Mercurial > repos > galaxyp > metaquantome_filter
comparison metaquantome_filter.xml @ 0:2ee495a1fc84 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
author | galaxyp |
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date | Thu, 25 Apr 2019 13:51:33 -0400 |
parents | |
children | deaf035bbe9f |
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1 <tool id="metaquantome_filter" name="metaQuantome: filter" version="@GVERSION@"> | |
2 <description>for quality, redundancy, and sample coverage</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements" /> | |
7 <command detect_errors="exit_code"><![CDATA[ | |
8 metaquantome filter | |
9 --samps '$samps' | |
10 --mode '$mode_args.mode' | |
11 #if $mode_args.mode == 'f' or $mode_args.mode == 'ft' | |
12 --ontology='$mode_args.ontology_args.ontology' | |
13 #end if | |
14 --expand_file '$expand_file' | |
15 --min_peptides $min_peptides | |
16 #if $min_pep_nsamp != "": | |
17 --min_pep_nsamp $min_pep_nsamp | |
18 #else | |
19 --min_pep_nsamp all | |
20 #end if | |
21 --min_children_non_leaf $min_children_non_leaf | |
22 #if $min_child_nsamp != "": | |
23 --min_child_nsamp $min_child_nsamp | |
24 #else | |
25 --min_child_nsamp all | |
26 #end if | |
27 --qthreshold $qthreshold | |
28 --outfile='$outfile' | |
29 ]]></command> | |
30 <inputs> | |
31 <conditional name="mode_args"> | |
32 <param argument="--mode" type="select" label="Mode"> | |
33 <option value="f">Functional analysis</option> | |
34 <option value="t">Taxonomic analysis</option> | |
35 <option value="ft">Functional-taxonomic interaction analysis</option> | |
36 </param> | |
37 <when value="f"> | |
38 <expand macro="ONTOLOGY_ARGS"/> | |
39 </when> | |
40 <when value="t"> | |
41 </when> | |
42 <when value="ft"> | |
43 <expand macro="ONTOLOGY_ARGS"/> | |
44 </when> | |
45 </conditional> | |
46 <expand macro="SAMPS"/> | |
47 <param argument="--expand_file" type="data" format="tabular" label="metaquantome expand file" | |
48 help=""/> | |
49 <param argument="--min_peptides" type="integer" value="0" min="0" label="min_peptides"> | |
50 <help> | |
51 Used for filtering to well-supported annotations. The | |
52 number of peptides providing evidence for a term is | |
53 the number of peptides directly annotated with that | |
54 term plus the number of peptides annotated with any of | |
55 its descendants. Terms with a number of peptides | |
56 greater than or equal to min_peptides are retained. | |
57 The default is 0. | |
58 </help> | |
59 </param> | |
60 <param argument="--min_pep_nsamp" type="integer" value="" min="0" optional="true" label="min_pep_nsamp"> | |
61 <help> | |
62 Number of samples per group that must meet or exceed | |
63 min_peptides. Default is 'all'. | |
64 </help> | |
65 </param> | |
66 <param argument="--min_children_non_leaf" type="integer" value="0" min="0" label="min_children_non_leaf"> | |
67 <help> | |
68 Used for filtering to informative annotations. A term | |
69 is retained if it has a number of children greater | |
70 than or equal to min_children_non_leaf. The default is 0. | |
71 </help> | |
72 </param> | |
73 <param argument="--min_child_nsamp" type="integer" value="" min="0" optional="true" label="min_child_nsamp"> | |
74 <help> | |
75 Number of samples per group that must meet or exceed | |
76 min_children_nsamp. The default is all samples. | |
77 </help> | |
78 </param> | |
79 <param argument="--qthreshold" type="integer" value="3" min="0" label="qthreshold"> | |
80 <help> | |
81 Minimum number of intensities in each sample group. | |
82 Any functional/taxonomic term with lower number of | |
83 per-group intensities will be filtered out. The | |
84 default is 3, because this is the minimum number for | |
85 t-tests. | |
86 </help> | |
87 </param> | |
88 </inputs> | |
89 <outputs> | |
90 <data format="tabular" name="outfile" label="${tool.name} on ${on_string} filtered"/> | |
91 </outputs> | |
92 <tests> | |
93 <test> | |
94 <param name="expand_file" value="go_expanded.tab" ftype="tabular"/> | |
95 <param name="mode" value="f" /> | |
96 <param name="ontology" value="go" /> | |
97 <param name="samps" value="samples_basic.tab" ftype="tabular"/> | |
98 <param name="min_peptides" value="2" /> | |
99 <param name="min_pep_nsamp" value="" /> | |
100 <param name="min_children_non_leaf" value="2" /> | |
101 <param name="min_child_nsamp" value="" /> | |
102 <param name="qthreshold" value="0" /> | |
103 <output name="outfile" file="go_filtered.tab" ftype="tabular"/> | |
104 </test> | |
105 </tests> | |
106 <help><![CDATA[ | |
107 metaQuantome filter | |
108 =================== | |
109 | |
110 The *filter* module is the second step in the metaQuantome analysis workflow. The | |
111 purpose of the filter module is to filter expanded terms to those that are | |
112 representative and well-supported by the data. Please see the manuscript for further | |
113 details about filtering. | |
114 | |
115 | |
116 Questions, Comments, Problems, Kudos | |
117 -------------------------------------- | |
118 | |
119 Please file any issues at https://github.com/galaxyproteomics/tools-galaxyp/issues. | |
120 ]]></help> | |
121 <expand macro="citations" /> | |
122 </tool> |