Mercurial > repos > iuc > qiime_validate_mapping_file

comparison validate_mapping_file.xml @ 7:bdf07e6d0108 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
author iuc
date Fri, 04 Aug 2017 18:24:23 -0400
parents e314b009545d
children 1cdbb21e086f
comparison
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6:4a920ba11575 7:bdf07e6d0108
1 <tool id="qiime_validate_mapping_file" name="Validate mapping file" version="@WRAPPER_VERSION@.0"> 1 <tool id="qiime_validate_mapping_file" name="Check user's metadata mapping file" version="@WRAPPER_VERSION@.0">
2 <description>to check for required data and format</description> 2 <description> for required data, valid format (validate_mapping_file)</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <version_command>validate_mapping_file.py --version</version_command> 7 <version_command>validate_mapping_file.py --version</version_command>
8 <command detect_errors="aggressive"><![CDATA[ 8 <command detect_errors="aggressive"><![CDATA[
9 validate_mapping_file.py 9 validate_mapping_file.py
10 --mapping_fp '$mapping_fp' 10 --mapping_fp '$mapping_fp'
11 -o validate_mapping_file_output 11 -o validate_mapping_file_output
12 $verbose 12 $verbose
13 --char_replace '$char_replace' 13 --char_replace '$char_replace'
14 $not_barcoded 14 $not_barcoded
15 $variable_len_barcodes 15 $variable_len_barcodes
16 $disable_primer_check 16 $disable_primer_check
17 #if str($added_demultiplex_field): 17 #if str($added_demultiplex_field):
18 --added_demultiplex_field '$added_demultiplex_field' 18 --added_demultiplex_field '$added_demultiplex_field'
19 #end if 19 #end if
20 $suppress_html 20 $suppress_html
21 21
22 #if not $suppress_html: 22 #if not $suppress_html:
23 && mkdir -p '$html_report.files_path' 23 && mkdir -p '$html_report.files_path'
24 && mv validate_mapping_file_output/*.html '$html_report' 24 && mv validate_mapping_file_output/*.html '$html_report'
25 && cp validate_mapping_file_output/overlib.js '$html_report.files_path' 25 && cp validate_mapping_file_output/overlib.js '$html_report.files_path'
26 #end if 26 #end if
27 ]]></command> 27 ]]></command>
28 <inputs> 28 <inputs>
29 <param argument="--mapping_fp" label="Metadata mapping filepath" type="data" format="tabular,csv,txt" help=""/> 29 <param argument="--mapping_fp" label="Metadata mapping filepath" type="data" format="tabular,csv,txt"/>
30 <param argument="--verbose" type="boolean" label="Enable printing information to standard out?" truevalue="-v" falsevalue="" checked="False"/> 30 <param argument="--verbose" type="boolean" truevalue="-v" falsevalue="" checked="false" label="Enable printing information to standard out?"/>
31 <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)"/> 31 <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)"/>
32 <param argument="--not_barcoded" type="boolean" label="Are barcodes present?" truevalue="" falsevalue="--not_barcoded" checked="True" help="BarcodeSequence header is still required in mapping file"/> 32 <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"/>
33 <param argument="--variable_len_barcodes" type="boolean" label="Are barcodes with variable length?" truevalue="" falsevalue="--variable_len_barcodes" checked="True" help=""/> 33 <param argument="--variable_len_barcodes" type="boolean" truevalue="" falsevalue="--variable_len_barcodes" checked="true" label="Are barcodes with variable length?"/>
34 <param argument="--disable_primer_check" type="boolean" label="Disable checks for primers?" truevalue="-disable_primer_check" falsevalue="" checked="False" help="LinkerPrimerSequence header is still required in mapping file"/> 34 <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"/>
35 <param argument="--added_demultiplex_field" type="text" 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'" optional="True"/> 35 <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'"/>
36 <param argument="--suppress_html" type="boolean" label="Disable html file generation?" truevalue="-s" falsevalue="" checked="False" help="It can be useful for extremely large mapping files"/> 36 <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"/>
37 </inputs> 37 </inputs>
38 <outputs> 38 <outputs>
39 <data name="html_report" format="html" label="${tool.name} on ${on_string}: html report"> 39 <data name="html_report" format="html" label="${tool.name} on ${on_string}: html report">
40 <filter>suppress_html is False</filter> 40 <filter>suppress_html is False</filter>
41 </data> 41 </data>