Mercurial > repos > dfornika > augur

annotate augur_parse.xml @ 1:892c6690a1e8 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/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
author dfornika
date Mon, 08 Apr 2019 13:27:08 -0400
parents 20ad934c5536
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
20ad934c5536 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit bd602c325bc1b6c6453f89cf243bd9cb2dd0c520-dirty
dfornika
parents:
diff changeset
1 <tool id="augur_parse" name="augur parse" version="@TOOL_VERSION@+galaxy0">
20ad934c5536 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit bd602c325bc1b6c6453f89cf243bd9cb2dd0c520-dirty
dfornika
parents:
diff changeset
2 <description></description>
20ad934c5536 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit bd602c325bc1b6c6453f89cf243bd9cb2dd0c520-dirty
dfornika
parents:
diff changeset
3 <macros>
20ad934c5536 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit bd602c325bc1b6c6453f89cf243bd9cb2dd0c520-dirty
dfornika
parents:
diff changeset
4 <import>macros.xml</import>
20ad934c5536 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit bd602c325bc1b6c6453f89cf243bd9cb2dd0c520-dirty
dfornika
parents:
diff changeset
5 </macros>
20ad934c5536 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit bd602c325bc1b6c6453f89cf243bd9cb2dd0c520-dirty
dfornika
parents:
diff changeset
6 <requirements>
20ad934c5536 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit bd602c325bc1b6c6453f89cf243bd9cb2dd0c520-dirty
dfornika
parents:
diff changeset
7 <requirement type="package" version="@TOOL_VERSION@">augur</requirement>
20ad934c5536 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit bd602c325bc1b6c6453f89cf243bd9cb2dd0c520-dirty
dfornika
parents:
diff changeset
8 </requirements>
20ad934c5536 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit bd602c325bc1b6c6453f89cf243bd9cb2dd0c520-dirty
dfornika
parents:
diff changeset
9 <version_command>augur --version</version_command>
20ad934c5536 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit bd602c325bc1b6c6453f89cf243bd9cb2dd0c520-dirty
dfornika
parents:
diff changeset
10 <command detect_errors="exit_code"><![CDATA[
20ad934c5536 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit bd602c325bc1b6c6453f89cf243bd9cb2dd0c520-dirty
dfornika
parents:
diff changeset
11 augur parse
20ad934c5536 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit bd602c325bc1b6c6453f89cf243bd9cb2dd0c520-dirty
dfornika
parents:
diff changeset
12 --sequences '$sequences'
20ad934c5536 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit bd602c325bc1b6c6453f89cf243bd9cb2dd0c520-dirty
dfornika
parents:
diff changeset
13 --fields $fields
20ad934c5536 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit bd602c325bc1b6c6453f89cf243bd9cb2dd0c520-dirty
dfornika
parents:
diff changeset
14 --separator '$separator'
20ad934c5536 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit bd602c325bc1b6c6453f89cf243bd9cb2dd0c520-dirty
dfornika
parents:
diff changeset
15 --output-sequences '$output_sequences'
20ad934c5536 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit bd602c325bc1b6c6453f89cf243bd9cb2dd0c520-dirty
dfornika
parents:
diff changeset
16 --output-metadata '$output_metadata'
20ad934c5536 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit bd602c325bc1b6c6453f89cf243bd9cb2dd0c520-dirty
dfornika
parents:
diff changeset
17 ]]></command>
20ad934c5536 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit bd602c325bc1b6c6453f89cf243bd9cb2dd0c520-dirty
dfornika
parents:
diff changeset
18 <inputs>
20ad934c5536 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit bd602c325bc1b6c6453f89cf243bd9cb2dd0c520-dirty
dfornika
parents:
diff changeset
19 <param name="sequences" type="data" format="fasta" label="Sequences"/>
20ad934c5536 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit bd602c325bc1b6c6453f89cf243bd9cb2dd0c520-dirty
dfornika
parents:
diff changeset
20 <param name="fields" type="text" label="Fields in fasta header"/>
1
892c6690a1e8 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
dfornika
parents: 0
diff changeset
21 <param name="separator" type="text" value="|" label="Separator in fasta header">
892c6690a1e8 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
dfornika
parents: 0
diff changeset
22 <sanitizer>
892c6690a1e8 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
dfornika
parents: 0
diff changeset
23 <valid initial="string.printable">
892c6690a1e8 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
dfornika
parents: 0
diff changeset
24 <remove value="&apos;"/>
892c6690a1e8 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
dfornika
parents: 0
diff changeset
25 </valid>
892c6690a1e8 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
dfornika
parents: 0
diff changeset
26 <mapping initial="none">
892c6690a1e8 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
dfornika
parents: 0
diff changeset
27 </mapping>
892c6690a1e8 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
dfornika
parents: 0
diff changeset
28 </sanitizer>
892c6690a1e8 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
dfornika
parents: 0
diff changeset
29 </param>
0
20ad934c5536 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit bd602c325bc1b6c6453f89cf243bd9cb2dd0c520-dirty
dfornika
parents:
diff changeset
30 </inputs>
20ad934c5536 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit bd602c325bc1b6c6453f89cf243bd9cb2dd0c520-dirty
dfornika
parents:
diff changeset
31 <outputs>
1
892c6690a1e8 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
dfornika
parents: 0
diff changeset
32 <data name="output_sequences" format="fasta" />
892c6690a1e8 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
dfornika
parents: 0
diff changeset
33 <data name="output_metadata" format="tabular" />
0
20ad934c5536 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit bd602c325bc1b6c6453f89cf243bd9cb2dd0c520-dirty
dfornika
parents:
diff changeset
34 </outputs>
20ad934c5536 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit bd602c325bc1b6c6453f89cf243bd9cb2dd0c520-dirty
dfornika
parents:
diff changeset
35 <tests>
20ad934c5536 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit bd602c325bc1b6c6453f89cf243bd9cb2dd0c520-dirty
dfornika
parents:
diff changeset
36 <test>
1
892c6690a1e8 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
dfornika
parents: 0
diff changeset
37 <param name="sequences" value="augur_parse_test_0_sequences.input.fasta" />
892c6690a1e8 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
dfornika
parents: 0
diff changeset
38 <param name="fields" value="strain country year" />
892c6690a1e8 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
dfornika
parents: 0
diff changeset
39 <output name="output_sequences" file="augur_parse_test_0_sequences.output.fasta" />
892c6690a1e8 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
dfornika
parents: 0
diff changeset
40 <output name="output_metadata" file="augur_parse_test_0_metadata.output.csv" />
0
20ad934c5536 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit bd602c325bc1b6c6453f89cf243bd9cb2dd0c520-dirty
dfornika
parents:
diff changeset
41 </test>
20ad934c5536 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit bd602c325bc1b6c6453f89cf243bd9cb2dd0c520-dirty
dfornika
parents:
diff changeset
42 </tests>
20ad934c5536 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit bd602c325bc1b6c6453f89cf243bd9cb2dd0c520-dirty
dfornika
parents:
diff changeset
43 <help><![CDATA[
20ad934c5536 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit bd602c325bc1b6c6453f89cf243bd9cb2dd0c520-dirty
dfornika
parents:
diff changeset
44 Parse delimited fields from FASTA sequence names into a TSV and FASTA file.
20ad934c5536 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit bd602c325bc1b6c6453f89cf243bd9cb2dd0c520-dirty
dfornika
parents:
diff changeset
45 ]]></help>
1
892c6690a1e8 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
dfornika
parents: 0
diff changeset
46 <expand macro="citations" />
0
20ad934c5536 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit bd602c325bc1b6c6453f89cf243bd9cb2dd0c520-dirty
dfornika
parents:
diff changeset
47 </tool>