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comparison Marea/marea_cluster.xml @ 4:cf3d3d8f4ef5 draft

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Modifica a xml
author bimib
date Tue, 13 Nov 2018 07:34:43 -0500
parents 02577e65dcca
children 146cb8e171b8
comparison
equal deleted inserted replaced
3:02577e65dcca 4:cf3d3d8f4ef5
1 <tool id="MaREA_cluester" name="MaREA cluster analysis"> 1 <tool id="MaREA_cluester" name="MaREA cluster analysis" version="1.0.0">
2 <description>of Reaction Activity Scores</description> 2 <description>of Reaction Activity Scores</description>
3 <macros> 3 <macros>
4 <import>marea_macros.xml</import> 4 <import>marea_macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
9 <requirement type="package">cobra</requirement> 9 <requirement type="package">cobra</requirement>
10 <requirement type="package">python-libsbml</requirement> 10 <requirement type="package">python-libsbml</requirement>
11 <requirement type="package">scikit-learn</requirement> 11 <requirement type="package">scikit-learn</requirement>
12 <requirement type="package">matplotlib</requirement> 12 <requirement type="package">matplotlib</requirement>
13 </requirements> 13 </requirements>
14 <command> 14 <command detect_errors="exit_code">
15 <![CDATA[ 15 <![CDATA[
16 python $__tool_directory__/marea_cluster.py 16 python $__tool_directory__/marea_cluster.py
17 --rules_selector $cond_rule.rules_selector 17 --rules_selector $cond_rule.rules_selector
18 #if $cond_rule.rules_selector == 'Custom': 18 #if $cond_rule.rules_selector == 'Custom':
19 --custom ${cond_rule.Custom_rules} 19 --custom ${cond_rule.Custom_rules}
37 <conditional name="cond_rule"> 37 <conditional name="cond_rule">
38 <expand macro="options"/> 38 <expand macro="options"/>
39 <when value="Custom"> 39 <when value="Custom">
40 <param name="Custom_rules" type="data" format="tabular, csv, tsv, xml" label="Custom rules" /> 40 <param name="Custom_rules" type="data" format="tabular, csv, tsv, xml" label="Custom rules" />
41 </when> 41 </when>
42 <when value="HMRcore">
43 </when>
44 <when value="Recon">
45 </when>
42 </conditional> 46 </conditional>
43 <param name="input" argument="--data" type="data" format="tabular, csv, tsv" label="RNAseq of all samples" /> 47 <param name="input" argument="--data" type="data" format="tabular, csv, tsv" label="RNAseq of all samples" />
44 <param name="name" argument="--name" type="text" label="Output name prefix" value="dataset" /> 48 <param name="name" argument="--name" type="text" label="Output name prefix" value="dataset" />
45 <param name="k_min" argument="--k_min" type="integer" size="20" value="3" min="2" max="30" label="Min number of clusters (k) to be tested (k-means)"/> 49 <param name="k_min" argument="--k_min" type="integer" size="20" value="3" min="2" max="30" label="Min number of clusters (k) to be tested (k-means)"/>
46 <param name="k_max" argument="--k_max" type="integer" size="20" value="3" min="2" max="30" label="Max number of clusters (k) to be tested (k-means)"/> 50 <param name="k_max" argument="--k_max" type="integer" size="20" value="3" min="2" max="30" label="Max number of clusters (k) to be tested (k-means)"/>
55 <option value="single" selected="true">Single: minimum distance between all observations of two sets</option> 59 <option value="single" selected="true">Single: minimum distance between all observations of two sets</option>
56 <option value="complete">Complete: maximum distance between all observations of two sets</option> 60 <option value="complete">Complete: maximum distance between all observations of two sets</option>
57 <option value="average">Average: average distance between all observations of two sets</option> 61 <option value="average">Average: average distance between all observations of two sets</option>
58 </param> 62 </param>
59 </when> 63 </when>
64 <when value="no">
65 </when>
60 </conditional> 66 </conditional>
61 </inputs> 67 </inputs>
62 68
63 <outputs> 69 <outputs>
64 <data format="txt" name="log" label="Log" /> 70 <data format="txt" name="log" label="Log" />
68 <data format="pdf" name="elbow" label="$name elbow evaluation method" /> 74 <data format="pdf" name="elbow" label="$name elbow evaluation method" />
69 <collection name="cluster_out" type="list" label="Clusters $k_min - $k_max"> 75 <collection name="cluster_out" type="list" label="Clusters $k_min - $k_max">
70 <discover_datasets pattern="__name_and_ext__" directory="cluster_out" /> 76 <discover_datasets pattern="__name_and_ext__" directory="cluster_out" />
71 </collection> 77 </collection>
72 </outputs> 78 </outputs>
73 79 <tests>
80 <test>
81 <param name="k_min" value="4"/>
82 <output name="log" file="log.txt"/>
83 </test>
84 </tests>
74 <help> 85 <help>
75 <![CDATA[ 86 <![CDATA[
76 87
77 What it does 88 What it does
78 ------------- 89 -------------