Mercurial > repos > azomics > flow_compensate

annotate flow-compensate.xml @ 0:ca7ba337b727 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
author azomics
date Tue, 25 May 2021 00:07:44 +0000
parents
children ffc083c86d44
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
1 <tool id="flow-compensate" name="Flow compensate" version="0.1.0+galaxy0" profile="19.01" python_template_version="3.5">
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
2 <description>
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
3 compensates a set of FCS objects through a compensation matrix
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
4 </description>
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
5 <requirements>
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
6 <requirement type="package" version="2.2.0">bioconductor-flowcore</requirement>
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
7 </requirements>
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
9 mkdir -p input_dir;
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
10 #for $fcs in $fcs_list:
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
11 ln -s '$fcs' input_dir/'$fcs.element_identifier';
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
12 #end for
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
13 mkdir -p output_dir;
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
14 Rscript '$compensate_script' '$compensation_matrix' input_dir output_dir
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
15 ]]></command>
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
16 <configfiles>
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
17 <configfile name="compensate_script"><![CDATA[
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
18 library(flowCore)
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
19
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
20 args <- commandArgs( TRUE )
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
21
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
22 if ( length( args ) != 3 ) {
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
23 cat( "ERROR: no arguments with directory, matrix file for compensation and out_dir",
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
24 file = stderr() )
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
25 stop()
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
26 }
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
27
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
28 comp_matrix <- read.table(file=args[[ 1 ]], sep="\t", header=TRUE, check.names = FALSE)
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
29 comp_matrix<-as.matrix(comp_matrix[,-1])
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
30 ## Square matrix, reuse colnames into rownames
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
31 rownames(comp_matrix)<-colnames(comp_matrix)
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
32 fcs_dir <- args[[ 2 ]]
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
33
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
34 samp<-read.flowSet(files=list.files(path=fcs_dir, pattern=".*.fcs\$"), path=fcs_dir)
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
35
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
36 samp<-compensate(samp, comp_matrix)
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
37
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
38 write.flowSet(samp, outdir=args[[ 3 ]])
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
39
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
40 ]]></configfile>
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
41 </configfiles>
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
42 <inputs>
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
43 <param type="data" name="fcs_list" format="fcs" multiple="true" label="FCS files" help="FCS files to compensate using the provided matrix"/>
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
44 <param type="data" name="compensation_matrix" format="tabular" label="Matrix to use for compensation" />
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
45 </inputs>
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
46 <outputs>
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
47 <collection name="compensated_fcs" format="fcs" label="${tool.name} compensated FCS files on ${on_string}" type="list">
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
48 <discover_datasets pattern="__designation_and_ext__" directory="output_dir" visible="true" />
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
49 </collection>
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
50 </outputs>
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
51 <help><![CDATA[
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
52 TODO: Fill in help.
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
53 ]]></help>
ca7ba337b727 "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit 386fcc6286d3e2d2769ac9856a653b04d5c6b0ad"
azomics
parents:
diff changeset
54 </tool>