Mercurial > repos > ebi-gxa > ct_combine_tool_outputs

annotate ct_macros.xml @ 6:844689a7f66e 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 a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
author ebi-gxa
date Fri, 27 Nov 2020 13:37:40 +0000
parents 846b34f8755e
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
7c7d1ef36bf6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
1 <macros>
6
844689a7f66e "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
ebi-gxa
parents: 4
diff changeset
2 <token name="@TOOL_VERSION@">1.1.1</token>
0
7c7d1ef36bf6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
3 <token name="@HELP@">More information can be found at https://github.com/ebi-gene-expression-group/cell-types-analysis</token>
7c7d1ef36bf6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
4 <token name="@PROFILE@">18.01</token>
7c7d1ef36bf6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
5 <xml name="requirements">
7c7d1ef36bf6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
6 <requirements>
6
844689a7f66e "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
ebi-gxa
parents: 4
diff changeset
7 <requirement type="package" version="0.1.9">cell-types-analysis</requirement>
0
7c7d1ef36bf6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
8 <yield/>
7c7d1ef36bf6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
9 </requirements>
7c7d1ef36bf6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
10 </xml>
7c7d1ef36bf6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
11 <xml name="version">
7c7d1ef36bf6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
12 <version_command><![CDATA[
7c7d1ef36bf6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
13 conda list | grep cell-types-analysis | egrep -o [0-9]\.[0-9]\.[0-9]
7c7d1ef36bf6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
14 ]]></version_command>
7c7d1ef36bf6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
15 </xml>
7c7d1ef36bf6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
16 <token name="@VERSION_HISTORY@"><![CDATA[
7c7d1ef36bf6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
17 **Version history**
6
844689a7f66e "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
ebi-gxa
parents: 4
diff changeset
18 0.1.6+galaxy0: Add removing non-alphanumeric characters from labels in metadata files
0
7c7d1ef36bf6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
19 0.0.5+galaxy0: Initial contribution. Andrey Solovyev, Expression Atlas team https://www.ebi.ac.uk/gxa/home at EMBL-EBI https://www.ebi.ac.uk/.
3
44b6219cba2d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 85476ee7f3b1d96e9d0afb972af1aaa67d990ce4"
ebi-gxa
parents: 1
diff changeset
20 0.0.5+galaxy1: Standardise input/output format into .txt.
0
7c7d1ef36bf6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
21 ]]></token>
4
846b34f8755e "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8c1bd2ab8a3f988e205677a3bb1ffda1e5694fe1"
ebi-gxa
parents: 3
diff changeset
22 <xml name="sem_siml_options">
846b34f8755e "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8c1bd2ab8a3f988e205677a3bb1ffda1e5694fe1"
ebi-gxa
parents: 3
diff changeset
23 <param type="select" name="sem_siml_metric" label="Semantic similarity metric" help="What semantic similarity metric should be used? NB: if include-sem-siml is set to True, make sure to use a metric that is in the [0;1] interval. See https://www.bioconductor.org/packages/release/bioc/html/Onassis.html for more detail.">
846b34f8755e "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8c1bd2ab8a3f988e205677a3bb1ffda1e5694fe1"
ebi-gxa
parents: 3
diff changeset
24 <option value="lin" selected="true">lin</option>
846b34f8755e "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8c1bd2ab8a3f988e205677a3bb1ffda1e5694fe1"
ebi-gxa
parents: 3
diff changeset
25 <option value="jaccard">jaccard</option>
846b34f8755e "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8c1bd2ab8a3f988e205677a3bb1ffda1e5694fe1"
ebi-gxa
parents: 3
diff changeset
26 <option value="jc_norm">jc_norm</option>
846b34f8755e "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8c1bd2ab8a3f988e205677a3bb1ffda1e5694fe1"
ebi-gxa
parents: 3
diff changeset
27 <option value="schlicker">schlicker</option>
846b34f8755e "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8c1bd2ab8a3f988e205677a3bb1ffda1e5694fe1"
ebi-gxa
parents: 3
diff changeset
28 <option value="edge_resnik">edge_resnik</option>
846b34f8755e "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8c1bd2ab8a3f988e205677a3bb1ffda1e5694fe1"
ebi-gxa
parents: 3
diff changeset
29 <option value="sim">sim</option>
846b34f8755e "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8c1bd2ab8a3f988e205677a3bb1ffda1e5694fe1"
ebi-gxa
parents: 3
diff changeset
30 <option value="edge_leachod">edge_leachod</option>
846b34f8755e "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8c1bd2ab8a3f988e205677a3bb1ffda1e5694fe1"
ebi-gxa
parents: 3
diff changeset
31 <option value="edge_slimani">edge_slimani</option>
846b34f8755e "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8c1bd2ab8a3f988e205677a3bb1ffda1e5694fe1"
ebi-gxa
parents: 3
diff changeset
32 <option value="edge_wupalmer">edge_wupalmer</option>
846b34f8755e "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8c1bd2ab8a3f988e205677a3bb1ffda1e5694fe1"
ebi-gxa
parents: 3
diff changeset
33 <option value="edge_rada_lca">edge_rada_lca</option>
846b34f8755e "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8c1bd2ab8a3f988e205677a3bb1ffda1e5694fe1"
ebi-gxa
parents: 3
diff changeset
34 <option value="edge_li">edge_li</option>
846b34f8755e "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8c1bd2ab8a3f988e205677a3bb1ffda1e5694fe1"
ebi-gxa
parents: 3
diff changeset
35 <option value="resnik">resnik</option>
846b34f8755e "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8c1bd2ab8a3f988e205677a3bb1ffda1e5694fe1"
ebi-gxa
parents: 3
diff changeset
36 </param>
846b34f8755e "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8c1bd2ab8a3f988e205677a3bb1ffda1e5694fe1"
ebi-gxa
parents: 3
diff changeset
37 </xml>
6
844689a7f66e "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
ebi-gxa
parents: 4
diff changeset
38 <xml name="sanitize_strings">
844689a7f66e "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
ebi-gxa
parents: 4
diff changeset
39 <sanitizer invalid_char="">
844689a7f66e "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
ebi-gxa
parents: 4
diff changeset
40 <valid initial="string.ascii_letters,string.digits">
844689a7f66e "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
ebi-gxa
parents: 4
diff changeset
41 <add value="_" />
844689a7f66e "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
ebi-gxa
parents: 4
diff changeset
42 <add value="-" />
844689a7f66e "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
ebi-gxa
parents: 4
diff changeset
43 <add value="[" />
844689a7f66e "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
ebi-gxa
parents: 4
diff changeset
44 <add value="]" />
844689a7f66e "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
ebi-gxa
parents: 4
diff changeset
45 <add value=" " />
844689a7f66e "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
ebi-gxa
parents: 4
diff changeset
46 </valid>
844689a7f66e "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
ebi-gxa
parents: 4
diff changeset
47 </sanitizer>
844689a7f66e "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
ebi-gxa
parents: 4
diff changeset
48 </xml>
0
7c7d1ef36bf6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
49 <xml name="citations">
7c7d1ef36bf6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
50 <citations>
7c7d1ef36bf6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
51 <citation type="bibtex">
7c7d1ef36bf6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
52 @misc{github-cell-types-analysis.git,
7c7d1ef36bf6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
53 author = {Andrey Solovyev, EBI Gene Expression Team},
7c7d1ef36bf6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
54 year = {2020},
7c7d1ef36bf6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
55 title = {Suite of scripts for analysis of scRNA-seq cell type classification tool outputs},
7c7d1ef36bf6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
56 publisher = {GitHub},
7c7d1ef36bf6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
57 journal = {GitHub repository},
7c7d1ef36bf6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
58 url = {https://github.com/ebi-gene-expression-group/cell-types-analysis.git},
7c7d1ef36bf6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
59 }
7c7d1ef36bf6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
60 </citation>
1
dc68e75e8ae3 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
ebi-gxa
parents: 0
diff changeset
61 <citation type="doi">10.1101/2020.04.08.032698</citation>
0
7c7d1ef36bf6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
62 <yield />
7c7d1ef36bf6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
63 </citations>
7c7d1ef36bf6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
64 </xml>
1
dc68e75e8ae3 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
ebi-gxa
parents: 0
diff changeset
65 </macros>