Mercurial > repos > bebatut > metaphlan2

annotate metaphlan2krona.xml @ 37:e7ed163633e1 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author bebatut
date Thu, 23 Feb 2017 08:13:41 -0500
parents 83f06bee818c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
31
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents: 30
diff changeset
1 <tool id="metaphlan2krona" name="Format MetaPhlAn2" version="@WRAPPER_VERSION@.0">
25
e8e0f835b4b6 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 11b919f18ba85a40ff0ff4df82aac9be6da188c5-dirty
bebatut
parents:
diff changeset
2
e8e0f835b4b6 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 11b919f18ba85a40ff0ff4df82aac9be6da188c5-dirty
bebatut
parents:
diff changeset
3 <description>output for Krona</description>
e8e0f835b4b6 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 11b919f18ba85a40ff0ff4df82aac9be6da188c5-dirty
bebatut
parents:
diff changeset
4
28
1d993cca38e3 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit b467108d731001d89920aee31433a5b0a623c251-dirty
bebatut
parents: 27
diff changeset
5 <macros>
1d993cca38e3 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit b467108d731001d89920aee31433a5b0a623c251-dirty
bebatut
parents: 27
diff changeset
6 <import>metaphlan2_macros.xml</import>
1d993cca38e3 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit b467108d731001d89920aee31433a5b0a623c251-dirty
bebatut
parents: 27
diff changeset
7 </macros>
25
e8e0f835b4b6 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 11b919f18ba85a40ff0ff4df82aac9be6da188c5-dirty
bebatut
parents:
diff changeset
8
28
1d993cca38e3 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit b467108d731001d89920aee31433a5b0a623c251-dirty
bebatut
parents: 27
diff changeset
9 <expand macro="requirements"/>
30
99fe591b59fb planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit c641bf32192cd4281a14f504fc97f1dc6edd6f7a-dirty
bebatut
parents: 29
diff changeset
10 <expand macro="stdio"/>
25
e8e0f835b4b6 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 11b919f18ba85a40ff0ff4df82aac9be6da188c5-dirty
bebatut
parents:
diff changeset
11
31
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents: 30
diff changeset
12 <version_command>metaphlan2krona.py -v</version_command>
25
e8e0f835b4b6 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 11b919f18ba85a40ff0ff4df82aac9be6da188c5-dirty
bebatut
parents:
diff changeset
13
e8e0f835b4b6 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 11b919f18ba85a40ff0ff4df82aac9be6da188c5-dirty
bebatut
parents:
diff changeset
14 <command>
30
99fe591b59fb planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit c641bf32192cd4281a14f504fc97f1dc6edd6f7a-dirty
bebatut
parents: 29
diff changeset
15 <![CDATA[
27
fb2dc25a832d planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 26
diff changeset
16 metaphlan2krona.py
31
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents: 30
diff changeset
17 --profile '$profile'
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents: 30
diff changeset
18 -k '$krona'
25
e8e0f835b4b6 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 11b919f18ba85a40ff0ff4df82aac9be6da188c5-dirty
bebatut
parents:
diff changeset
19 ]]>
e8e0f835b4b6 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 11b919f18ba85a40ff0ff4df82aac9be6da188c5-dirty
bebatut
parents:
diff changeset
20 </command>
e8e0f835b4b6 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 11b919f18ba85a40ff0ff4df82aac9be6da188c5-dirty
bebatut
parents:
diff changeset
21
e8e0f835b4b6 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 11b919f18ba85a40ff0ff4df82aac9be6da188c5-dirty
bebatut
parents:
diff changeset
22 <inputs>
31
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents: 30
diff changeset
23 <param argument="--profile" type="data" format="tabular,txt" label="Input file (MetaPhlAN2 output)"/>
25
e8e0f835b4b6 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 11b919f18ba85a40ff0ff4df82aac9be6da188c5-dirty
bebatut
parents:
diff changeset
24 </inputs>
e8e0f835b4b6 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 11b919f18ba85a40ff0ff4df82aac9be6da188c5-dirty
bebatut
parents:
diff changeset
25
e8e0f835b4b6 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 11b919f18ba85a40ff0ff4df82aac9be6da188c5-dirty
bebatut
parents:
diff changeset
26 <outputs>
30
99fe591b59fb planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit c641bf32192cd4281a14f504fc97f1dc6edd6f7a-dirty
bebatut
parents: 29
diff changeset
27 <data format="tabular" name="krona" label="${tool.name} on ${on_string}: Formatted file for Krona" />
25
e8e0f835b4b6 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 11b919f18ba85a40ff0ff4df82aac9be6da188c5-dirty
bebatut
parents:
diff changeset
28 </outputs>
e8e0f835b4b6 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 11b919f18ba85a40ff0ff4df82aac9be6da188c5-dirty
bebatut
parents:
diff changeset
29
27
fb2dc25a832d planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 26
diff changeset
30 <tests>
fb2dc25a832d planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 26
diff changeset
31 <test>
31
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents: 30
diff changeset
32 <param name="profile" value="community_profile.tabular"/>
29
713a83023626 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents: 28
diff changeset
33 <output name="krona" file="formatted_to_krona.tabular"/>
30
99fe591b59fb planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit c641bf32192cd4281a14f504fc97f1dc6edd6f7a-dirty
bebatut
parents: 29
diff changeset
34 </test>
25
e8e0f835b4b6 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 11b919f18ba85a40ff0ff4df82aac9be6da188c5-dirty
bebatut
parents:
diff changeset
35 </tests>
e8e0f835b4b6 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 11b919f18ba85a40ff0ff4df82aac9be6da188c5-dirty
bebatut
parents:
diff changeset
36
e8e0f835b4b6 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 11b919f18ba85a40ff0ff4df82aac9be6da188c5-dirty
bebatut
parents:
diff changeset
37 <help><![CDATA[
e8e0f835b4b6 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 11b919f18ba85a40ff0ff4df82aac9be6da188c5-dirty
bebatut
parents:
diff changeset
38
e8e0f835b4b6 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 11b919f18ba85a40ff0ff4df82aac9be6da188c5-dirty
bebatut
parents:
diff changeset
39 **What it does**
e8e0f835b4b6 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 11b919f18ba85a40ff0ff4df82aac9be6da188c5-dirty
bebatut
parents:
diff changeset
40
30
99fe591b59fb planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit c641bf32192cd4281a14f504fc97f1dc6edd6f7a-dirty
bebatut
parents: 29
diff changeset
41 MetaPhlAn is a computational tool to profile the structure and the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data with species level resolution. For more information, check the `user manual <https://bitbucket.org/biobakery/metaphlan2/>`_.
25
e8e0f835b4b6 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 11b919f18ba85a40ff0ff4df82aac9be6da188c5-dirty
bebatut
parents:
diff changeset
42
30
99fe591b59fb planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit c641bf32192cd4281a14f504fc97f1dc6edd6f7a-dirty
bebatut
parents: 29
diff changeset
43 This tool formats MetaPhlAn2 output to be ready for Krona.
25
e8e0f835b4b6 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 11b919f18ba85a40ff0ff4df82aac9be6da188c5-dirty
bebatut
parents:
diff changeset
44
e8e0f835b4b6 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 11b919f18ba85a40ff0ff4df82aac9be6da188c5-dirty
bebatut
parents:
diff changeset
45 ]]></help>
e8e0f835b4b6 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 11b919f18ba85a40ff0ff4df82aac9be6da188c5-dirty
bebatut
parents:
diff changeset
46
31
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents: 30
diff changeset
47 <expand macro="citations"/>
30
99fe591b59fb planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit c641bf32192cd4281a14f504fc97f1dc6edd6f7a-dirty
bebatut
parents: 29
diff changeset
48 </tool>