Mercurial > repos > jjohnson > qiime

comparison check_id_map.xml @ 0:e5c3175506b7 default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Initial tool configs for qiime, most need work.
author Jim Johnson <jj@umn.edu>
date Sun, 17 Jul 2011 10:30:11 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:e5c3175506b7
1 <tool id="check_id_map" name="check_id_map" version="1.2.0">
2 <description>Checks user's metadata mapping file for required data, valid format</description>
3 <requirements>
4 <requirement type="binary">check_id_map.py</requirement>
5 </requirements>
6 <command interpreter="python">
7 qiime_wrapper.py
8 --galaxy_outputdir='$log.extra_files_path'
9 --galaxy_datasets='^\S+_corrected\.txt$:'$corrected_mapping,'^\S+\.log:'$log
10 check_id_map.py
11 --map=$map
12 --output_dir='$log.extra_files_path'
13 --char_replace=$char_replace
14 $not_barcoded
15 $variable_len_barcodes
16 $disable_primer_check
17 $verbose
18 </command>
19 <inputs>
20 <param name="map" type="data" format="tabular" label="map"
21 help="Metadata mapping file filepath [REQUIRED]"/>
22 <param name="char_replace" type="text" value="_" label="char_replace"
23 help="Changes the default character used to replace invalid characters found in the mapping file. Must be a valid character (alphanumeric or underscore). NOT IMPLEMENTED CURRENTLY [default: _]"/>
24 <param name="not_barcoded" type="boolean" truevalue="--not_barcoded" falsevalue="" checked="false" label="not_barcoded"
25 help="Use -b if barcodes are not present. [default: False]"/>
26 <param name="variable_len_barcodes" type="boolean" truevalue="--variable_len_barcodes" falsevalue="" checked="false" label="variable_len_barcodes"
27 help="Use -B if variable length barcodes are present to suppress warnings about barcodes of unequal length. [default: False]"/>
28 <param name="disable_primer_check" type="boolean" truevalue="--disable_primer_check" falsevalue="" checked="false" label="disable_primer_check"
29 help="Use -p to disable checks for primers. [default: False]"/>
30 <param name="verbose" type="boolean" truevalue="" falsevalue="--verbose" checked="false" label="verbose"
31 help="Turn on this flag to disable verbose output. [default: True]"/>
32 </inputs>
33 <outputs>
34 <data format="txt" name="log"/>
35 <data format="tabular" name="corrected_mapping" label="${tool.name} on ${on_string}: corrected_mapping"/>
36 </outputs>
37 <tests>
38 </tests>
39 <help>
40
41 </help>
42 </tool>
43