Mercurial > repos > iuc > qiime_validate_mapping_file

annotate validate_mapping_file.xml @ 9:1cdbb21e086f draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c845cb240f57663cf1e2240c5c506ea0b294872c"
author iuc
date Thu, 05 Dec 2019 12:32:01 +0000
parents bdf07e6d0108
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
9
1cdbb21e086f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c845cb240f57663cf1e2240c5c506ea0b294872c"
iuc
parents: 7
diff changeset
1 <tool id="qiime_validate_mapping_file" name="Check user's metadata mapping file" version="@WRAPPER_VERSION@.0" profile="@PROFILE@">
7
bdf07e6d0108 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
iuc
parents: 0
diff changeset
2 <description> for required data, valid format (validate_mapping_file)</description>
0
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
3 <macros>
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
4 <import>macros.xml</import>
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
5 </macros>
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
6 <expand macro="requirements"/>
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
7 <version_command>validate_mapping_file.py --version</version_command>
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
8 <command detect_errors="aggressive"><![CDATA[
9
1cdbb21e086f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c845cb240f57663cf1e2240c5c506ea0b294872c"
iuc
parents: 7
diff changeset
9 @MPLBACKEND@
7
bdf07e6d0108 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
iuc
parents: 0
diff changeset
10 validate_mapping_file.py
bdf07e6d0108 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
iuc
parents: 0
diff changeset
11 --mapping_fp '$mapping_fp'
bdf07e6d0108 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
iuc
parents: 0
diff changeset
12 -o validate_mapping_file_output
bdf07e6d0108 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
iuc
parents: 0
diff changeset
13 $verbose
bdf07e6d0108 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
iuc
parents: 0
diff changeset
14 --char_replace '$char_replace'
bdf07e6d0108 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
iuc
parents: 0
diff changeset
15 $not_barcoded
bdf07e6d0108 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
iuc
parents: 0
diff changeset
16 $variable_len_barcodes
bdf07e6d0108 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
iuc
parents: 0
diff changeset
17 $disable_primer_check
bdf07e6d0108 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
iuc
parents: 0
diff changeset
18 #if str($added_demultiplex_field):
bdf07e6d0108 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
iuc
parents: 0
diff changeset
19 --added_demultiplex_field '$added_demultiplex_field'
bdf07e6d0108 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
iuc
parents: 0
diff changeset
20 #end if
bdf07e6d0108 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
iuc
parents: 0
diff changeset
21 $suppress_html
0
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
22
7
bdf07e6d0108 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
iuc
parents: 0
diff changeset
23 #if not $suppress_html:
bdf07e6d0108 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
iuc
parents: 0
diff changeset
24 && mkdir -p '$html_report.files_path'
bdf07e6d0108 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
iuc
parents: 0
diff changeset
25 && mv validate_mapping_file_output/*.html '$html_report'
bdf07e6d0108 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
iuc
parents: 0
diff changeset
26 && cp validate_mapping_file_output/overlib.js '$html_report.files_path'
bdf07e6d0108 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
iuc
parents: 0
diff changeset
27 #end if
0
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
28 ]]></command>
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
29 <inputs>
7
bdf07e6d0108 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
iuc
parents: 0
diff changeset
30 <param argument="--mapping_fp" label="Metadata mapping filepath" type="data" format="tabular,csv,txt"/>
bdf07e6d0108 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
iuc
parents: 0
diff changeset
31 <param argument="--verbose" type="boolean" truevalue="-v" falsevalue="" checked="false" label="Enable printing information to standard out?"/>
0
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
32 <param argument="--char_replace" type="text" value="_" label="Default character used to replace invalid characters found in the mapping file" help="Must be a valid character (alphanumeric, period, or underscore)"/>
7
bdf07e6d0108 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
iuc
parents: 0
diff changeset
33 <param argument="--not_barcoded" type="boolean" truevalue="" falsevalue="--not_barcoded" checked="true" label="Are barcodes present?" help="BarcodeSequence header is still required in mapping file"/>
bdf07e6d0108 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
iuc
parents: 0
diff changeset
34 <param argument="--variable_len_barcodes" type="boolean" truevalue="" falsevalue="--variable_len_barcodes" checked="true" label="Are barcodes with variable length?"/>
bdf07e6d0108 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
iuc
parents: 0
diff changeset
35 <param argument="--disable_primer_check" type="boolean" truevalue="-disable_primer_check" falsevalue="" checked="false" label="Disable checks for primers?" help="LinkerPrimerSequence header is still required in mapping file"/>
bdf07e6d0108 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
iuc
parents: 0
diff changeset
36 <param argument="--added_demultiplex_field" type="text" optional="true" label="Field to use in the mapping file as additional demultiplexing (optional)" help="It can be used with or without barcodes. All combinations of barcodes/primers and 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 'run_prefix' and set the run prefix to be used as the data under the column header 'run_prefix'"/>
bdf07e6d0108 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
iuc
parents: 0
diff changeset
37 <param argument="--suppress_html" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Disable html file generation?" help="It can be useful for extremely large mapping files"/>
0
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
38 </inputs>
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
39 <outputs>
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
40 <data name="html_report" format="html" label="${tool.name} on ${on_string}: html report">
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
41 <filter>suppress_html is False</filter>
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
42 </data>
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
43 <data name="log" format="txt" from_work_dir="validate_mapping_file_output/*.log" label="${tool.name} on ${on_string}: log"/>
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
44 <data format="tabular" name="mapping_fp_corrected" from_work_dir="validate_mapping_file_output/*corrected.txt" label="${tool.name} on ${on_string}: corrected map"/>
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
45 </outputs>
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
46 <tests>
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
47 <test>
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
48 <param name="mapping_fp" value="validate_mapping_file/map.tsv"/>
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
49 <param name="verbose" value=""/>
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
50 <param name="char_replace" value="_"/>
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
51 <param name="not_barcoded" value=""/>
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
52 <param name="variable_len_barcodes" value=""/>
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
53 <param name="disable_primer_check" value=""/>
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
54 <param name="suppress_html" value=""/>
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
55 <output name="log" file="validate_mapping_file/log.txt"/>
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
56 <output name="mapping_fp_corrected" file="validate_mapping_file/corrected_map.tabular"/>
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
57 </test>
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
58 </tests>
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
59 <help><![CDATA[
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
60 **What it does**
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
61
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
62 This tool checks user’s metadata mapping file for required data, valid format
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
63
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
64 Specifically, it checks that:
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
65
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
66 - The BarcodeSequence, LinkerPrimerSequences, and ReversePrimer fields have valid IUPAC DNA characters, and BarcodeSequence characters are non-degenerate (error)
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
67 - The SampleID, BarcodeSequence, LinkerPrimerSequence, and Description headers are present. (error)
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
68 - There are not duplicate header fields (error)
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
69 - There are not duplicate barcodes (error)
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
70 - Barcodes are of the same length. Suppressed when variable_len_barcode flag is passed (warning)
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
71 - The headers do not contain invalid characters (alphanumeric and underscore only) (warning)
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
72 - The data fields do not contain invalid characters (alphanumeric, underscore, space, and +-%./:,; characters) (warning)
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
73 - SampleID fields are MIENS compliant (only alphanumeric and . characters). (warning)
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
74 - There are no duplicates when the primer and variable length barcodes are appended (error)
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
75 - There are no duplicates when barcodes and added demultiplex fields (-j option) are combined (error)
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
76 - Data fields are not found beyond the Description column (warning)
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
77
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
78 More information about this tool is available on
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
79 `QIIME documentation <http://qiime.org/scripts/validate_mapping_file.html>`_.
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
80 ]]></help>
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
81 <citations>
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
82 <expand macro="citations"/>
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
83 </citations>
e314b009545d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
84 </tool>