Mercurial > repos > iuc > mlst

annotate mlst_list.xml @ 3:022dc4bbc27e draft

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/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
author iuc
date Mon, 15 Oct 2018 07:41:28 -0400
parents 11e1af1f7f35
children 7eb5e58d2263
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
1 <tool id="mlst_list" name="MLST List" version="@VERSION@">
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
2 <description>Lists available schemes for the MLST tool.</description>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
3 <macros>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
4 <import>macros.xml</import>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
5 </macros>
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
6 <expand macro="requirements" />
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
7 <expand macro="version_command" />
0
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
8
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
9 <command detect_errors="exit_code"><![CDATA[
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
10 mlst $list_type > "$report"
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
11 ]]></command>
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
12
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
13 <inputs>
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
14 <param name="list_type" type="boolean" label="Output allele information" truevalue="--longlist" falsevalue="--list"
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
15 help="Selecting 'Yes' will provide the alleles for all MLST schemes" optional="false" />
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
16 </inputs>
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
17
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
18 <outputs>
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
19 <data format="txt" name="report" label="${tool.name} - list of schemes"/>
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
20 </outputs>
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
21
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
22 <tests>
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
23 <!-- Test the longlist option -->
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
24 <test>
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
25 <param name="list_type" value="true" />
1
681a5aa83361 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 47ad236b09eaf7541fbd7dd5b95e970800d545a5
iuc
parents: 0
diff changeset
26 <output name="report" ftype="txt" >
681a5aa83361 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 47ad236b09eaf7541fbd7dd5b95e970800d545a5
iuc
parents: 0
diff changeset
27 <assert_contents>
681a5aa83361 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 47ad236b09eaf7541fbd7dd5b95e970800d545a5
iuc
parents: 0
diff changeset
28 <has_text text="saureus" />
681a5aa83361 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 47ad236b09eaf7541fbd7dd5b95e970800d545a5
iuc
parents: 0
diff changeset
29 </assert_contents>
681a5aa83361 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 47ad236b09eaf7541fbd7dd5b95e970800d545a5
iuc
parents: 0
diff changeset
30 </output>
0
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
31 </test>
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
32
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
33 <!-- Test the list option -->
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
34 <test>
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
35 <param name="list_type" value="false" />
1
681a5aa83361 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 47ad236b09eaf7541fbd7dd5b95e970800d545a5
iuc
parents: 0
diff changeset
36 <output name="report" ftype="txt" >
681a5aa83361 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 47ad236b09eaf7541fbd7dd5b95e970800d545a5
iuc
parents: 0
diff changeset
37 <assert_contents>
681a5aa83361 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 47ad236b09eaf7541fbd7dd5b95e970800d545a5
iuc
parents: 0
diff changeset
38 <has_text text="saureus" />
681a5aa83361 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 47ad236b09eaf7541fbd7dd5b95e970800d545a5
iuc
parents: 0
diff changeset
39 </assert_contents>
681a5aa83361 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 47ad236b09eaf7541fbd7dd5b95e970800d545a5
iuc
parents: 0
diff changeset
40 </output>
0
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
41 </test>
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
42 </tests>
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
43
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
44 <help><![CDATA[
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
45 **What it does**
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
46
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
47 MLST List will list all the scheme names used by MLST. Selecting the long list option will also provide the alleles for all MLST schemes.
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
48
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
49 ]]></help>
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
50
3
022dc4bbc27e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
iuc
parents: 2
diff changeset
51 <expand macro="citations" />
0
d99b37191518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
iuc
parents:
diff changeset
52 </tool>