annotate blast2html.xml @ 41:637f96ffb9a4

more dependency updates, now including the python package dependencies
author Jan Kanis <jan.code@jankanis.nl>
date Mon, 19 May 2014 18:22:24 +0200
parents 91008923c402
children 1d49bce1e4bb
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
38
91008923c402 add repository dependency; add <stdio> tag; update version
Jan Kanis <jan.code@jankanis.nl>
parents: 37
diff changeset
1 <tool id="blast2html" name="blast2html" version="0.0.4">
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>
637f96ffb9a4 more dependency updates, now including the python package dependencies
Jan Kanis <jan.code@jankanis.nl>
parents: 38
diff changeset
7 <requirement name="package" version="1.2.1">argparse</requirement>
637f96ffb9a4 more dependency updates, now including the python package dependencies
Jan Kanis <jan.code@jankanis.nl>
parents: 38
diff changeset
8 <requirement name="package" version="2.2.3">lxml</requirement>
637f96ffb9a4 more dependency updates, now including the python package dependencies
Jan Kanis <jan.code@jankanis.nl>
parents: 38
diff changeset
9 <requirement name="package" version="2.7.2">jinja2</requirement>
28
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
10 </requirements>
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
11
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
12 <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
13
91008923c402 add repository dependency; add <stdio> tag; update version
Jan Kanis <jan.code@jankanis.nl>
parents: 37
diff changeset
14 <stdio>
91008923c402 add repository dependency; add <stdio> tag; update version
Jan Kanis <jan.code@jankanis.nl>
parents: 37
diff changeset
15 <!-- 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
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 <exit_code range=":-1" />
91008923c402 add repository dependency; add <stdio> tag; update version
Jan Kanis <jan.code@jankanis.nl>
parents: 37
diff changeset
18 </stdio>
28
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
19
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
20 <inputs>
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
21 <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
22 </inputs>
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
23
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
24 <outputs>
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
25 <data format="html" name="output" />
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
26 </outputs>
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
27
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
28 <tests>
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
29 <test>
32
ce8f29efc0a1 fix tests
Jan Kanis <jan.code@jankanis.nl>
parents: 29
diff changeset
30 <param name="input" value="blast xml example1.xml"/>
ce8f29efc0a1 fix tests
Jan Kanis <jan.code@jankanis.nl>
parents: 29
diff changeset
31 <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
32 </test>
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
33 <test>
32
ce8f29efc0a1 fix tests
Jan Kanis <jan.code@jankanis.nl>
parents: 29
diff changeset
34 <param name="input" value="blast xml example2.xml"/>
ce8f29efc0a1 fix tests
Jan Kanis <jan.code@jankanis.nl>
parents: 29
diff changeset
35 <output name="out_file1" file="blast xml example2.html"/>
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 <test>
ce8f29efc0a1 fix tests
Jan Kanis <jan.code@jankanis.nl>
parents: 29
diff changeset
38 <param name="input" value="blast xml example3.xml"/>
ce8f29efc0a1 fix tests
Jan Kanis <jan.code@jankanis.nl>
parents: 29
diff changeset
39 <output name="out_file1" file="blast xml example3.html"/>
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 <test>
ce8f29efc0a1 fix tests
Jan Kanis <jan.code@jankanis.nl>
parents: 29
diff changeset
42 <param name="input" value="blast xml example4.xml"/>
ce8f29efc0a1 fix tests
Jan Kanis <jan.code@jankanis.nl>
parents: 29
diff changeset
43 <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
44 </test>
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
45 </tests>
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
46
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
47 <help>
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
48 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
49 </help>
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
50
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
51 </tool>