Mercurial > repos > ebi-gxa > garnett_get_std_output

annotate garnett_macros.xml @ 4:212976eeca07 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 660486ba0e1ef2f0195e7c6f75448221ba4640f7"
author ebi-gxa
date Tue, 28 Apr 2020 15:11:36 +0000
parents b108a059b7f7
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
c5f5e64d9666 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
1 <macros>
c5f5e64d9666 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
2 <token name="@TOOL_VERSION@">0.2.8</token>
c5f5e64d9666 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
3 <token name="@HELP@">More information can be found at https://cole-trapnell-lab.github.io/garnett/docs/</token>
c5f5e64d9666 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
4 <token name="@PROFILE@">18.01</token>
c5f5e64d9666 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
5 <xml name="requirements">
c5f5e64d9666 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
6 <requirements>
2
f5c6f85d35bf "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
ebi-gxa
parents: 1
diff changeset
7 <requirement type="package" version="0.0.5">garnett-cli</requirement>
0
c5f5e64d9666 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
8 <yield/>
c5f5e64d9666 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
9 </requirements>
c5f5e64d9666 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
10 </xml>
c5f5e64d9666 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
11 <xml name="version">
c5f5e64d9666 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
12 <version_command><![CDATA[
c5f5e64d9666 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
13 echo $(R --version | grep version | grep -v GNU)", garnett version" $(R --vanilla --slave -e "library(garnett); cat(sessionInfo()\$otherPkgs\$garnett\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
c5f5e64d9666 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
14 ]]></version_command>
c5f5e64d9666 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
15 </xml>
c5f5e64d9666 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
16 <token name="@VERSION_HISTORY@"><![CDATA[
c5f5e64d9666 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
17 **Version history**
c5f5e64d9666 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
18 0.2.8+galaxy0: Initial contribution. Andrey Solovyev, Expression Atlas team https://www.ebi.ac.uk/gxa/home at EMBL-EBI https://www.ebi.ac.uk/.
3
b108a059b7f7 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 85476ee7f3b1d96e9d0afb972af1aaa67d990ce4"
ebi-gxa
parents: 2
diff changeset
19 0.2.8+galaxy1: Minor improvements and bug fixes in IO.
0
c5f5e64d9666 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
20 ]]></token>
c5f5e64d9666 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
21 <xml name="citations">
c5f5e64d9666 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
22 <citations>
c5f5e64d9666 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
23 <citation type="bibtex">
c5f5e64d9666 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
24 @article{,
1
418dfedcf3f1 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 3fc448754d6720855f781caa7938e33d3961b092"
ebi-gxa
parents: 0
diff changeset
25 url = {https://doi.org/10.1038/s41592-019-0535-3},
0
c5f5e64d9666 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
26 author = {Hannah A. Pliner and Jay Shendure and Cole Trapnell},
c5f5e64d9666 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
27 title = {Supervised classification enables rapid annotation of cell atlases},
c5f5e64d9666 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
28 journal = {Nature Methods}
c5f5e64d9666 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
29 }
c5f5e64d9666 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
30 </citation>
c5f5e64d9666 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
31 <citation type="bibtex">
c5f5e64d9666 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
32 @misc{githubgarnett-cli.git,
c5f5e64d9666 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
33 author = {Andrey Solovyev, EBI Gene Expression Team},
c5f5e64d9666 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
34 year = {2019},
c5f5e64d9666 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
35 title = {garnett-cli: command line interface for Garnett tool},
c5f5e64d9666 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
36 publisher = {GitHub},
c5f5e64d9666 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
37 journal = {GitHub repository},
c5f5e64d9666 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
38 url = {https://github.com/ebi-gene-expression-group/garnett-cli.git},
c5f5e64d9666 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
39 }
c5f5e64d9666 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
40 </citation>
c5f5e64d9666 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
41 <yield />
1
418dfedcf3f1 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 3fc448754d6720855f781caa7938e33d3961b092"
ebi-gxa
parents: 0
diff changeset
42 <citation type="doi">10.1101/2020.04.08.032698</citation>
0
c5f5e64d9666 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
43 </citations>
c5f5e64d9666 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
44 </xml>
c5f5e64d9666 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
45 </macros>