Mercurial > repos > bimib > marea

comparison Marea/marea_cluster.xml @ 0:23ac9cf12788 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author bimib
date Tue, 06 Nov 2018 03:16:21 -0500
parents
children 9e63d5f02d62
comparison
equal deleted inserted replaced
-1:000000000000 0:23ac9cf12788
1 <tool id="MaREA_cluester" name="MaREA cluster analysis">
2 <description>of Reaction Activity Scores</description>
3 <requirements>
4 <requirement type="package">pandas</requirement>
5 <requirement type="package">scikit-learn</requirement>
6 <requirement type="package">scipy</requirement>
7 <requirement type="package">matplotlib</requirement>
8 <requirement type="package">cobrapy</requirement>
9 <requirement type="package">python-libsbml</requirement>
10 </requirements>
11 <command>
12 <![CDATA[
13 python $__tool_directory__/marea_cluster.py
14 --rules_selector $cond_rule.rules_selector
15 #if $cond_rule.rules_selector == 'Custom':
16 --custom ${cond_rule.Custom_rules}
17 #end if
18 --cond_hier $cond_hier.hier
19 #if $cond_hier.hier == 'yes':
20 --linkage ${cond_hier.linkage}
21 --dendro $dendrogram
22 #end if
23 --k_max $k_max
24 --k_min $k_min
25 --data $input
26 --name $name
27 --none $None
28 --tool_dir $__tool_directory__
29 --out_log $log
30 --elbow $elbow
31 ]]>
32 </command>
33 <inputs>
34 <conditional name="cond_rule">
35 <param name="rules_selector" type="select" label="Gene-Protein-Reaction rules:">
36 <option value="HMRcore" selected="true">HMRcore rules</option>
37 <option value="Recon">Recon 2.2 rules</option>
38 <option value="Custom">Custom rules</option>
39 </param>
40 <when value="Custom">
41 <param name="Custom_rules" type="data" format="tabular, csv, tsv, xml" label="Custom rules"/>
42 </when>
43 </conditional>
44 <param name="input" type="data" format="tabular, csv, tsv" label="RNAseq of all samples"/>
45 <param name="name" type="text" label="Output name prefix" value = "dataset"/>
46 <param name="k_min" type="integer" size="20" value="3" min="2" max="30" label="min number of clusters (k) to be tested (k-means)"/>
47 <param name="k_max" type="integer" size="20" value="3" min="2" max="30" label="max number of clusters (k) to be tested (k-means)"/>
48 <param name="None" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" help="if NO is selected (A and NaN) is solved as (NaN)"/>
49 <conditional name="cond_hier">
50 <param name="hier" type="select" label="Produce dendrogram (hierarchical clustering):">
51 <option value="no" selected="true">no</option>
52 <option value="yes">yes</option>
53 </param>
54 <when value="yes">
55 <param name="linkage" type="select" label="Linkage type:">
56 <option value="single" selected="true">Single: minimum distance between all observations of two sets</option>
57 <option value="complete">Complete: maximum distance between all observations of two sets</option>
58 <option value="average">Average: average distance between all observations of two sets</option>
59 </param>
60 </when>
61 </conditional>
62 </inputs>
63 <outputs>
64 <data format="txt" name="log" label="Log"/>
65 <data format="pdf" name="dendrogram" label="$name dendrogram">
66 <filter>cond_hier['hier'] == 'yes'</filter>
67 </data>
68 <data format="pdf" name="elbow" label="$name elbow evaluation method"/>
69 <collection name="cluster_out" type="list" label="Clusters $k_min - $k_max">
70 <discover_datasets pattern="__name_and_ext__" directory="cluster_out"/>
71 </collection>
72 </outputs>
73 <help>
74
75 .. class:: warningmark
76
77 This tool expects input datasets consisting of tab-delimited columns.
78
79 .. class:: infomark
80
81 **TIP:** If your data is not TAB delimited, use *Text Manipulation > Convert delimiters to TAB*
82
83 </help>
84 </tool>
85
86
87
88
89
90
91
92
93
94
95
96
97