Mercurial > repos > iuc > chewbbaca_extractcgmlst

annotate ExtractCgMLST.xml @ 3:9c4c2191b550 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/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
author iuc
date Wed, 25 Sep 2024 14:13:48 +0000
parents a302f0fef852
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
1 <tool id="chewbbaca_extractcgmlst" name="chewBBACA ExtractCgMLST" version="@CHEW_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
2 <description>Determine the set of loci that constitute the core genome</description>
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
3 <macros>
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
4 <import>macros.xml</import>
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
5 </macros>
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
6 <expand macro="requirements" />
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
8 chewBBACA.py ExtractCgMLST
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
9 --t $threshold
1
a302f0fef852 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 2564b0ca982636c6c6f221d0c5072f52d39e6751
iuc
parents: 0
diff changeset
10 #if $genes2remove:
a302f0fef852 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 2564b0ca982636c6c6f221d0c5072f52d39e6751
iuc
parents: 0
diff changeset
11 --r '$genes2remove'
0
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
12 #end if
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
13 #if $genomes2remove:
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
14 --g '$genomes2remove'
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
15 #end if
1
a302f0fef852 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 2564b0ca982636c6c6f221d0c5072f52d39e6751
iuc
parents: 0
diff changeset
16 -i '$input_file' -o 'output'
0
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
17 ]]></command>
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
18 <inputs>
1
a302f0fef852 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 2564b0ca982636c6c6f221d0c5072f52d39e6751
iuc
parents: 0
diff changeset
19 <param argument="--input-file" type="data" label="Allelic Profiles" format="tabular"/>
0
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
20 <section name="advanced" title="Advanced options">
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
21 <param argument="--genomes2remove" type="data" format="txt" label="Genomes/rows to remove from the matrix" optional="true" help="One genome identifier per line"/>
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
22 <param argument="--threshold" type="text" value="0.95 0.99 1" label="threshold" help="Genes that constitute the core genome must be in a proportion of genomes that is at least equal to this value. Users can provide multiple values as a space-separated list.">
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
23 <validator type="regex">[ .0-9]+</validator>
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
24 </param>
1
a302f0fef852 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 2564b0ca982636c6c6f221d0c5072f52d39e6751
iuc
parents: 0
diff changeset
25 <param argument="--genes2remove" type="data" format="tabular" label="List of genes to exclude from analysis" optional="true" help="the list of genes listed in the &quot;paralogous_counts.tsv&quot; file created by the AlleleCall process."/>
0
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
26 </section>
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
27 </inputs>
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
28 <outputs>
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
29 <collection name="output_collection" type="list" format="html,tsv,txt" label="${tool.name} on ${on_string}">
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
30 <discover_datasets pattern="__name_and_ext__" directory="output"/>
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
31 </collection>
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
32 </outputs>
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
33 <tests>
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
34 <test>
1
a302f0fef852 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 2564b0ca982636c6c6f221d0c5072f52d39e6751
iuc
parents: 0
diff changeset
35 <param name="input_file" value="results_alleles.tsv"/>
0
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
36 <output_collection name="output_collection" type="list">
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
37 <element name="missing_loci_stats">
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
38 <assert_contents>
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
39 <has_text_matching expression="GCA_000007265"/>
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
40 </assert_contents>
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
41 </element>
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
42 <element name="presence_absence">
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
43 <assert_contents>
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
44 <has_text_matching expression="GCA_000007265"/>
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
45 </assert_contents>
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
46 </element>
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
47 </output_collection>
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
48 </test>
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
49 </tests>
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
50 <help>
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
51 chewBBACA is a software suite for the creation and evaluation of core genome and whole genome MultiLocus Sequence Typing (cg/wgMLST) schemas and results.
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
52
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
53 cgMLST schemas are defined as the set of loci that are present in all strains under analysis or, due to sequencing/assembly limitations, >95% of strains analyzed. In order to have a robust definition of a cgMLST schema for a given bacterial species, a set of representative strains of the diversity of a given species should be selected.
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
54
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
55 .. class:: infomark
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
56
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
57 **Note**
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
58
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
59 The user can define a **space-separated** list of values for --threshold
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
60 </help>
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
61 <expand macro="citations" />
743125c3ac12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
parents:
diff changeset
62 </tool>