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comparison validate_mapping_file.xml @ 0:c1bd0c560018 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
author bebatut
date Tue, 02 Feb 2016 05:50:37 -0500
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1 <tool id="qiime_validate_mapping_file" name="Validate mapping file" version="1.9.1">
2 <description>to check for required data and format</description>
3
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7
8 <expand macro="requirements" />
9
10 <version_command><![CDATA[
11 validate_mapping_file.py --version
12 ]]></version_command>
13
14 <command><![CDATA[
15 validate_mapping_file.py
16 -m $mapping_fp
17 -o validate_mapping_file_output
18 $verbose
19 -c $char_replace
20 $not_barcoded
21 $variable_len_barcodes
22 $disable_primer_check
23
24 #if str($added_demultiplex_field):
25 -j $added_demultiplex_field
26 #end if
27
28 $suppress_html
29
30 #if not $suppress_html:
31 &&
32 mkdir -p $html_report.files_path
33 &&
34 cp validate_mapping_file_output/*.html $html_report.files_path
35 &&
36 cp "validate_mapping_file_output/overlib.js" "$html_report.extra_files_path"
37 &&
38 mv $html_report.files_path/*.html $html_report
39 #end if
40 ]]>
41 </command>
42
43 <inputs>
44 <param name="mapping_fp" label="Metadata mapping filepath" type="data"
45 format="tabular,csv,txt,tsv" help="(-m/--mapping_fp)"/>
46
47 <param name="verbose" type="boolean" label="Enable printing information
48 to standard out?" truevalue="-v" falsevalue="" checked="False"
49 help="(-v/--verbose)" />
50
51 <param name="char_replace" type="text" value="_" label="Default character
52 used to replace invalid characters found in the mapping file"
53 help="Must be a valid character (alphanumeric, period, or underscore).
54 (-c/--char_replace)"/>
55
56 <param name="not_barcoded" type="boolean" label="Are barcodes present?"
57 truevalue="" falsevalue="--not_barcoded" checked="True"
58 help="BarcodeSequence header is still required in mapping file
59 (-b/--not_barcoded)"/>
60
61 <param name="variable_len_barcodes" type="boolean" label="Are barcodes with
62 variable length?" truevalue="" falsevalue="--variable_len_barcodes"
63 checked="True" help="(-B/--variable_len_barcodes)"/>
64
65 <param name="disable_primer_check" type="boolean" label="Disable checks
66 for primers?" truevalue="-disable_primer_check" falsevalue=""
67 checked="False" help="LinkerPrimerSequence header is still required
68 in mapping file (-p/--disable_primer_check)"/>
69
70 <param name="added_demultiplex_field" type="text" label="Field
71 to use in the mapping file as additional demultiplexing (optional)"
72 help="It can be used with or without barcodes. All combinations of
73 barcodes/primers and these fields must be unique. The fields must contain
74 values that can be parsed from the fasta labels such as 'plate=R_2008_12_09'.
75 In this case, 'plate' would be the column header and 'R_2008_12_09'
76 would be the field data (minus quotes) in the mapping file.
77 To use the run prefix from the fasta label, such as 'FLP3FBN01ELBSX',
78 where 'FLP3FBN01' is generated from the run ID, use 'run_prefix' and
79 set the run prefix to be used as the data under the column header
80 'run_prefix' (-j/--added_demultiplex_field)" optional="True"/>
81
82 <param name="suppress_html" type="boolean" label="Disable html file
83 generation?" truevalue="-s" falsevalue="" checked="False"
84 help="It can be useful for extremely large mapping files
85 (-s/--suppress_html)"/>
86 </inputs>
87
88 <outputs>
89 <data name="html_report" format="html"
90 label="${tool.name} on ${on_string}: html report">
91 <filter>suppress_html is False</filter>
92 </data>
93 <data name="log" format="txt"
94 from_work_dir="validate_mapping_file_output/*.log"
95 label="${tool.name} on ${on_string}: log"/>
96 <data format="tabular" name="mapping_fp_corrected"
97 from_work_dir="validate_mapping_file_output/*corrected.txt"
98 label="${tool.name} on ${on_string}: corrected map" />
99 </outputs>
100
101 <tests>
102 <test>
103 <param name="mapping_fp" value="map.tsv"/>
104 <param name="verbose" value="" />
105 <param name="char_replace" value="_" />
106 <param name="not_barcoded" value="" />
107 <param name="variable_len_barcodes" value="" />
108 <param name="disable_primer_check" value="" />
109 <param name="suppress_html" value="" />
110
111 <output name="log" file="validate_mapping_file_log.txt"/>
112 <output name="mapping_fp_corrected"
113 file="validate_mapping_file_corrected_map.tabular"/>
114 </test>
115 </tests>
116
117 <help><![CDATA[
118 **What it does?**
119
120 This tool checks user’s metadata mapping file for required data, valid format
121
122 Specifically, it checks that:
123
124 - The BarcodeSequence, LinkerPrimerSequences, and ReversePrimer fields have valid IUPAC DNA characters, and BarcodeSequence characters are non-degenerate (error)
125 - The SampleID, BarcodeSequence, LinkerPrimerSequence, and Description headers are present. (error)
126 - There are not duplicate header fields (error)
127 - There are not duplicate barcodes (error)
128 - Barcodes are of the same length. Suppressed when variable_len_barcode flag is passed (warning)
129 - The headers do not contain invalid characters (alphanumeric and underscore only) (warning)
130 - The data fields do not contain invalid characters (alphanumeric, underscore, space, and +-%./:,; characters) (warning)
131 - SampleID fields are MIENS compliant (only alphanumeric and . characters). (warning)
132 - There are no duplicates when the primer and variable length barcodes are appended (error)
133 - There are no duplicates when barcodes and added demultiplex fields (-j option) are combined (error)
134 - Data fields are not found beyond the Description column (warning)
135
136 More information about this tool is available on
137 `QIIME documentation <http://qiime.org/scripts/validate_mapping_file.html>`_.
138 ]]>
139 </help>
140
141 <citations>
142 <expand macro="citations" />
143 </citations>
144
145 </tool>