annotate Marea/marea_cluster.xml @ 5:146cb8e171b8 draft

revision: xml requirement version
author bimib
date Thu, 15 Nov 2018 04:52:09 -0500
parents cf3d3d8f4ef5
children 5721182715a7
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
cf3d3d8f4ef5 Modifica a xml
bimib
parents: 3
diff changeset
1 <tool id="MaREA_cluester" name="MaREA cluster analysis" version="1.0.0">
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
2 <description>of Reaction Activity Scores</description>
1
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
3 <macros>
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
4 <import>marea_macros.xml</import>
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
5 </macros>
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
6 <requirements>
5
146cb8e171b8 revision: xml requirement version
bimib
parents: 4
diff changeset
7 <requirement type="package" version="0.23.0">pandas</requirement>
146cb8e171b8 revision: xml requirement version
bimib
parents: 4
diff changeset
8 <requirement type="package" version="1.1.0">scipy</requirement>
146cb8e171b8 revision: xml requirement version
bimib
parents: 4
diff changeset
9 <requirement type="package" version="0.11.3">cobra</requirement>
146cb8e171b8 revision: xml requirement version
bimib
parents: 4
diff changeset
10 <requirement type="package" version="5.17.0">python-libsbml</requirement>
146cb8e171b8 revision: xml requirement version
bimib
parents: 4
diff changeset
11 <requirement type="package" version="0.19.1">scikit-learn</requirement>
146cb8e171b8 revision: xml requirement version
bimib
parents: 4
diff changeset
12 <requirement type="package" version="2.2.2">matplotlib</requirement>
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
13 </requirements>
4
cf3d3d8f4ef5 Modifica a xml
bimib
parents: 3
diff changeset
14 <command detect_errors="exit_code">
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
15 <![CDATA[
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
16 python $__tool_directory__/marea_cluster.py
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
17 --rules_selector $cond_rule.rules_selector
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
18 #if $cond_rule.rules_selector == 'Custom':
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
19 --custom ${cond_rule.Custom_rules}
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
20 #end if
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
21 --cond_hier $cond_hier.hier
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
22 #if $cond_hier.hier == 'yes':
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
23 --linkage ${cond_hier.linkage}
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
24 --dendro $dendrogram
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
25 #end if
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
26 --k_max $k_max
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
27 --k_min $k_min
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
28 --data $input
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
29 --name $name
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
30 --none $None
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
31 --tool_dir $__tool_directory__
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
32 --out_log $log
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
33 --elbow $elbow
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
34 ]]>
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
35 </command>
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
36 <inputs>
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
37 <conditional name="cond_rule">
2
3b3d0e5d0802 Uploaded
bimib
parents: 1
diff changeset
38 <expand macro="options"/>
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
39 <when value="Custom">
1
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
40 <param name="Custom_rules" type="data" format="tabular, csv, tsv, xml" label="Custom rules" />
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
41 </when>
4
cf3d3d8f4ef5 Modifica a xml
bimib
parents: 3
diff changeset
42 <when value="HMRcore">
cf3d3d8f4ef5 Modifica a xml
bimib
parents: 3
diff changeset
43 </when>
cf3d3d8f4ef5 Modifica a xml
bimib
parents: 3
diff changeset
44 <when value="Recon">
cf3d3d8f4ef5 Modifica a xml
bimib
parents: 3
diff changeset
45 </when>
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
46 </conditional>
1
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
47 <param name="input" argument="--data" type="data" format="tabular, csv, tsv" label="RNAseq of all samples" />
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
48 <param name="name" argument="--name" type="text" label="Output name prefix" value="dataset" />
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
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)"/>
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
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)"/>
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
51 <param name="None" argument="--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)" />
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
52 <conditional name="cond_hier">
1
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
53 <param name="hier" argument="--cond_hier" type="select" label="Produce dendrogram (hierarchical clustering):">
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
54 <option value="no" selected="true">no</option>
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
55 <option value="yes">yes</option>
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
56 </param>
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
57 <when value="yes">
1
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
58 <param name="linkage" argument="--linkage" type="select" label="Linkage type:">
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
59 <option value="single" selected="true">Single: minimum distance between all observations of two sets</option>
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
60 <option value="complete">Complete: maximum distance between all observations of two sets</option>
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
61 <option value="average">Average: average distance between all observations of two sets</option>
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
62 </param>
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
63 </when>
4
cf3d3d8f4ef5 Modifica a xml
bimib
parents: 3
diff changeset
64 <when value="no">
cf3d3d8f4ef5 Modifica a xml
bimib
parents: 3
diff changeset
65 </when>
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
66 </conditional>
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
67 </inputs>
1
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
68
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
69 <outputs>
1
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
70 <data format="txt" name="log" label="Log" />
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
71 <data format="pdf" name="dendrogram" label="$name dendrogram">
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
72 <filter>cond_hier['hier'] == 'yes'</filter>
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
73 </data>
1
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
74 <data format="pdf" name="elbow" label="$name elbow evaluation method" />
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
75 <collection name="cluster_out" type="list" label="Clusters $k_min - $k_max">
1
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
76 <discover_datasets pattern="__name_and_ext__" directory="cluster_out" />
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
77 </collection>
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
78 </outputs>
4
cf3d3d8f4ef5 Modifica a xml
bimib
parents: 3
diff changeset
79 <tests>
cf3d3d8f4ef5 Modifica a xml
bimib
parents: 3
diff changeset
80 <test>
cf3d3d8f4ef5 Modifica a xml
bimib
parents: 3
diff changeset
81 <param name="k_min" value="4"/>
cf3d3d8f4ef5 Modifica a xml
bimib
parents: 3
diff changeset
82 <output name="log" file="log.txt"/>
cf3d3d8f4ef5 Modifica a xml
bimib
parents: 3
diff changeset
83 </test>
cf3d3d8f4ef5 Modifica a xml
bimib
parents: 3
diff changeset
84 </tests>
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
85 <help>
1
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
86 <![CDATA[
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
87
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
88 What it does
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
89 -------------
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
90
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
91 This tool performs cluster analysis of RNA-seq dataset(s) based of Graudenzi et al."`MaREA`_: Metabolic feature extraction, enrichment and visualization of RNAseq data" bioRxiv (2018): 248724.
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
92
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
93 Accepted files are:
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
94 1) For "Recon 2.2 rules" or "HMRcore rules" options: RNA-seq dataset. The user can specify a label of output prefix (as e.g. "K=3 *dataset*" and "K=4 *MyDataset*");
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
95 2) For "Custom rules" option: custom rules dataset, custom map (.svg) and RNA-seq dataset. The user can specify a label of output prefix (as e.g. "K=3 *dataset*" and "K=4 *MyDataset*").
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
96
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
97 Optional files:
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
98 - custom GPR (Gene-Protein-Reaction) rules. Two accepted formats:
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
99
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
100 * (Cobra Toolbox and CobraPy compliant) xml of metabolic model;
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
101 * .csv file specifyig for each reaction ID (column 1) the corresponding GPR rule (column 2).
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
102 - custom svg map. Graphical elements must have the same IDs of reactions. See HmrCore svg map for an example.
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
103
1
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
104 The tool generates:
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
105 1) Clusters n1 - n2 (n1 and n2 refer to min and max number of clusters): class-files (as many files as the chosen different number of clusters k to be tested) specifying the class/condition each sample belongs to;
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
106 2) Log: a log file (.txt);
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
107 3) *dataset* elbow evaluation method: diagram (.pdf) of elbow evaluation method;
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
108 4) *dataset* dendrogram (optional): dendrogram (.pdf) if the user chooses to produce a dendrogram (hierachical clustering).
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
109
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
110 RNA-seq datasets format: tab-separated text files, reporting the expression level (e.g., TPM, RPKM, ...) of each gene (row) for a given sample (column). Header: sample ID.
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
111
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
112
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
113 Example input
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
114 -------------
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
115
1
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
116 **RNA-seq dataset**:
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
117
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
118 @DATASET_EXEMPLE@
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
119
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
120 **Custom Rules Dataset**:
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
121
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
122 @CUSTOM_RULES_EXEMPLE@
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
123
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
124 **Custom Map**:
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
125
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
126 *see the generated HMRcore .svg map for example*
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
127
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
128
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
129
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
130 .. class:: infomark
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
131
1
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
132 **TIP**: If your data is not TAB delimited, use `Convert delimiters to TAB`_.
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
133
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
134 .. class:: warningmark
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
135
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
136 If dendrogram it's too populated, each path and label can be not clear.
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
137
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
138 @REFERENCE@
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
139
1
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
140 .. _MaREA: https://www.biorxiv.org/content/early/2018/01/16/248724
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
141 .. _Convert delimiters to TAB: https://usegalaxy.org/?tool_id=Convert+characters1&version=1.0.0&__identifer=6t22teyofhj
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
142
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
143
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
144 ]]>
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
145 </help>
1
9e63d5f02d62 Uploaded
bimib
parents: 0
diff changeset
146 <expand macro="citations" />
0
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
147 </tool>
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
148
23ac9cf12788 Uploaded
bimib
parents:
diff changeset
149