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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier commit f7363f7c391bd501fc4d1c10aaf372ec2bd82732
author artbio
date Mon, 12 Feb 2024 23:57:01 +0000
parents fec313f5c889
children
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0:fec313f5c889 1:0960bd1161fa
1 <tool id="pathifier" name="Pathifier" version="1.0.1"> 1 <tool id="pathifier" name="Pathifier" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>: Quantify deregulation of pathways in cancer</description> 2 <description>: Quantify deregulation of pathways in cancer</description>
3 <macros>
4 <token name="@TOOL_VERSION@">1.40.0</token>
5 <token name="@VERSION_SUFFIX@">0</token>
6 <token name="@PROFILE@">23.0</token>
7 </macros>
3 <requirements> 8 <requirements>
4 <requirement type="package" version="1.6.2=r35h6115d3f_0">r-optparse</requirement> 9 <requirement type="package" version="@TOOL_VERSION@">bioconductor-pathifier</requirement>
5 <requirement type="package" version="1.22.0=r351_0">bioconductor-pathifier</requirement> 10 <requirement type="package" version="1.7.4">r-optparse</requirement>
6 <requirement type="package" version="1.0.12=r351h6115d3f_0">r-pheatmap</requirement> 11 <requirement type="package" version="1.0.12">r-pheatmap</requirement>
7 <requirement type="package" version="0.3_41=r351h6115d3f_0">r-scatterplot3d</requirement> 12 <requirement type="package" version="0.3_44">r-scatterplot3d</requirement>
8 <requirement type="package" version="0.4.7=r35h6115d3f_0">r-circlize</requirement> 13 <requirement type="package" version="0.4.15">r-circlize</requirement>
9 </requirements> 14 </requirements>
10 <stdio> 15 <stdio>
11 <exit_code range="1:" level="fatal" description="Tool exception" /> 16 <exit_code range="1:" level="fatal" description="Tool exception" />
12 </stdio> 17 </stdio>
13 <command detect_errors="exit_code"><![CDATA[ 18 <command detect_errors="exit_code"><![CDATA[
14 Rscript $__tool_directory__/pathifier.R 19 Rscript '$__tool_directory__/pathifier.R'
15 --exp '$input' 20 --exp '$input'
16 --sep '$input_sep' 21 --sep '$input_sep'
17 --genes '$genes' 22 --genes '$genes'
18 23
19 #if $reference.is_normal == "Yes": 24 #if str($reference.reference_selector) == 'TRUE':
20 --is_normal 'TRUE' 25 --is_normal '$reference.reference_selector'
21 --normals '$reference.normals' 26 --normals '$reference.normals'
22 #end if 27 #end if
23 28
24 --max_stability '$max_stability' 29 --max_stability '$max_stability'
25 --attempts '$attempts' 30 --attempts '$attempts'
33 38
34 --pds '$pds' 39 --pds '$pds'
35 --logfile '$logfile' 40 --logfile '$logfile'
36 --plot '$plot' 41 --plot '$plot'
37 --rdata '$rdatafile' 42 --rdata '$rdatafile'
38
39 ]]></command> 43 ]]></command>
40 <inputs> 44 <inputs>
41 <param name="input" type="data" format="txt,tabular" label="expression data"/> 45 <param name="input" type="data" format="txt,tabular" label="expression data"/>
42 <param name="input_sep" type="select" label="Input column separator"> 46 <param name="input_sep" type="select" label="Input column separator">
43 <option value="tab" selected="true">Tabs</option> 47 <option value="tab" selected="true">Tabs</option>
44 <option value=",">Comma</option> 48 <option value=",">Comma</option>
45 </param> 49 </param>
46 <param name="genes" type="data" format="txt" label="Gene sets Pathways" 50 <param name="genes" type="data" format="txt" label="Gene sets Pathways"
47 help="Must be in gmt format (one pathway per line : Name, description, genes (one by column), tab separated)" /> 51 help="Must be in gmt format (one pathway per line : Name, description, genes (one by column), tab separated)" />
48 <conditional name="reference"> 52 <conditional name="reference">
49 <param name="is_normal" label="Do you have non cancer transcriptomes in your data set ?" type="boolean" truevalue="Yes" falsevalue="" checked="false" 53 <param name="reference_selector" label="Do you have non cancer transcriptomes in your data set ?" type="select"
50 help="If set the starting curve depends on the matrix of points with in a certain row order (first 'normal' then 'cancer' samples), otherwise the first principal component is used. See help for more informations"/> 54 help="Yes, if the starting curve depends on the matrix of points with in a certain row order
51 <when value="Yes"> 55 (first 'normal' then 'cancer' samples), otherwise (No) the first principal component is used. See help section for more informations">
56 <option selected="True" value="TRUE">Yes</option>
57 <option value="">No</option>
58 </param>
59 <when value="TRUE">
52 <param name="normals" type="data" format="tabular" label="Sample status" 60 <param name="normals" type="data" format="tabular" label="Sample status"
53 help="A two-column data frame, first column contains data labels, second column the levels of sample status : 1 = Healthy, 0 = Tumor (no header)" /> 61 help="A two-column data frame, first column contains data labels, second column the levels of sample status : 1 = Healthy, 0 = Tumor (no header)" />
54 </when> 62 </when>
55 <when value=""> 63 <when value="">
56 </when> 64 </when>
72 </param> 80 </param>
73 <param label="Return Pathifier S4 object" name="rdata" type="select" > 81 <param label="Return Pathifier S4 object" name="rdata" type="select" >
74 <option value="no" selected="True">No</option> 82 <option value="no" selected="True">No</option>
75 <option value="yes">Yes</option> 83 <option value="yes">Yes</option>
76 </param> 84 </param>
77
78 </inputs> 85 </inputs>
79 <outputs> 86 <outputs>
80 <data name="pds" format="tabular" label="Pathifier Deregulation Score (PDS) of ${on_string}" /> 87 <data name="pds" format="tabular" label="Pathifier Deregulation Score (PDS) of ${on_string}" />
81 <data name="logfile" format="txt" label="Pathifier log file of ${on_string}" > 88 <data name="logfile" format="txt" label="Pathifier log file of ${on_string}" >
82 <filter>log == 'yes'</filter> 89 <filter>log == 'yes'</filter>
83 </data> 90 </data>
84 <data name="plot" format="pdf" label="Pathifier vizualization of ${on_string}" /> 91 <data name="plot" format="pdf" label="Pathifier vizualization of ${on_string}" />
85 <data name="rdatafile" format="rdata" label="Pathifier S4 object of ${on_string}" > 92 <data name="rdatafile" format="rdata" label="Pathifier S4 object of ${on_string}" >
86 <filter>rds == 'yes'</filter> 93 <filter>rdata == 'yes'</filter>
87 </data> 94 </data>
88 </outputs> 95 </outputs>
89 <tests> 96 <tests>
90 <test> 97 <test expect_num_outputs="3">
91 <param name="input" value="sheffer.tsv" ftype="tabular"/> 98 <param name="input" value="sheffer.tsv" ftype="tabular"/>
92 <param name="genes" value="kegg_pathways.gmt" ftype="txt" /> 99 <param name="genes" value="kegg_pathways.gmt" ftype="txt" />
93 <param name="is_normal" value="True" /> 100 <param name="reference_selector" value="TRUE" />
94 <param name="normals" value="normals.tsv" ftype="tabular" /> 101 <param name="normals" value="normals.tsv" ftype="tabular" />
95 <param name="log" value="yes" /> 102 <param name="log" value="yes" />
96 <param name="attempts" value="100" /> 103 <param name="attempts" value="100" />
97 <output name="logfile" file="sheffer.kegg.log" ftype="txt" compare="sim_size" /> 104 <output name="logfile" file="sheffer.kegg.log" ftype="txt" compare="sim_size" />
98 <output name="pds" file="sheffer.kegg.tsv" ftype="tabular"/> 105 <output name="pds" file="sheffer.kegg.tsv" ftype="tabular"/>
99 <output name="plot" file="plot.pdf" ftype="pdf" compare="sim_size" /> 106 <output name="plot" file="plot.pdf" ftype="pdf" compare="sim_size" />
100 </test> 107 </test>
101 <test> 108 <test expect_num_outputs="3">
102 <param name="input" value="sheffer_noref.tsv" ftype="tabular"/> 109 <param name="input" value="sheffer_noref.tsv" ftype="tabular"/>
103 <param name="genes" value="kegg_pathways.gmt" ftype="txt" /> 110 <param name="genes" value="kegg_pathways.gmt" ftype="txt" />
104 <param name="is_normal" value="" /> 111 <param name="reference_selector" value="" />
105 <param name="log" value="no" /> 112 <param name="log" value="no" />
106 <param name="rdata" value="yes" /> 113 <param name="rdata" value="yes" />
107 <param name="attempts" value="50" /> 114 <param name="attempts" value="50" />
108 <param name="min_exp" value="data" /> 115 <param name="min_exp" value="data" />
109 <param name="min_std" value="data" /> 116 <param name="min_std" value="data" />