Mercurial > repos > earlhaminst > ete

annotate ete_gene_cnv.xml @ 14:d40b9a7debe5 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 71b9c1035f713be174bfcf5ecb20804495f39258
author earlhaminst
date Thu, 07 Mar 2024 19:39:30 +0000
parents 16e925bf567e
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
8
16e925bf567e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit ed32f2e6d8174873cefcbe141084f857f84b0586"
earlhaminst
parents:
diff changeset
1 <tool id="ete_gene_csv_finder" name="Gene Copy Number Finder" version="@VERSION@">
16e925bf567e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit ed32f2e6d8174873cefcbe141084f857f84b0586"
earlhaminst
parents:
diff changeset
2 <description>from a genetree using the ETE Toolkit</description>
16e925bf567e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit ed32f2e6d8174873cefcbe141084f857f84b0586"
earlhaminst
parents:
diff changeset
3 <macros>
16e925bf567e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit ed32f2e6d8174873cefcbe141084f857f84b0586"
earlhaminst
parents:
diff changeset
4 <import>ete_macros.xml</import>
16e925bf567e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit ed32f2e6d8174873cefcbe141084f857f84b0586"
earlhaminst
parents:
diff changeset
5 </macros>
14
d40b9a7debe5 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 71b9c1035f713be174bfcf5ecb20804495f39258
earlhaminst
parents: 8
diff changeset
6 <expand macro="bio_tools"/>
8
16e925bf567e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit ed32f2e6d8174873cefcbe141084f857f84b0586"
earlhaminst
parents:
diff changeset
7 <expand macro="requirements" />
16e925bf567e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit ed32f2e6d8174873cefcbe141084f857f84b0586"
earlhaminst
parents:
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
16e925bf567e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit ed32f2e6d8174873cefcbe141084f857f84b0586"
earlhaminst
parents:
diff changeset
9 python '$__tool_directory__/ete_gene_cnv.py'
16e925bf567e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit ed32f2e6d8174873cefcbe141084f857f84b0586"
earlhaminst
parents:
diff changeset
10 --genetree '$genetreeFile'
16e925bf567e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit ed32f2e6d8174873cefcbe141084f857f84b0586"
earlhaminst
parents:
diff changeset
11 --speciesorder '$speciesorder'
16e925bf567e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit ed32f2e6d8174873cefcbe141084f857f84b0586"
earlhaminst
parents:
diff changeset
12 > '$genes'
16e925bf567e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit ed32f2e6d8174873cefcbe141084f857f84b0586"
earlhaminst
parents:
diff changeset
13 ]]></command>
16e925bf567e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit ed32f2e6d8174873cefcbe141084f857f84b0586"
earlhaminst
parents:
diff changeset
14 <inputs>
16e925bf567e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit ed32f2e6d8174873cefcbe141084f857f84b0586"
earlhaminst
parents:
diff changeset
15 <param name="genetreeFile" type="data" format="nhx" label="GeneTree file" help="GeneTree in nhx format, where nodes are in form of geneid_species" />
16e925bf567e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit ed32f2e6d8174873cefcbe141084f857f84b0586"
earlhaminst
parents:
diff changeset
16 <param name="speciesorder" type="text" label="Species in order" help="Comma-separated species list" />
16e925bf567e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit ed32f2e6d8174873cefcbe141084f857f84b0586"
earlhaminst
parents:
diff changeset
17 </inputs>
16e925bf567e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit ed32f2e6d8174873cefcbe141084f857f84b0586"
earlhaminst
parents:
diff changeset
18 <outputs>
16e925bf567e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit ed32f2e6d8174873cefcbe141084f857f84b0586"
earlhaminst
parents:
diff changeset
19 <data name="genes" format="tabular" label="${tool.name} on ${on_string}"/>
16e925bf567e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit ed32f2e6d8174873cefcbe141084f857f84b0586"
earlhaminst
parents:
diff changeset
20 </outputs>
16e925bf567e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit ed32f2e6d8174873cefcbe141084f857f84b0586"
earlhaminst
parents:
diff changeset
21 <tests>
16e925bf567e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit ed32f2e6d8174873cefcbe141084f857f84b0586"
earlhaminst
parents:
diff changeset
22 <test>
16e925bf567e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit ed32f2e6d8174873cefcbe141084f857f84b0586"
earlhaminst
parents:
diff changeset
23 <param name="genetreeFile" ftype="nhx" value="test.nhx" />
16e925bf567e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit ed32f2e6d8174873cefcbe141084f857f84b0586"
earlhaminst
parents:
diff changeset
24 <param name="speciesorder" value="w,x,y,z,zz" />
16e925bf567e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit ed32f2e6d8174873cefcbe141084f857f84b0586"
earlhaminst
parents:
diff changeset
25 <output name="genes" file="test.tsv" />
16e925bf567e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit ed32f2e6d8174873cefcbe141084f857f84b0586"
earlhaminst
parents:
diff changeset
26 </test>
16e925bf567e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit ed32f2e6d8174873cefcbe141084f857f84b0586"
earlhaminst
parents:
diff changeset
27 </tests>
16e925bf567e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit ed32f2e6d8174873cefcbe141084f857f84b0586"
earlhaminst
parents:
diff changeset
28 <help><![CDATA[
16e925bf567e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit ed32f2e6d8174873cefcbe141084f857f84b0586"
earlhaminst
parents:
diff changeset
29 Find copy number for genes from GeneTree by utilising the `ETE Toolkit`_. Input can be single GeneTree or multiple GeneTree in a file with one GeneTree per line.
16e925bf567e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit ed32f2e6d8174873cefcbe141084f857f84b0586"
earlhaminst
parents:
diff changeset
30
16e925bf567e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit ed32f2e6d8174873cefcbe141084f857f84b0586"
earlhaminst
parents:
diff changeset
31 .. _ETE Toolkit: http://etetoolkit.org/
16e925bf567e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit ed32f2e6d8174873cefcbe141084f857f84b0586"
earlhaminst
parents:
diff changeset
32 ]]></help>
16e925bf567e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit ed32f2e6d8174873cefcbe141084f857f84b0586"
earlhaminst
parents:
diff changeset
33 <expand macro="citations" />
16e925bf567e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit ed32f2e6d8174873cefcbe141084f857f84b0586"
earlhaminst
parents:
diff changeset
34 </tool>