Mercurial > repos > dfornika > match_plasmid_to_reference

annotate match_plasmid_to_reference.xml @ 4:826ddf832bef 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/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
author dfornika
date Wed, 06 Nov 2019 13:52:40 -0500
parents d56b4f743779
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents:
diff changeset
1 <tool id="match_plasmid_to_reference" name="Match plasmid to reference" version="0.1.0">
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents:
diff changeset
2 <description>Pick plasmids containing specific genes</description>
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents:
diff changeset
3 <requirements>
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents:
diff changeset
4 </requirements>
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents:
diff changeset
5 <command detect_errors="exit_code"><![CDATA[
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents:
diff changeset
6 '$__tool_directory__/match_plasmid_to_reference.py'
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents:
diff changeset
7 --plasmid '${plasmid}'
4
826ddf832bef "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents: 3
diff changeset
8 --reference_plasmids_genbank
826ddf832bef "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents: 3
diff changeset
9 #for $reference_plasmid in $reference_plasmids_genbank:
826ddf832bef "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents: 3
diff changeset
10 '${reference_plasmid}'
826ddf832bef "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents: 3
diff changeset
11 #end for
826ddf832bef "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents: 3
diff changeset
12 --reference_plasmids_fasta
826ddf832bef "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents: 3
diff changeset
13 #for $reference_plasmid in $reference_plasmids_fasta:
0
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents:
diff changeset
14 '${reference_plasmid}'
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents:
diff changeset
15 #end for
2
faf74a1bbd5f "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents: 1
diff changeset
16 --mob_typer_report '${concatenated_mob_typer_reports}'
0
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents:
diff changeset
17 --outdir outdir
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents:
diff changeset
18 ]]></command>
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents:
diff changeset
19 <inputs>
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents:
diff changeset
20 <param name="plasmid" type="data" format="fasta" />
4
826ddf832bef "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents: 3
diff changeset
21 <param name="reference_plasmids_genbank" type="data_collection" collection_type="list" format="genbank" />
826ddf832bef "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents: 3
diff changeset
22 <param name="reference_plasmids_fasta" type="data_collection" collection_type="list" format="fasta" />
0
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents:
diff changeset
23 <param name="concatenated_mob_typer_reports" type="data" format="tabular" />
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents:
diff changeset
24 </inputs>
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents:
diff changeset
25 <outputs>
3
d56b4f743779 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents: 2
diff changeset
26 <data name="output_plasmid" from_work_dir="outdir/plasmid.fasta" label="Plasmid" format="fasta"/>
4
826ddf832bef "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents: 3
diff changeset
27 <data name="matched_reference_plasmid_genbank" from_work_dir="outdir/reference_plasmid.gbk" label="Reference Plasmid (genbank)" format="genbank"/>
826ddf832bef "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents: 3
diff changeset
28 <data name="matched_reference_plasmid_fasta" from_work_dir="outdir/reference_plasmid.fasta" label="Reference Plasmid (fasta)" format="fasta"/>
3
d56b4f743779 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents: 2
diff changeset
29 <data name="matched_mob_typer_record" from_work_dir="outdir/mob_typer_record.tsv" label="Matched MOB-Typer Record" format="tabular"/>
0
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents:
diff changeset
30 </outputs>
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents:
diff changeset
31 <tests>
1
3616b6eda1da "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents: 0
diff changeset
32 <test>
3616b6eda1da "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents: 0
diff changeset
33 <param name="plasmid" value="SRR9113487_plasmid_2719.fasta"/>
4
826ddf832bef "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents: 3
diff changeset
34 <param name="reference_plasmids_genbank">
1
3616b6eda1da "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents: 0
diff changeset
35 <collection type="list">
2
faf74a1bbd5f "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents: 1
diff changeset
36 <element name="CP008719" value="CP008719.gbk" ftype="genbank" />
faf74a1bbd5f "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents: 1
diff changeset
37 <element name="JQ739157" value="JQ739157.gbk" ftype="genbank" />
1
3616b6eda1da "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents: 0
diff changeset
38 </collection>
3616b6eda1da "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents: 0
diff changeset
39 </param>
4
826ddf832bef "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents: 3
diff changeset
40 <param name="reference_plasmids_fasta">
826ddf832bef "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents: 3
diff changeset
41 <collection type="list">
826ddf832bef "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents: 3
diff changeset
42 <element name="CP008719" value="CP008719.fa" ftype="fasta" />
826ddf832bef "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents: 3
diff changeset
43 <element name="JQ739157" value="JQ739157.fa" ftype="fasta" />
826ddf832bef "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents: 3
diff changeset
44 </collection>
826ddf832bef "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents: 3
diff changeset
45 </param>
2
faf74a1bbd5f "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents: 1
diff changeset
46 <param name="concatenated_mob_typer_reports" value="concatenated_mob_typer_reports.tsv" />
faf74a1bbd5f "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents: 1
diff changeset
47 <output name="output_plasmid" file="outdir/plasmid.fasta" />
4
826ddf832bef "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents: 3
diff changeset
48 <output name="matched_reference_plasmid_genbank" file="outdir/reference_plasmid.gbk" />
826ddf832bef "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents: 3
diff changeset
49 <output name="matched_reference_plasmid_fasta" file="outdir/reference_plasmid.fasta" />
2
faf74a1bbd5f "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents: 1
diff changeset
50 <output name="matched_mob_typer_record" file="outdir/mob_typer_record.tsv" />
1
3616b6eda1da "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents: 0
diff changeset
51 </test>
0
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents:
diff changeset
52 </tests>
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents:
diff changeset
53 <help><![CDATA[
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents:
diff changeset
54 ]]></help>
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents:
diff changeset
55 <citations>
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents:
diff changeset
56 </citations>
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
parents:
diff changeset
57 </tool>