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comparison Marea/marea_cluster.xml @ 1:9e63d5f02d62 draft

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author bimib
date Wed, 07 Nov 2018 07:07:46 -0500
parents 23ac9cf12788
children 3b3d0e5d0802
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0:23ac9cf12788 1:9e63d5f02d62
1 <tool id="MaREA_cluester" name="MaREA cluster analysis"> 1 <tool id="MaREA_cluester" name="MaREA cluster analysis">
2 <description>of Reaction Activity Scores</description> 2 <description>of Reaction Activity Scores</description>
3 <macros>
4 <import>marea_macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
3 <requirements> 7 <requirements>
4 <requirement type="package">pandas</requirement>
5 <requirement type="package">scikit-learn</requirement> 8 <requirement type="package">scikit-learn</requirement>
6 <requirement type="package">scipy</requirement>
7 <requirement type="package">matplotlib</requirement> 9 <requirement type="package">matplotlib</requirement>
8 <requirement type="package">cobrapy</requirement>
9 <requirement type="package">python-libsbml</requirement>
10 </requirements> 10 </requirements>
11 <command> 11 <command>
12 <![CDATA[ 12 <![CDATA[
13 python $__tool_directory__/marea_cluster.py 13 python $__tool_directory__/marea_cluster.py
14 --rules_selector $cond_rule.rules_selector 14 --rules_selector $cond_rule.rules_selector
30 --elbow $elbow 30 --elbow $elbow
31 ]]> 31 ]]>
32 </command> 32 </command>
33 <inputs> 33 <inputs>
34 <conditional name="cond_rule"> 34 <conditional name="cond_rule">
35 <param name="rules_selector" type="select" label="Gene-Protein-Reaction rules:"> 35 <expand macro="options" />
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"> 36 <when value="Custom">
41 <param name="Custom_rules" type="data" format="tabular, csv, tsv, xml" label="Custom rules"/> 37 <param name="Custom_rules" type="data" format="tabular, csv, tsv, xml" label="Custom rules" />
42 </when> 38 </when>
43 </conditional> 39 </conditional>
44 <param name="input" type="data" format="tabular, csv, tsv" label="RNAseq of all samples"/> 40 <param name="input" argument="--data" type="data" format="tabular, csv, tsv" label="RNAseq of all samples" />
45 <param name="name" type="text" label="Output name prefix" value = "dataset"/> 41 <param name="name" argument="--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)"/> 42 <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)"/>
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)"/> 43 <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)"/>
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)"/> 44 <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)" />
49 <conditional name="cond_hier"> 45 <conditional name="cond_hier">
50 <param name="hier" type="select" label="Produce dendrogram (hierarchical clustering):"> 46 <param name="hier" argument="--cond_hier" type="select" label="Produce dendrogram (hierarchical clustering):">
51 <option value="no" selected="true">no</option> 47 <option value="no" selected="true">no</option>
52 <option value="yes">yes</option> 48 <option value="yes">yes</option>
53 </param> 49 </param>
54 <when value="yes"> 50 <when value="yes">
55 <param name="linkage" type="select" label="Linkage type:"> 51 <param name="linkage" argument="--linkage" type="select" label="Linkage type:">
56 <option value="single" selected="true">Single: minimum distance between all observations of two sets</option> 52 <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> 53 <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> 54 <option value="average">Average: average distance between all observations of two sets</option>
59 </param> 55 </param>
60 </when> 56 </when>
61 </conditional> 57 </conditional>
62 </inputs> 58 </inputs>
59
63 <outputs> 60 <outputs>
64 <data format="txt" name="log" label="Log"/> 61 <data format="txt" name="log" label="Log" />
65 <data format="pdf" name="dendrogram" label="$name dendrogram"> 62 <data format="pdf" name="dendrogram" label="$name dendrogram">
66 <filter>cond_hier['hier'] == 'yes'</filter> 63 <filter>cond_hier['hier'] == 'yes'</filter>
67 </data> 64 </data>
68 <data format="pdf" name="elbow" label="$name elbow evaluation method"/> 65 <data format="pdf" name="elbow" label="$name elbow evaluation method" />
69 <collection name="cluster_out" type="list" label="Clusters $k_min - $k_max"> 66 <collection name="cluster_out" type="list" label="Clusters $k_min - $k_max">
70 <discover_datasets pattern="__name_and_ext__" directory="cluster_out"/> 67 <discover_datasets pattern="__name_and_ext__" directory="cluster_out" />
71 </collection> 68 </collection>
72 </outputs> 69 </outputs>
70
73 <help> 71 <help>
72 <![CDATA[
73
74 What it does
75 -------------
76
77 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.
78
79 Accepted files are:
80 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*");
81 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*").
82
83 Optional files:
84 - custom GPR (Gene-Protein-Reaction) rules. Two accepted formats:
85
86 * (Cobra Toolbox and CobraPy compliant) xml of metabolic model;
87 * .csv file specifyig for each reaction ID (column 1) the corresponding GPR rule (column 2).
88 - custom svg map. Graphical elements must have the same IDs of reactions. See HmrCore svg map for an example.
89
90 The tool generates:
91 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;
92 2) Log: a log file (.txt);
93 3) *dataset* elbow evaluation method: diagram (.pdf) of elbow evaluation method;
94 4) *dataset* dendrogram (optional): dendrogram (.pdf) if the user chooses to produce a dendrogram (hierachical clustering).
95
96 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.
97
98
99 Example input
100 -------------
101
102 **RNA-seq dataset**:
103
104 @DATASET_EXEMPLE@
105
106 **Custom Rules Dataset**:
107
108 @CUSTOM_RULES_EXEMPLE@
109
110 **Custom Map**:
111
112 *see the generated HMRcore .svg map for example*
113
114
115
116 .. class:: infomark
117
118 **TIP**: If your data is not TAB delimited, use `Convert delimiters to TAB`_.
74 119
75 .. class:: warningmark 120 .. class:: warningmark
76 121
77 This tool expects input datasets consisting of tab-delimited columns. 122 If dendrogram it's too populated, each path and label can be not clear.
78 123
79 .. class:: infomark 124 @REFERENCE@
80 125
81 **TIP:** If your data is not TAB delimited, use *Text Manipulation > Convert delimiters to TAB* 126 .. _MaREA: https://www.biorxiv.org/content/early/2018/01/16/248724
127 .. _Convert delimiters to TAB: https://usegalaxy.org/?tool_id=Convert+characters1&version=1.0.0&__identifer=6t22teyofhj
82 128
129
130 ]]>
83 </help> 131 </help>
132 <expand macro="citations" />
84 </tool> 133 </tool>
85 134
86 135
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