Mercurial > repos > iuc > maker_map_ids

annotate map_ids.xml @ 0:060ea7339911 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
author iuc
date Thu, 19 Oct 2017 15:59:20 -0400
parents
children e906fa778440
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents:
diff changeset
2 <tool id="maker_map_ids" name="Map annotation ids" profile="16.04" version="@VERSION@">
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents:
diff changeset
3 <description>on a Maker annotation</description>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents:
diff changeset
4 <macros>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents:
diff changeset
5 <import>macros.xml</import>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents:
diff changeset
6 </macros>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents:
diff changeset
7 <expand macro="requirements"/>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents:
diff changeset
8 <command><![CDATA[
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents:
diff changeset
9 cp '${maker_gff}' '${renamed}' &&
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents:
diff changeset
10 maker_map_ids --prefix '${prefix}' --justify ${justify} '${maker_gff}' > '${id_map}' &&
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents:
diff changeset
11 map_gff_ids '${id_map}' '${renamed}'
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents:
diff changeset
12 ]]></command>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents:
diff changeset
13 <inputs>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents:
diff changeset
14 <param name="maker_gff" type="data" format="gff" label="Maker annotation where to change ids"/>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents:
diff changeset
15 <param name="prefix" type="text" label="Prefix for ids"/>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents:
diff changeset
16 <param name="justify" type="integer" value="6" min="2" max="20" label="Justify numeric ids to this length"/>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents:
diff changeset
17 </inputs>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents:
diff changeset
18 <outputs>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents:
diff changeset
19 <data format="gff" name="renamed" label="${tool.name} on ${on_string}: renamed GFF"/>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents:
diff changeset
20 <data format="tabular" name="id_map" label="${tool.name} on ${on_string}: ID map"/>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents:
diff changeset
21 </outputs>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents:
diff changeset
22 <tests>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents:
diff changeset
23 <test>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents:
diff changeset
24 <param name="maker_gff" value="annot.gff3"/>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents:
diff changeset
25 <param name="prefix" value="YES"/>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents:
diff changeset
26 <param name="justify" value="6"/>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents:
diff changeset
27 <output name="renamed" file="annot_mapped.gff3"/>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents:
diff changeset
28 <output name="id_map" file="id_map.tsv"/>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents:
diff changeset
29 </test>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents:
diff changeset
30 </tests>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents:
diff changeset
31 <help><![CDATA[
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents:
diff changeset
32 MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MAKER is also easily trainable: outputs of preliminary runs can be used to automatically retrain its gene prediction algorithm, producing higher quality gene-models on seusequent runs. MAKER's inputs are minimal and its ouputs can be directly loaded into a GMOD database. They can also be viewed in the Apollo genome browser; this feature of MAKER provides an easy means to annotate, view and edit individual contigs and BACs without the overhead of a database. MAKER should prove especially useful for emerging model organism projects with minimal bioinformatics expertise and computer resources.
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents:
diff changeset
33
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents:
diff changeset
34 This tool will automatically assign new ids to a Maker annotation respecting a specified pattern.
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents:
diff changeset
35
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents:
diff changeset
36 .. _Maker: http://www.yandell-lab.org/software/maker.html
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents:
diff changeset
37 ]]></help>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents:
diff changeset
38 <expand macro="citations"/>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents:
diff changeset
39 </tool>