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comparison viscorvar_matcoraddvar.xml @ 2:c8533e9298e5 draft

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"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
author ppericard
date Fri, 23 Oct 2020 10:15:56 +0000
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children df8428358b7f
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1:e93350dc99f1 2:c8533e9298e5
1 <tool id="viscorvar_matcoraddvar" name="visCorVar matCorAddVar" version="@TOOL_VERSION@+galaxy1" profile="16.04" workflow_compatible="true">
2
3 <description>determine the correlation circles that can be overlaid and compute the correlations</description>
4
5 <macros>
6 <import>macros.xml</import>
7 <import>macros_viscorvar.xml</import>
8 </macros>
9
10 <expand macro="requirements"/>
11 <expand macro="stdio"/>
12
13 <command detect_errors="aggressive"><![CDATA[
14
15 @COMMAND_RSCRIPT@/viscorvar_matcoraddvar.R
16
17 --input_rdata ${input_rdata}
18 --block_Y_file ${block_Y}
19
20 ##--cutoff_comp ${cutoff_comp}
21 --cutoff_comp 0.75
22 #if str($var_of_interest_file) !='':
23 --interest_var_file ${var_of_interest_file}
24 #end if
25
26 --output_rdata ${output_rdata}
27 --output_response_var ${output_response_var}
28 --output_blocks_comb ${output_blocks_comb}
29
30 @COMMAND_LOG_EXIT@
31
32 ]]></command>
33
34 <inputs>
35 <param name="input_rdata" type="data" format="rdata"
36 label="Input RData file from block.SPLSDA"
37 help="This is the RData output file from the block.splsda function." />
38 <param name="block_Y" type="data" format="tabular"
39 label="Block Y"
40 help="[block_Y] (tabular format) This table contains the name of the samples in the first column. The other columns correspond to phenotypes. For each of these other columns, a column determines which sample is associated with this phenotype (value equals to 1) or not (value equals to 0). The name of the samples in Block Y (transposed), in the sample metadata (transposed) and for all datasets have to be in the same order" />
41 <!-- Fichier avec noms de gènes/variables, donné par l'utilisateur -->
42 <param name="var_of_interest_file" type="data" format="txt" optional="true"
43 label="Variables of interest (Optional)"
44 help="variables not belonging to any block will not be considered"/>
45 <!-- <param name="cutoff_comp" type="float" value="0.775" min="0" max="1"
46 label="Cutoff comp"
47 help="[cutoff_comp] Two correlation circles will be superimposed if the correlation of their first and second axis is greater than cutoff_comp in absolute value." /> -->
48 </inputs>
49
50 <outputs>
51 <data name="output_rdata" format="rdata" label="${tool.name}_output.RData" />
52 <data name="output_response_var" format="tabular" label="${tool.name}_response_var.tsv" />
53 <data name="output_blocks_comb" format="tabular" label="${tool.name}_blocks_comb.tsv" />
54 </outputs>
55
56 <tests>
57 </tests>
58
59 <help><![CDATA[
60
61 @HELP_AUTHORS@
62
63 ======================
64 visCorVar matCorAddVar
65 ======================
66
67 -----------
68 Description
69 -----------
70
71 Bla bla...
72
73 -----------------
74 Workflow position
75 -----------------
76
77 **Upstream tools**
78
79 ======================= =================================== ========
80 Name Output file Format
81 ======================= =================================== ========
82 mixOmics.block.splsda mixomics_blocksplsda_output.RData rdata
83 ======================= =================================== ========
84
85 **Downstream tools**
86
87 ================================ ========================================= ========
88 Name Output file Format
89 ================================ ========================================= ========
90 visCorVar.circleCor viscorvar_matcoraddvar_output.RData rdata
91 -------------------------------- ----------------------------------------- --------
92 visCorVar.computeMatSimilarity viscorvar_matcoraddvar_output.RData rdata
93 -------------------------------- ----------------------------------------- --------
94 visCorVar.networkVar viscorvar_matcoraddvar_response_var.tsv tabular
95 ================================ ========================================= ========
96
97 ---------------------------------------------------
98
99 -----------
100 Input files
101 -----------
102
103 +---------------------------------+------------+
104 | Parameter : num + label | Format |
105 +=================================+============+
106 | 1 : Rdata block.splsda output | Rdata |
107 +---------------------------------+------------+
108 | 2 : Block Y | tabular |
109 +---------------------------------+------------+
110 | 3 : [opt] Variables of interest | txt |
111 +---------------------------------+------------+
112
113 ----------
114 Parameters
115 ----------
116
117 @HELP_MANUAL@
118
119 ------------
120 Output files
121 ------------
122
123 viscorvar_matcoraddvar_output.RData
124 RData output
125
126 viscorvar_matcoraddvar_response_var.tsv
127
128
129 viscorvar_matcoraddvar_blocks_comb.tsv
130
131
132 ]]></help>
133
134 <expand macro="citations" />
135
136 </tool>