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comparison filter_fasta.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_filter_fasta" name="filter fasta" version="1.9.1galaxy1">
2 <description>This script can be applied to remove sequences from a fasta or
3 fastq file based on input criteria.</description>
4
5 <macros>
6 <import>macros.xml</import>
7 </macros>
8
9 <expand macro="requirements" />
10
11 <command>
12 <![CDATA[
13 filter_fasta.py
14 -f $input_fasta_fp
15 -o $output_fasta_fp
16 #if str($otu_map) != 'None':
17 -m $otu_map
18 #end if
19
20 #if str($seq_id_fp) != 'None':
21 -s $seq_id_fp
22 #end if
23
24 #if str($biom_fp) != 'None':
25 -b $biom_fp
26 #end if
27
28 #if str($subject_fasta_fp) != 'None':
29 -a $subject_fasta_fp
30 #end if
31
32 #if str($seq_id_prefix):
33 -p $seq_id_prefix
34 #end if
35
36 #if str($sample_id_fp) != 'None':
37 --sample_id_fp=$sample_id_fp
38 #end if
39
40 #if $negate:
41 -n
42 #end if
43
44 #if str($mapping_fp) != 'None':
45 --mapping_fp=$mapping_fp
46 #end if
47
48 #if str($valid_states):
49 --valid_states=$valid_states
50 #end if
51 ]]>
52 </command>
53
54 <inputs>
55 <param label="-f/--input_fasta_fp: path to the input fasta file"
56 name="input_fasta_fp" optional="False" type="data"/>
57 <param label="-m/--otu_map: an OTU map where sequences ids are those
58 which should be retained" name="otu_map" optional="True" type="data"/>
59 <param label="-s/--seq_id_fp: A list of sequence identifiers (or tab-delimited
60 lines with a seq identifier in the first field) which should be retained"
61 name="seq_id_fp" optional="True" type="data"/>
62 <param label="-b/--biom_fp: A biom file where otu identifiers should be
63 retained" name="biom_fp" optional="True" type="data"/>
64 <param label="-a/--subject_fasta_fp: A fasta file where the seq ids should
65 be retained." name="subject_fasta_fp" optional="True" type="data"/>
66 <param label="-p/--seq_id_prefix: keep seqs where seq_id starts with this
67 prefix" name="seq_id_prefix" optional="True" type="text"/>
68 <param label="--sample_id_fp: keep seqs where seq_id starts with a sample
69 id listed in this file" name="sample_id_fp" optional="True"
70 type="data"/>
71 <param label="-n/--negate: discard passed seq ids rather than keep passed
72 seq ids [default: False]" name="negate" selected="False"
73 type="boolean"/>
74 <param label="--mapping_fp: mapping file path (for use with --valid_states)
75 [default: None]" name="mapping_fp" optional="True" type="data"/>
76 <param label="--valid_states: description of sample ids to retain (for use
77 with --mapping_fp) [default: None]" name="valid_states" optional="True"
78 type="text"/>
79 </inputs>
80
81 <outputs>
82 <data format="txt" name="output_fasta_fp"/>
83 </outputs>
84
85 <tests>
86 <test>
87 </test>
88 </tests>
89
90 <help>
91 <![CDATA[
92
93 **What it does**
94
95
96 ]]>
97 </help>
98
99 <citations>
100 <expand macro="citations" />
101 </citations>
102 </tool>