Mercurial > repos > ebi-gxa > gtf2gene_list
annotate gtf2featureAnnotation.xml @ 7:14b3f2a4523b draft default tip
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml commit 5a62f18c80ddd55cfcc9d64546fde4e20be3e070"
author | ebi-gxa |
---|---|
date | Mon, 19 Jul 2021 08:00:24 +0000 |
parents | 1a642de6db01 |
children |
rev | line source |
---|---|
7
14b3f2a4523b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml commit 5a62f18c80ddd55cfcc9d64546fde4e20be3e070"
ebi-gxa
parents:
6
diff
changeset
|
1 <tool id="_ensembl_gtf2gene_list" name="GTF2GeneList" version="1.52.0+galaxy0" profile="18.01"> |
1
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
2 <description>extracts a complete annotation table or subsets thereof from an Ensembl GTF using rtracklayer</description> |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
3 <requirements> |
7
14b3f2a4523b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml commit 5a62f18c80ddd55cfcc9d64546fde4e20be3e070"
ebi-gxa
parents:
6
diff
changeset
|
4 <requirement type="package" version="1.0.1">atlas-gene-annotation-manipulation</requirement> |
1
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
5 </requirements> |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
6 <command detect_errors="exit_code"><![CDATA[ |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
7 ln -s '$gtf_input' input.gtf; |
7
14b3f2a4523b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml commit 5a62f18c80ddd55cfcc9d64546fde4e20be3e070"
ebi-gxa
parents:
6
diff
changeset
|
8 gtf2featureAnnotation.R --gtf-file input.gtf |
1
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
9 #if $noheader |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
10 --no-header |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
11 #end if |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
12 #if $version_transcripts |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
13 --version-transcripts |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
14 #end if |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
15 #if $mito.mark_mito |
6
1a642de6db01
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml commit bf9021c853da640771202920cde38f77cdeaf368"
ebi-gxa
parents:
5
diff
changeset
|
16 --mito --mito-chr "${mito.mito_chr}" --mito-biotypes "${mito.mito_biotypes}" |
1
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
17 #end if |
7
14b3f2a4523b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml commit 5a62f18c80ddd55cfcc9d64546fde4e20be3e070"
ebi-gxa
parents:
6
diff
changeset
|
18 #if $cdnas.parse_cdnas |
14b3f2a4523b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml commit 5a62f18c80ddd55cfcc9d64546fde4e20be3e070"
ebi-gxa
parents:
6
diff
changeset
|
19 --parse-cdnas "${cdnas.fasta_input}" --parse-cdna-field "${cdnas.cdnas_field}" |
1
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
20 #if $cdnas.filter_cdnas |
7
14b3f2a4523b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml commit 5a62f18c80ddd55cfcc9d64546fde4e20be3e070"
ebi-gxa
parents:
6
diff
changeset
|
21 --filter-cdnas-output "${fasta_output}" |
14b3f2a4523b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml commit 5a62f18c80ddd55cfcc9d64546fde4e20be3e070"
ebi-gxa
parents:
6
diff
changeset
|
22 #end if |
14b3f2a4523b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml commit 5a62f18c80ddd55cfcc9d64546fde4e20be3e070"
ebi-gxa
parents:
6
diff
changeset
|
23 #if $cdnas.parse_cdna_names |
14b3f2a4523b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml commit 5a62f18c80ddd55cfcc9d64546fde4e20be3e070"
ebi-gxa
parents:
6
diff
changeset
|
24 --parse-cdna-names |
14b3f2a4523b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml commit 5a62f18c80ddd55cfcc9d64546fde4e20be3e070"
ebi-gxa
parents:
6
diff
changeset
|
25 #end if |
14b3f2a4523b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml commit 5a62f18c80ddd55cfcc9d64546fde4e20be3e070"
ebi-gxa
parents:
6
diff
changeset
|
26 #if $fill_empty |
14b3f2a4523b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml commit 5a62f18c80ddd55cfcc9d64546fde4e20be3e070"
ebi-gxa
parents:
6
diff
changeset
|
27 --fill-empty "${fill_empty}" |
14b3f2a4523b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml commit 5a62f18c80ddd55cfcc9d64546fde4e20be3e070"
ebi-gxa
parents:
6
diff
changeset
|
28 #end if |
1
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
29 #end if |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
30 --feature-type "${feature_type}" --first-field "${first_field}" --output-file annotation.txt --fields "${fields}" |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
31 ]]></command> |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
32 |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
33 <inputs> |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
34 <param name="gtf_input" type="data" format="gff" label="Ensembl GTF file" /> |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
35 <param name="feature_type" type="text" optional='true' value="gene" label="Feature type for which to derive annotation"/> |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
36 <param name="first_field" type="text" optional='true' value="gene_id" label="Field to place first in output table"/> |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
37 <param name="noheader" type="boolean" checked="false" label="Suppress header line in output?"/> |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
38 <param name="fields" type="text" optional='true' value="" label="Comma-separated list of field names to extract from the GTF (default: use all fields)"/> |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
39 <param name="version_transcripts" type="boolean" checked="false" label="Append version to transcript identifiers?" help="For transcript feature type only: where the GTF contains transcript versions, should these be appended to transcript identifiers? Useful when generating transcript/gene mappings for use with transcriptomes"/> |
7
14b3f2a4523b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml commit 5a62f18c80ddd55cfcc9d64546fde4e20be3e070"
ebi-gxa
parents:
6
diff
changeset
|
40 <param name="fill_empty" type="text" optional='true' value="" label="Column to be used to fill empty values in other fields" help="Only when output fields are defined, useful when you need to guarantee a value, for example a gene ID for a transcript/gene mapping."/> |
1
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
41 <conditional name="mito"> |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
42 <param name="mark_mito" type="boolean" checked="true" label="Flag mitochondrial features?"/> |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
43 <when value="true"> |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
44 <param name="mito_chr" type="text" optional='true' value="mt,mitochondrion_genome,mito,m,chrM,chrMt" label="Comma-separated list of possible mitochondrial chromosome names (case insensitive)"/> |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
45 <param name="mito_biotypes" type="text" optional='true' value="mt_trna,mt_rrna,mt_trna_pseudogene" label="Comma-separated list of possible mitochondrial biotypes (case insensitive)"/> |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
46 </when> |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
47 <when value="false" /> |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
48 </conditional> |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
49 <conditional name="cdnas"> |
7
14b3f2a4523b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml commit 5a62f18c80ddd55cfcc9d64546fde4e20be3e070"
ebi-gxa
parents:
6
diff
changeset
|
50 <param name="parse_cdnas" type="boolean" checked="false" label="Provide a cDNA file for extracting annotations and/ or possible filtering?" help="For some applications, e.g. transcriptome mappers, its useful to match a cDNAs file to an annotation list (e.g. transcript-to-gene mapping)"/> |
1
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
51 <when value="true"> |
3
b95e6a9bb15c
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552-dirty
ebi-gxa
parents:
2
diff
changeset
|
52 <param name="fasta_input" type="data" format="fasta,fasta.gz" label="FASTA-format cDNA/ transcript file" /> |
7
14b3f2a4523b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml commit 5a62f18c80ddd55cfcc9d64546fde4e20be3e070"
ebi-gxa
parents:
6
diff
changeset
|
53 <param name="cdnas_field" type="text" optional='true' value="transcript_id" label="Annotation field in GTF to match with sequences."/> |
14b3f2a4523b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml commit 5a62f18c80ddd55cfcc9d64546fde4e20be3e070"
ebi-gxa
parents:
6
diff
changeset
|
54 <param name="parse_cdna_names" type="boolean" checked="false" label="Parse the FASTA headers for annotation info?" help="e.g. to find gene IDs for transcripts not present in the GTF. May only work for Ensembl GTFs."/> |
14b3f2a4523b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml commit 5a62f18c80ddd55cfcc9d64546fde4e20be3e070"
ebi-gxa
parents:
6
diff
changeset
|
55 <param name="filter_cdnas" type="boolean" checked="false" label="Filter the cDNA file to match the annotations?" /> |
1
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
56 </when> |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
57 <when value="false" /> |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
58 </conditional> |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
59 </inputs> |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
60 |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
61 <outputs> |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
62 <data name="feature_annotation" format="tsv" from_work_dir="annotation.txt" label="${tool.name} on ${on_string}: annotation table"/> |
3
b95e6a9bb15c
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552-dirty
ebi-gxa
parents:
2
diff
changeset
|
63 <data name="fasta_output" format="fasta.gz" from_work_dir="filtered.fa.gz" label="${tool.name} on ${on_string}: annotation-matched sequences"> |
4
b6354c917ef9
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit ab0f820986e34953ac7a309d76adb178a315b98f
ebi-gxa
parents:
3
diff
changeset
|
64 <filter>cdnas['filter_cdnas']</filter> |
1
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
65 </data> |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
66 </outputs> |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
67 <tests> |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
68 <test> |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
69 <param name="gtf_input" ftype="gtf" value="test.gtf"/> |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
70 <output name="feature_annotation" file="annotation.txt"/> |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
71 </test> |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
72 </tests> |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
73 |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
74 |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
75 <help><![CDATA[ |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
76 .. class:: infomark |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
77 |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
78 **What it does** |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
79 |
7
14b3f2a4523b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml commit 5a62f18c80ddd55cfcc9d64546fde4e20be3e070"
ebi-gxa
parents:
6
diff
changeset
|
80 Given an Ensembl GTF file, it will extract all information on chromosomes, coordinates, and attributes provided at the specified feature level. Mitochondrial features can also be flagged. See https://github.com/ebi-gene-expression-group/atlas-gene-annotation-manipulation. |
1
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
81 |
7
14b3f2a4523b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml commit 5a62f18c80ddd55cfcc9d64546fde4e20be3e070"
ebi-gxa
parents:
6
diff
changeset
|
82 You can also supply a fasta-format file of sequences, which can be filtered by identifier to match annotation and/or used a source of information for transcripts un-annotated in the GTF. This can be useful for tools such as Alevin which need a transcript-to-gene mapping and a transcriptome file without any missing entries (with respect to annotation). |
1
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
83 |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
84 |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
85 **Inputs** |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
86 |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
87 * Ensembl GTF file |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
88 |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
89 ----- |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
90 |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
91 **Outputs** |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
92 |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
93 * Gene annotations in tsv. |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
94 ]]></help> |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
95 <citations> |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
96 <citation type="bibtex"> |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
97 @misc{github-hinxton-single-cell, |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
98 author = {Jonathan Manning, EBI Gene Expression Team}, |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
99 year = {2019}, |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
100 title = {Hinxton Single Cell Anlysis Environment}, |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
101 publisher = {GitHub}, |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
102 journal = {GitHub repository}, |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
103 url = {https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary}, |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
104 }</citation> |
7
14b3f2a4523b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml commit 5a62f18c80ddd55cfcc9d64546fde4e20be3e070"
ebi-gxa
parents:
6
diff
changeset
|
105 <citation type="doi">10.1101/2020.04.08.032698</citation> |
1
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
106 </citations> |
247b439a78f7
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552
ebi-gxa
parents:
diff
changeset
|
107 </tool> |