Mercurial > repos > iuc > dropletutils
annotate dropletutils.xml @ 2:58105e5efa8d draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 4d89eb1eb951ef094d1f77c46824d9c38be4445b"
| author | iuc |
|---|---|
| date | Fri, 06 Sep 2019 10:55:49 -0400 |
| parents | 94ee8160ace3 |
| children | 2bbf0052aaa9 |
| rev | line source |
|---|---|
|
0
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
1 <?xml version="1.0" encoding="utf-8"?> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
2 <tool id="dropletutils" name="DropletUtils" version="@PACKAGE_VERSION@+@GALAXY_VERSION@" > |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
3 <description>Utilities for handling droplet-based single-cell RNA-seq data</description> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
4 <macros> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
5 <token name="@PACKAGE_VERSION@" >1.2.1</token> |
|
2
58105e5efa8d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 4d89eb1eb951ef094d1f77c46824d9c38be4445b"
iuc
parents:
1
diff
changeset
|
6 <token name="@GALAXY_VERSION@" >3</token> |
|
0
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
7 <token name="@TXIN@">tenx.input</token> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
8 <token name="@TXOUT@">tenx.output</token> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
9 <xml name="test_dirin" > |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
10 <conditional name="tenx_format"> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
11 <param name="use" value="directory" /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
12 <param name="input" value="in_matrix.mtx" /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
13 <param name="input_genes" value="in_genes.tsv" /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
14 <param name="input_barcodes" value="in_barcodes.tsv" /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
15 </conditional> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
16 </xml> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
17 </macros> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
18 <requirements> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
19 <requirement type="package" version="@PACKAGE_VERSION@">bioconductor-dropletutils</requirement> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
20 <requirement type="package" version="1.2_17" >r-matrix</requirement> |
|
1
94ee8160ace3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 40d4a92c62d75fe931baba8657cde006a26d84cf"
iuc
parents:
0
diff
changeset
|
21 <requirement type="package" version="1.10.1" >bioconductor-scater</requirement> |
|
0
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
22 </requirements> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
23 <version_command><![CDATA[ |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
24 Rscript -e 'packageVersion("DropletUtils")' | grep -oP '\d\.\d\.\d' |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
25 ]]> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
26 </version_command> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
27 <command detect_errors='exit_code'><![CDATA[ |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
28 #if str($tenx_format.use) == 'directory': |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
29 mkdir '@TXIN@' && |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
30 ln -s '$tenx_format.input' '@TXIN@/matrix.mtx' && |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
31 ln -s '$tenx_format.input_genes' '@TXIN@/genes.tsv' && |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
32 ln -s '$tenx_format.input_barcodes' '@TXIN@/barcodes.tsv' && |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
33 #end if |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
34 |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
35 #if str($operation.use) == 'filter': |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
36 #if str($operation.outformat) == 'directory': |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
37 mkdir '@TXOUT@' && |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
38 #end if |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
39 #end if |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
40 |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
41 Rscript '$__tool_directory__/scripts/dropletutils.Rscript' '$droplet_conf' |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
42 ]]> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
43 </command> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
44 <configfiles> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
45 <configfile name="droplet_conf" > |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
46 ## defaults |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
47 empty.fdr_threshold = 0.01 |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
48 eparams=formals(emptyDrops) |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
49 dparams=formals(defaultDrops) |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
50 bparams=formals(barcodeRanks) |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
51 |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
52 ## File params |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
53 in.type='$tenx_format.use' |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
54 out.type=NULL |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
55 |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
56 files=list() |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
57 files\$table='$table' |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
58 files\$plot='$plot' |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
59 files\$out=NULL |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
60 |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
61 #if str($tenx_format.use) == 'directory': |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
62 files\$infile='@TXIN@' |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
63 #else |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
64 files\$infile='$input' |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
65 #end if |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
66 |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
67 #if str($operation.use) == 'filter': |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
68 #if str($operation.method.use) == 'defaultdrops': |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
69 do.method="defaultDrops" |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
70 dparams\$expected=as.integer('$operation.method.expected') |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
71 dparams\$upper.quant=as.numeric('$operation.method.upperquant') |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
72 dparams\$lower.prop=as.numeric('$operation.method.lowerprop') |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
73 #else if str($operation.method.use) == 'emptydrops': |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
74 do.method="emptyDrops" |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
75 eparams\$lower=as.integer('$operation.method.lower') |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
76 empty.fdr_threshold=as.numeric('$operation.method.fdr_thresh') |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
77 #end if |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
78 |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
79 out.type='$operation.outformat' |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
80 #if str($operation.outformat) == 'directory': |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
81 files\$out='@TXOUT@' |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
82 #else if str($operation.outformat) == 'h5ad': |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
83 files\$out='$fileout_h5ad' |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
84 #else if str($operation.outformat) == 'tsv': |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
85 files\$out='$fileout_tsv' |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
86 #end if |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
87 |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
88 #else if str($operation.use) == 'barcode_rank': |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
89 do.method="barcodeRankings" |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
90 bparams\$lower=as.integer('$operation.lower') |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
91 #end if |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
92 |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
93 seed.val=as.integer('$seed') |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
94 |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
95 </configfile> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
96 </configfiles> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
97 <inputs> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
98 <conditional name="tenx_format"> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
99 <param name="use" type="select" label="Format for the input matrix"> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
100 <option value="directory" >Bundled (barcodes.tsv, genes.tsv, matrix.mtx)</option> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
101 <option value="h5ad" selected="true" >AnnData/H5</option> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
102 <option value="tsv">Tabular</option> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
103 </param> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
104 <when value="directory"> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
105 <param name="input" type="data" format="mtx,txt" label="Count Data"/> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
106 <param name="input_genes" type="data" format="tabular,tsv,txt" label="Genes List"/> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
107 <param name="input_barcodes" type="data" format="tabular,tsv,txt" label="Barcodes List"/> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
108 </when> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
109 <when value="h5ad"> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
110 <param name="input" type="data" format="h5ad" label="Count Data"/> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
111 </when> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
112 <when value="tsv"> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
113 <param name="input" type="data" format="tabular,tsv" label="Count Data" help="The first column must contain gene names, and the first row must contain barcode identifiers." /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
114 </when> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
115 </conditional> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
116 <conditional name="operation" > |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
117 <param name="use" type="select" label="Operation" help="The filtering uses intelligent methods to generate output 10X matrices as would be otherwise generated by CellRanger. The ranking option serves to illustrate the number of detected barcodes in the sample."> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
118 <option value="filter" selected="true">Filter for Barcodes</option> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
119 <option value="barcode_rank">Rank Barcodes</option> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
120 </param> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
121 <when value="filter"> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
122 <conditional name="method"> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
123 <param name="use" type="select" label="Method" help="The DefaultDrops method calls cells according to the number of UMIs associated with each barcode as implemented by CellRanger. The EmptyDrops method identifies empty droplets using a smart ambient background model." > |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
124 <option value="defaultdrops" selected="true">DefaultDrops</option> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
125 <option value="emptydrops">EmptyDrops</option> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
126 </param> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
127 <when value="defaultdrops"> |
|
2
58105e5efa8d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 4d89eb1eb951ef094d1f77c46824d9c38be4445b"
iuc
parents:
1
diff
changeset
|
128 <param name="expected" type="integer" min="1" value="3000" label="Expected Number of Cells" help="The expected number of cells in the sample." /> |
|
58105e5efa8d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 4d89eb1eb951ef094d1f77c46824d9c38be4445b"
iuc
parents:
1
diff
changeset
|
129 <param name="upperquant" type="float" min="0" max="1.0" value="0.99" label="Upper Quantile" help="The quantile of the top expected barcodes to consider." /> |
|
58105e5efa8d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 4d89eb1eb951ef094d1f77c46824d9c38be4445b"
iuc
parents:
1
diff
changeset
|
130 <param name="lowerprop" type="float" min="0" max="1.0" value="0.1" label="Lower Proportion" help="The fraction of molecules of the upper quantile that must be exceeded for a cell barcode to be detected." /> |
|
0
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
131 </when> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
132 <when value="emptydrops"> |
|
2
58105e5efa8d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 4d89eb1eb951ef094d1f77c46824d9c38be4445b"
iuc
parents:
1
diff
changeset
|
133 <param name="lower" type="integer" min="1" value="100" label="Lower-bound Threshold" help="The lower-bound threshold of the total UMI count at which barcodes beneath this are assumed to be empty droplets." /> |
|
58105e5efa8d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 4d89eb1eb951ef094d1f77c46824d9c38be4445b"
iuc
parents:
1
diff
changeset
|
134 <param name="fdr_thresh" type="float" min="0" max="1" value="0.01" label="FDR Threshold" help="False Discovery Rate threshold at which droplets with significant deviations from the ambient profile are detected at this threshold. If set to 0, the threshold is ignored." /> |
|
0
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
135 </when> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
136 </conditional> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
137 <param name="outformat" type="select" label="Format for output matrices"> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
138 <option value="directory" >Bundled (barcodes.tsv, genes.tsv, matrix.mtx)</option> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
139 <option value="h5ad" selected="true" >AnnData/H5</option> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
140 <option value="tsv">Tabular</option> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
141 </param> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
142 </when> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
143 <when value="barcode_rank"> |
|
2
58105e5efa8d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 4d89eb1eb951ef094d1f77c46824d9c38be4445b"
iuc
parents:
1
diff
changeset
|
144 <param name="lower" type="integer" min="1" value="100" label="Lower Bound" help="Lower bound on the total UMI count, at or below which all barcodes are assumed to correspond to empty droplets."/> |
|
0
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
145 </when> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
146 </conditional> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
147 <param name="seed" type="integer" value="100" label="Random Seed" /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
148 </inputs> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
149 <outputs> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
150 <data name="fileout_tsv" format="tsv" label="${tool.name} Count Matrix on ${on_string}"> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
151 <filter>operation['use']=='filter' and operation['outformat'] == 'tsv' </filter> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
152 </data> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
153 <data name="fileout_h5ad" format="h5ad" label="${tool.name} AnnData on ${on_string}"> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
154 <filter>operation['use']=='filter' and operation['outformat'] == 'h5ad'</filter> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
155 </data> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
156 <data name="barcodes_out" format="tsv" from_work_dir="@TXOUT@/barcodes.tsv" label="${tool.name} 10X Barcodes on ${on_string}" > |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
157 <filter>operation['use']=='filter' and operation['outformat'] == 'directory'</filter> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
158 </data> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
159 <data name="genes_out" format="tsv" from_work_dir="@TXOUT@/genes.tsv" label="${tool.name} 10X Genes on ${on_string}" > |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
160 <filter>operation['use']=='filter' and operation['outformat'] == 'directory'</filter> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
161 </data> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
162 <data name="matrix_out" format="mtx" from_work_dir="@TXOUT@/matrix.mtx" label="${tool.name} 10X Matrices on ${on_string}" > |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
163 <filter>operation['use']=='filter' and operation['outformat'] == 'directory'</filter> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
164 </data> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
165 <data name="plot" format="png" label="${tool.name} Plot on ${on_string}"> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
166 <filter>(operation['use']=='filter' and operation['method']['use']=="emptydrops") or operation['use']=='barcode_rank'</filter> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
167 </data> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
168 <data name="table" format="tsv" label="${tool.name} Table on ${on_string}"> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
169 <filter>operation['use']=='filter' and operation['method']['use']=="emptydrops"</filter> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
170 </data> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
171 </outputs> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
172 <tests> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
173 <!-- Directory input tests --> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
174 <!-- ::: Default Drops --> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
175 <test expect_num_outputs="1"> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
176 <expand macro="test_dirin" /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
177 <conditional name="operation"> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
178 <param name="use" value="filter" /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
179 <param name="outformat" value="h5ad" /><!-- H5AD --> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
180 </conditional> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
181 <output name="fileout_h5ad" value="defs_defaultdrops.h5ad" compare="sim_size" delta="10" /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
182 </test> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
183 <test expect_num_outputs="1"> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
184 <expand macro="test_dirin" /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
185 <conditional name="operation"> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
186 <param name="use" value="filter" /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
187 <param name="outformat" value="tsv" /><!-- TSV --> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
188 </conditional> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
189 <output name="fileout_tsv" > |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
190 <assert_contents> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
191 <has_n_columns n="1026" /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
192 <has_text_matching expression="^\sTCGCCAAGAA\sGGACTTAGAA\sTGCGCCTGAA\sACGGACACAA\sGCGGACACAA" /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
193 <has_text_matching expression="GENE50\s4\s0\s0\s0\s0\s5\s11\s8\s5" /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
194 <has_text_matching expression="GENE100\s6\s3\s5\s0\s0\s16\s31\s15\s26" /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
195 </assert_contents> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
196 </output> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
197 </test> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
198 <!-- :: Barcode Ranks --> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
199 <test expect_num_outputs="1"> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
200 <expand macro="test_dirin" /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
201 <conditional name="operation"> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
202 <param name="use" value="barcode_rank" /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
203 <param name="lower" value="120" /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
204 </conditional> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
205 <output name="plot" value="defs_barcoderankings.png" compare="sim_size" delta="200"/> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
206 </test> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
207 <!-- ::: Empty Drops --> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
208 <test expect_num_outputs="3"> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
209 <expand macro="test_dirin" /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
210 <conditional name="operation"> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
211 <param name="use" value="filter" /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
212 <param name="outformat" value="h5ad" /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
213 <conditional name="method"> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
214 <param name="use" value="emptydrops" /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
215 <param name="lower" value="150" /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
216 <param name="fdr_thresh" value="0.02" /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
217 </conditional> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
218 </conditional> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
219 <output name="fileout_h5ad" value="defs_emptydrops_150_0002.h5ad" compare="sim_size" delta="10" /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
220 <output name="table" > |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
221 <assert_contents> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
222 <has_n_columns n="9" /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
223 <has_line_matching expression="^\sbar.names\sTotal\sLogProb\sPValue\sLimited\sFDR\sis.Cell\sis.CellAndLimited" /> |
|
2
58105e5efa8d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 4d89eb1eb951ef094d1f77c46824d9c38be4445b"
iuc
parents:
1
diff
changeset
|
224 <has_line_matching expression="^994\sGGCATTACAA\s338\s-246.922772388055\s9.99900009999e-05\sTRUE\s9.99900009999e-05\sTRUE\sTRUE" /> |
|
58105e5efa8d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 4d89eb1eb951ef094d1f77c46824d9c38be4445b"
iuc
parents:
1
diff
changeset
|
225 <has_line_matching expression="^998\sCATGAAGCAA\s151\s-166.644236503983\s9.99900009999e-05\sTRUE\s9.99900009999e-05\sTRUE\sTRUE" /> |
|
0
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
226 </assert_contents> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
227 </output> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
228 <output name="plot" value="defs_emptydrops_150_0002.png" compare="sim_size" delta="100" /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
229 </test> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
230 <!-- Other format input tests --> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
231 <!-- ::: Empty Drops, same as above but input is h5ad --> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
232 <test expect_num_outputs="3"> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
233 <conditional name="tenx_format" > |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
234 <param name="use" value="h5ad" /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
235 <param name="input" value="in_matrix.h5ad" /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
236 </conditional> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
237 <conditional name="operation"> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
238 <param name="use" value="filter" /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
239 <param name="outformat" value="h5ad" /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
240 <conditional name="method"> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
241 <param name="use" value="emptydrops" /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
242 <param name="lower" value="150" /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
243 <param name="fdr_thresh" value="0.02" /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
244 </conditional> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
245 </conditional> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
246 <output name="fileout_h5ad" value="defs_emptydrops_150_0002a.h5ad" compare="sim_size" delta="200" /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
247 <output name="table" > |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
248 <assert_contents> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
249 <has_n_columns n="9" /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
250 <has_line_matching expression="^\sbar.names\sTotal\sLogProb\sPValue\sLimited\sFDR\sis.Cell\sis.CellAndLimited" /> |
|
2
58105e5efa8d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 4d89eb1eb951ef094d1f77c46824d9c38be4445b"
iuc
parents:
1
diff
changeset
|
251 <has_line_matching expression="^1100\sCCGGAAGCAA\s169\s-198.117943099773\s9.99900009999e-05\sTRUE\s0.000126279506880773\sTRUE\sTRUE" /> |
|
58105e5efa8d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 4d89eb1eb951ef094d1f77c46824d9c38be4445b"
iuc
parents:
1
diff
changeset
|
252 <has_line_matching expression="^1114\sTCCGAAGCAA\s182\s-196.181449214729\s9.99900009999e-05\sTRUE\s0.000126279506880773\sTRUE\sTRUE" /> |
|
0
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
253 </assert_contents> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
254 </output> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
255 <output name="plot" value="defs_emptydrops_150_0002a.png" compare="sim_size" delta="100" /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
256 </test> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
257 <!-- Output a directory --> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
258 <test expect_num_outputs="3"> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
259 <conditional name="tenx_format" > |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
260 <param name="use" value="tsv" /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
261 <param name="input" value="in_matrix.tsv" /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
262 </conditional> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
263 <conditional name="operation"> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
264 <param name="use" value="filter" /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
265 <param name="outformat" value="directory" /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
266 <conditional name="method"> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
267 <param name="use" value="defaultdrops" /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
268 <param name="expected" value="2000" /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
269 <param name="upperquant" value="0.85" /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
270 <param name="lowerpopr" value="0.2" /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
271 </conditional> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
272 </conditional> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
273 <output name="genes_out" file="in_genes.tsv" ftype="tsv" /><!-- same as the input in this case --> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
274 <output name="barcodes_out" ftype="tsv" > |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
275 <assert_contents> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
276 <has_n_columns n="1" /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
277 <has_line line="GGAAGAAGAA" /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
278 <has_line line="TCGAATGGAA" /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
279 </assert_contents> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
280 </output> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
281 <output name="matrix_out" ftype="mtx" > |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
282 <assert_contents> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
283 <has_line_matching expression="^100\s2650\s64072$" /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
284 <has_line_matching expression="^19\s1\s1$" /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
285 <has_line_matching expression="^100\s2650\s1$" /> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
286 </assert_contents> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
287 </output> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
288 </test> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
289 </tests> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
290 <help><![CDATA[ |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
291 Utilities to process 10X data in a variety of formats. Methods include: |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
292 |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
293 *Filter data:* |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
294 |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
295 * **DefaultDrops** emulates the native 10X method to produce a filtered count matrix |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
296 * **EmptyDrops** is a more informative quantile-based approach to produce a filtered count matrix. |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
297 |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
298 *Metrics:* |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
299 |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
300 * **RankBarcodes** produces a gap statistic plot to estimate the number of barcodes detected in the sample matrix. |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
301 |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
302 *Background* |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
303 |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
304 Droplet-based single-cell RNA sequencing (scRNA-seq) technologies allow researchers to obtain transcriptome-wide expression profiles for thousands of cells at once. Briefly, each cell is encapsulated in a droplet in a oil-water emulsion, along with a bead containing reverse transcription primers with a unique barcode sequence. After reverse transcription inside the droplet, each cell’s cDNA is labelled with that barcode (referred to a “cell barcode”). Bursting of the droplets yields a pool of cDNA for library preparation and sequencing. Debarcoding of the sequences can then be performed to obtain the expression profile for each cell. |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
305 |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
306 This tool implements some general utilities for handling these data after quantification of expression. In particular, we focus on the 10X Genomics platform, providing functions to load in the matrix of unique molecule identifier (UMI) counts as well as the raw molecule information. Functions are also available for downsampling the UMI count matrix or the raw reads; for distinguishing cells from empty droplets, based on the UMI counts; and to eliminate the effects of barcode swapping on Illumina 4000 sequencing machine. |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
307 ]]></help> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
308 <citations> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
309 <citation type="doi">10.1186/s13059-019-1662-y</citation> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
310 </citations> |
|
1335bf5bcd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
iuc
parents:
diff
changeset
|
311 </tool> |