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comparison extract_seqs_by_sample_id.xml @ 0:e5c3175506b7 default tip

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Initial tool configs for qiime, most need work.
author Jim Johnson <jj@umn.edu>
date Sun, 17 Jul 2011 10:30:11 -0500
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1 <tool id="extract_seqs_by_sample_id" name="extract_seqs_by_sample_id" version="1.2.0">
2 <description>Extract sequences based on the SampleID</description>
3 <requirements>
4 <requirement type="binary">extract_seqs_by_sample_id.py</requirement>
5 </requirements>
6 <command interpreter="python">
7 qiime_wrapper.py
8 --galaxy_tmpdir='$__new_file_path__'
9 extract_seqs_by_sample_id.py
10 --input_fasta_fp=$input_fasta_fp
11 --sample_ids=$sample_ids
12 --output_fasta_fp=$output_fasta_fp
13 $negate
14 </command>
15 <inputs>
16 <param name="input_fasta_fp" type="data" format="fasta" label="input_fasta_fp"
17 help="path to the input fasta file [REQUIRED]"/>
18 <param name="sample_ids" type="text" label="sample_ids"
19 help="comma-separated sample_ids to include in output fasta file(or exclude if -n=True) [REQUIRED]"/>
20 <param name="negate" type="boolean" truevalue="--negate" falsevalue="" checked="false" label="negate"
21 help="negate the sample ID list (i.e., output sample ids not passed via -s) [default: False]"/>
22 </inputs>
23 <outputs>
24 <data format="txt" name="output_fasta_fp"/>
25 </outputs>
26 <tests>
27 </tests>
28 <help>
29
30 </help>
31 </tool>
32