comparison scran_normalize.xml @ 2:6864acb21714 draft default tip

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize commit a14fb3d106b647c4f1dea2c8d3ac7c1e8848b21c
author artbio
date Sun, 10 Dec 2023 00:27:45 +0000
parents fb2f1b8b0013
children
comparison
equal deleted inserted replaced
1:fb2f1b8b0013 2:6864acb21714
1 <tool id="scran_normalize" name="scran_normalize" version="0.2.1"> 1 <tool id="scran_normalize" name="scran_normalize" version="1.28.1+galaxy0">
2 <description>Normalize raw counts expression values using deconvolution size factors</description> 2 <description>Normalize raw counts expression values using deconvolution size factors</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.6.2">r-optparse</requirement> 4 <requirement type="package" version="1.28.1">bioconductor-scran</requirement>
5 <requirement type="package" version="1.12.1=r36he1b5a44_0">bioconductor-scran</requirement> 5 <requirement type="package" version="1.63_1">r-dynamictreecut</requirement>
6 <requirement type="package" version="1.7.3">r-optparse</requirement>
6 </requirements> 7 </requirements>
7 <stdio> 8 <stdio>
8 <exit_code range="1:" level="fatal" description="Tool exception" /> 9 <exit_code range="1:" level="fatal" description="Tool exception" />
9 </stdio> 10 </stdio>
10 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
11 Rscript $__tool_directory__/scran-normalize.R 12 Rscript $__tool_directory__/scran-normalize.R
12 --data '$input' 13 --data '$input'
13 --sep '$input_sep'
14 #if $metacell.cluster == "Yes": 14 #if $metacell.cluster == "Yes":
15 --cluster 15 --cluster
16 --method '$metacell.method' 16 --method '$metacell.method'
17 --size '$metacell.size' 17 --size '$metacell.size'
18 #end if 18 #end if
19 -o '${output}' 19 -o '${output}'
20 ]]></command> 20 ]]></command>
21 <inputs> 21 <inputs>
22 <param name="input" type="data" format="txt,tabular" label="Raw counts of expression data" help = "Must have an header"/> 22 <param name="input" type="data" format="tabular" label="Raw counts of expression data" help = "A tsv file that must have an header line"/>
23 <param name="input_sep" type="select" label="Input column separator">
24 <option value="tab" selected="true">Tabulation</option>
25 <option value=",">Comma</option>
26 </param>
27 <conditional name="metacell"> 23 <conditional name="metacell">
28 <param name="cluster" type="select" label = "Do you want to cluster cells ?" help="Perform scaling method on metacell, see Details"> 24 <param name="cluster" type="select" label = "Do you want to cluster cells ?" help="Perform scaling method on metacell, see Details">
29 <option value="Yes">Yes</option> 25 <option value="Yes">Yes</option>
30 <option value="No" selected="true">No</option> 26 <option value="No" selected="true">No</option>
31 </param> 27 </param>
43 <data name="output" format="tabular" label="Normalized Log counts of ${on_string}"> 39 <data name="output" format="tabular" label="Normalized Log counts of ${on_string}">
44 </data> 40 </data>
45 </outputs> 41 </outputs>
46 <tests> 42 <tests>
47 <test> 43 <test>
48 <param name="input" value="counts.tab" ftype="tabular"/> 44 <param name="input" value="counts.tsv" ftype="tabular"/>
49 <output name="output" file="logcounts.tab" ftype="tabular"/> 45 <output name="output" file="logcounts.tsv" ftype="tabular"/>
50 </test> 46 </test>
51 <test> 47 <test>
52 <param name="input" value="counts.tab" ftype="tabular"/> 48 <param name="input" value="counts.tsv" ftype="tabular"/>
53 <param name="cluster" value="Yes"/> 49 <param name="cluster" value="Yes"/>
54 <param name="method" value="igraph"/> 50 <param name="method" value="igraph"/>
55 <param name="size" value="25"/> 51 <param name="size" value="25"/>
56 <output name="output" file="logcounts_igraph.tsv" ftype="tabular"/> 52 <output name="output" file="logcounts_igraph.tsv" ftype="tabular"/>
57 </test> 53 </test>
58 <test> 54 <test>
59 <param name="input" value="counts.tab" ftype="tabular"/> 55 <param name="input" value="counts.tsv" ftype="tabular"/>
60 <param name="cluster" value="Yes"/> 56 <param name="cluster" value="Yes"/>
61 <param name="method" value="hclust"/> 57 <param name="method" value="hclust"/>
62 <param name="size" value="25"/> 58 <param name="size" value="25"/>
63 <output name="output" file="logcounts_hclust.tsv" ftype="tabular"/> 59 <output name="output" file="logcounts_hclust.tsv" ftype="tabular"/>
64 </test> 60 </test>