Mercurial > repos > jankanis > blast2html

annotate blast2html.xml @ 122:5f104d05aa23

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
fix python 2.6 issue with array type codes
author Jan Kanis <jan.code@jankanis.nl>
date Thu, 31 Jul 2014 17:24:10 +0200
parents 8ae714069687
children 532aa200dbe9
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
117
8ae714069687 increase version to 0.0.14
Jan Kanis <jan.code@jankanis.nl>
parents: 115
diff changeset
1 <tool id="blast2html" name="blast2html" version="0.0.14">
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>
85
2edb77030a9e re-include backed out revisions and update version numbers
Jan Kanis <jan.code@jankanis.nl>
parents: 84
diff changeset
6 <requirement name="package" version="0.2">blast2html_venv</requirement>
28
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
7 </requirements>
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
8
100
be7c94e29cd8 add --db-config-dir switch to wrapper; update version number
Jan Kanis <jan.code@jankanis.nl>
parents: 85
diff changeset
9 <command interpreter="python">blast2html.py -i "${input}" -o "${output}" --db-config-dir "${GALAXY_DATA_INDEX_DIR}"</command>
38
91008923c402 add repository dependency; add <stdio> tag; update version
Jan Kanis <jan.code@jankanis.nl>
parents: 37
diff changeset
10
91008923c402 add repository dependency; add <stdio> tag; update version
Jan Kanis <jan.code@jankanis.nl>
parents: 37
diff changeset
11 <stdio>
91008923c402 add repository dependency; add <stdio> tag; update version
Jan Kanis <jan.code@jankanis.nl>
parents: 37
diff changeset
12 <!-- 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
13 <exit_code range="1:" />
91008923c402 add repository dependency; add <stdio> tag; update version
Jan Kanis <jan.code@jankanis.nl>
parents: 37
diff changeset
14 <exit_code range=":-1" />
91008923c402 add repository dependency; add <stdio> tag; update version
Jan Kanis <jan.code@jankanis.nl>
parents: 37
diff changeset
15 </stdio>
28
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
16
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
17 <inputs>
66
e3dd39906eef fix input format
Jan Kanis <jan.code@jankanis.nl>
parents: 61
diff changeset
18 <param format="blastxml" name="input" type="data" label="Source file"/>
28
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
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
21 <outputs>
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
22 <data format="html" name="output" />
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
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
25 <tests>
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
26 <test>
32
ce8f29efc0a1 fix tests
Jan Kanis <jan.code@jankanis.nl>
parents: 29
diff changeset
27 <param name="input" value="blast xml example1.xml"/>
105
b3b5ee557170 update test
Jan Kanis <jan.code@jankanis.nl>
parents: 100
diff changeset
28 <output name="output" file="blast xml example1.html"/>
28
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
29 </test>
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
30 <test>
32
ce8f29efc0a1 fix tests
Jan Kanis <jan.code@jankanis.nl>
parents: 29
diff changeset
31 <param name="input" value="blast xml example2.xml"/>
105
b3b5ee557170 update test
Jan Kanis <jan.code@jankanis.nl>
parents: 100
diff changeset
32 <output name="output" file="blast xml example2.html"/>
32
ce8f29efc0a1 fix tests
Jan Kanis <jan.code@jankanis.nl>
parents: 29
diff changeset
33 </test>
ce8f29efc0a1 fix tests
Jan Kanis <jan.code@jankanis.nl>
parents: 29
diff changeset
34 <test>
ce8f29efc0a1 fix tests
Jan Kanis <jan.code@jankanis.nl>
parents: 29
diff changeset
35 <param name="input" value="blast xml example3.xml"/>
105
b3b5ee557170 update test
Jan Kanis <jan.code@jankanis.nl>
parents: 100
diff changeset
36 <output name="output" file="blast xml example3.html"/>
32
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 <test>
ce8f29efc0a1 fix tests
Jan Kanis <jan.code@jankanis.nl>
parents: 29
diff changeset
39 <param name="input" value="blast xml example4.xml"/>
105
b3b5ee557170 update test
Jan Kanis <jan.code@jankanis.nl>
parents: 100
diff changeset
40 <output name="output" file="blast xml example4.html"/>
28
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
41 </test>
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
42 </tests>
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
43
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
44 <help>
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
45 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
46 </help>
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
47
8a8c0c71b5d1 add blast2html.xml config setting
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
48 </tool>