Mercurial > repos > jankanis > blast2html

annotate blast2html.xml @ 53:4217bb9cf1d3

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
depend on python 3; fix internal links with multiple iterations
author Jan Kanis <jan.code@jankanis.nl>
date Mon, 26 May 2014 13:07:13 +0200
parents d6c7b5de2833
children d2fb88c1e866
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
53
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations
Jan Kanis <jan.code@jankanis.nl>
parents: 52
diff changeset
1 <tool id="blast2html" name="blast2html" version="0.0.8">
28
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
2
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
3 <description>Convert BLAST XML to HTML</description>
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
4
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
5 <requirements>
41
637f96ffb9a4 more dependency updates, now including the python package dependencies
Jan Kanis <jan.code@jankanis.nl>
parents: 38
diff changeset
6 <requirement type="package" version="v0.0.18">blast_datatypes</requirement>
53
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations
Jan Kanis <jan.code@jankanis.nl>
parents: 52
diff changeset
7 <requirement name="package" version="3.4.1">python3</requirement>
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations
Jan Kanis <jan.code@jankanis.nl>
parents: 52
diff changeset
8 <requirement name="package" version="0.1">blast2html_venv</requirement>
28
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
9 </requirements>
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
10
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
11 <command interpreter="python">blast2html.py -i "${input}" -o "${output}"</command>
38
91008923c402 add repository dependency; add <stdio> tag; update version
Jan Kanis <jan.code@jankanis.nl>
parents: 37
diff changeset
12
91008923c402 add repository dependency; add <stdio> tag; update version
Jan Kanis <jan.code@jankanis.nl>
parents: 37
diff changeset
13 <stdio>
91008923c402 add repository dependency; add <stdio> tag; update version
Jan Kanis <jan.code@jankanis.nl>
parents: 37
diff changeset
14 <!-- Any exit code other than 0 is an error -->
91008923c402 add repository dependency; add <stdio> tag; update version
Jan Kanis <jan.code@jankanis.nl>
parents: 37
diff changeset
15 <exit_code range="1:" />
91008923c402 add repository dependency; add <stdio> tag; update version
Jan Kanis <jan.code@jankanis.nl>
parents: 37
diff changeset
16 <exit_code range=":-1" />
91008923c402 add repository dependency; add <stdio> tag; update version
Jan Kanis <jan.code@jankanis.nl>
parents: 37
diff changeset
17 </stdio>
28
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
18
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
19 <inputs>
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
20 <param format="blast" name="input" type="data" label="Source file"/>
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
21 </inputs>
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
22
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
23 <outputs>
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
24 <data format="html" name="output" />
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
25 </outputs>
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
26
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
27 <tests>
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
28 <test>
32
ce8f29efc0a1 fix tests
Jan Kanis <jan.code@jankanis.nl>
parents: 29
diff changeset
29 <param name="input" value="blast xml example1.xml"/>
ce8f29efc0a1 fix tests
Jan Kanis <jan.code@jankanis.nl>
parents: 29
diff changeset
30 <output name="out_file1" file="blast xml example1.html"/>
28
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
31 </test>
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
32 <test>
32
ce8f29efc0a1 fix tests
Jan Kanis <jan.code@jankanis.nl>
parents: 29
diff changeset
33 <param name="input" value="blast xml example2.xml"/>
ce8f29efc0a1 fix tests
Jan Kanis <jan.code@jankanis.nl>
parents: 29
diff changeset
34 <output name="out_file1" file="blast xml example2.html"/>
ce8f29efc0a1 fix tests
Jan Kanis <jan.code@jankanis.nl>
parents: 29
diff changeset
35 </test>
ce8f29efc0a1 fix tests
Jan Kanis <jan.code@jankanis.nl>
parents: 29
diff changeset
36 <test>
ce8f29efc0a1 fix tests
Jan Kanis <jan.code@jankanis.nl>
parents: 29
diff changeset
37 <param name="input" value="blast xml example3.xml"/>
ce8f29efc0a1 fix tests
Jan Kanis <jan.code@jankanis.nl>
parents: 29
diff changeset
38 <output name="out_file1" file="blast xml example3.html"/>
ce8f29efc0a1 fix tests
Jan Kanis <jan.code@jankanis.nl>
parents: 29
diff changeset
39 </test>
ce8f29efc0a1 fix tests
Jan Kanis <jan.code@jankanis.nl>
parents: 29
diff changeset
40 <test>
ce8f29efc0a1 fix tests
Jan Kanis <jan.code@jankanis.nl>
parents: 29
diff changeset
41 <param name="input" value="blast xml example4.xml"/>
ce8f29efc0a1 fix tests
Jan Kanis <jan.code@jankanis.nl>
parents: 29
diff changeset
42 <output name="out_file1" file="blast xml example4.html"/>
28
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
43 </test>
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
44 </tests>
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
45
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
46 <help>
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
47 This tool converts the default BLAST XML result into a HTML document
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
48 </help>
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
49
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
50 </tool>