Mercurial > repos > p.lucas > clermontyping

annotate ClermonTyping_wrapper.xml @ 1:cec55ef9cce5 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Use env clermont instead of requirements in the wrapper
author p.lucas
date Mon, 14 Feb 2022 14:20:05 +0000
parents e93c20bad6b0
children 07fe3c343426
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
e93c20bad6b0 First upload wrapper
p.lucas
parents:
diff changeset
1 <tool id="ClermonTyping" name="ClermonTyping" version="1">
e93c20bad6b0 First upload wrapper
p.lucas
parents:
diff changeset
2 <description>
e93c20bad6b0 First upload wrapper
p.lucas
parents:
diff changeset
3 ClermonTyping: an easy-to-use and accurate in silico method for Escherichia genus strain phylotyping
e93c20bad6b0 First upload wrapper
p.lucas
parents:
diff changeset
4 </description>
e93c20bad6b0 First upload wrapper
p.lucas
parents:
diff changeset
5 <command detect_errors="exit_code"><![CDATA[
1
cec55ef9cce5 Use env clermont instead of requirements in the wrapper
p.lucas
parents: 0
diff changeset
6 source /home/galaxy/data/_conda/bin/activate Ab-HADDOCK;
cec55ef9cce5 Use env clermont instead of requirements in the wrapper
p.lucas
parents: 0
diff changeset
7 /home/galaxy/ClermonTyping/clermonTyping.sh --fasta ${input} --name Analyse;
cec55ef9cce5 Use env clermont instead of requirements in the wrapper
p.lucas
parents: 0
diff changeset
8 source /home/galaxy/data/_conda/bin/deactivate;
0
e93c20bad6b0 First upload wrapper
p.lucas
parents:
diff changeset
9 ]]></command>
e93c20bad6b0 First upload wrapper
p.lucas
parents:
diff changeset
10 <inputs>
e93c20bad6b0 First upload wrapper
p.lucas
parents:
diff changeset
11 <param name="input" format="fasta" type="data" label="Select contigs file in fasta format." help="Fasta format containing contigs."/>
e93c20bad6b0 First upload wrapper
p.lucas
parents:
diff changeset
12 </inputs>
e93c20bad6b0 First upload wrapper
p.lucas
parents:
diff changeset
13 <outputs>
e93c20bad6b0 First upload wrapper
p.lucas
parents:
diff changeset
14 <data name="html" format="html" label="html output file" from_work_dir="Analyse/Analyse.html"/>
e93c20bad6b0 First upload wrapper
p.lucas
parents:
diff changeset
15 <data name="phylogroup" format="tsv" label="Phylogroup found" from_work_dir="Analyse/Analyse_phylogroups.txt"/>
e93c20bad6b0 First upload wrapper
p.lucas
parents:
diff changeset
16 </outputs>
e93c20bad6b0 First upload wrapper
p.lucas
parents:
diff changeset
17 <help>
e93c20bad6b0 First upload wrapper
p.lucas
parents:
diff changeset
18 Script usage :
e93c20bad6b0 First upload wrapper
p.lucas
parents:
diff changeset
19 -h : print this message and exit
e93c20bad6b0 First upload wrapper
p.lucas
parents:
diff changeset
20 -v : print the version and exit
e93c20bad6b0 First upload wrapper
p.lucas
parents:
diff changeset
21 --fasta : fasta contigs file(s). If multiple files, they must be separated by an arobase (@) value
e93c20bad6b0 First upload wrapper
p.lucas
parents:
diff changeset
22 --name : name for this analysis (optional)
e93c20bad6b0 First upload wrapper
p.lucas
parents:
diff changeset
23 --threshold : option for ClermontTyping, do not use contigs under this size (optional)
e93c20bad6b0 First upload wrapper
p.lucas
parents:
diff changeset
24 --minimal : output a minimal set of files (optional)
e93c20bad6b0 First upload wrapper
p.lucas
parents:
diff changeset
25 --fastafile : file with path of fasta contig file. One file by line (optional)
e93c20bad6b0 First upload wrapper
p.lucas
parents:
diff changeset
26 --summary : file with path of *_phylogroups.txt. One file by line (optional)
e93c20bad6b0 First upload wrapper
p.lucas
parents:
diff changeset
27 </help>
e93c20bad6b0 First upload wrapper
p.lucas
parents:
diff changeset
28 </tool>