. Barcodes are of the same length. Suppressed when
76 variable_len_barcode flag is passed (warning)
77
78 6. The headers do not contain invalid characters (alphanumeric and
79 underscore only) (warning)
80
81 7. The data fields do not contain invalid characters (alphanumeric,
82 underscore, space, and +-%./:,; characters) (warning)
83
84 8. SampleID fields are MIENS compliant (only alphanumeric
85 and . characters). (warning)
86
87 9. There are no duplicates when the primer and variable length
88 barcodes are appended (error)
89
90 10. There are no duplicates when barcodes and added demultiplex
91 fields (-j option) are combined (error)
92
93 11. Data fields are not found beyond the Description column (warning)
94
95 Details about the metadata mapping file format can be found here:
96 http://www.qiime.org/documentation/file_formats.html#metadata-mapping-files
97
98 Errors and warnings are saved to a log file. Errors can be caused
99 by problems with the headers, invalid characters in barcodes or
100 primers, or by duplications in SampleIDs or barcodes.
101
102 Warnings can arise from invalid characters and variable length
103 barcodes that are not specified with the --variable_len_barcode.
104 Warnings will contain a reference to the cell (row,column) that
105 the warning arose from.
106
107 In addition to the log file, a 'corrected_mapping' file will be
108 created. Any invalid characters will be replaced with '.'
109 characters in the SampleID fields (to enforce MIENS compliance)
110 and text in other data fields will be replaced with the character
111 specified by the -c parameter, which is an underscore '_' by
112 default.
113
114 If pooled primers are used, separate with a comma. For instance,
115 a pooled set of three 27f primers (used to increase taxonomic
116 coverage) could be specified in the LinkerPrimerSequence fields as
117 such:
118 AGGGTTCGATTCTGGCTCAG,AGAGTTTGATCCTGGCTTAG,AGAATTTGATCTTGGTTCAG
119 </help>
120 </tool>