Mercurial > repos > immuneml > immuneml_tools

annotate immuneml_yaml.xml @ 3:ed3932e6d616 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
author immuneml
date Thu, 01 Jul 2021 16:51:28 +0000
parents 629e7e403e19
children 2d3dd9ff7e84
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
1 <tool id="immune_ml" name="Run immuneML with any YAML specification" version="@VERSION@.0">
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
2 <description></description>
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
3 <macros>
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
4 <import>prod_macros.xml</import>
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
5 </macros>
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
6 <expand macro="requirements" />
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
7 <command><![CDATA[
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
8
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
9 #if $iml_input
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
10 cp -r ${iml_input.extra_files_path}/result/* . &&
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
11 (mv repertoires/* . &>/dev/null || :) &&
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
12 rm -rf repertoires &&
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
13 #end if
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
14
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
15 #set $input_orig_names = []
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
16 #if $data_input
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
17 #for $input in $data_input
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
18 #set input_orig_names += [str($input.element_identifier)]
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
19 ([ -e ./"$input.element_identifier" ] && echo "File '$input.element_identifier' already exists in the input folder, skipping." || ln -s $input "$input.element_identifier") &&
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
20 #end for#
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
21 #end if
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
22
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
23 cp "$yaml_input" yaml_copy &&
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
24 immune-ml ./yaml_copy ${html_outfile.files_path} --tool GalaxyYamlTool &&
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
25 mv ${html_outfile.files_path}/index.html ${html_outfile} &&
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
26 mv ${html_outfile.files_path}/immuneML_output.zip $archive
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
27
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
28 ]]>
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
29 </command>
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
30 <inputs>
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
31 <param name="yaml_input" type="data" format="txt" label="YAML specification" multiple="false"/>
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
32 <param name="data_input" type="data" multiple="true" label="Additional files" optional="true" help="This field should include individual repertoire files, metadata files, receptor data and others."/>
3
ed3932e6d616 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents: 0
diff changeset
33 <param name="iml_input" type="data" format="immuneml_receptors" label="ImmuneML dataset" optional="true" help="This field accepts ImmuneML datasets, as created by the Create Dataset tool."/>
0
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
34 </inputs>
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
35 <outputs>
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
36 <data format="zip" name="archive" label="Archive: immuneML Analysis"/>
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
37 <data format="html" name="html_outfile" label="Summary: immuneML analysis"/>
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
38 </outputs>
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
39
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
40
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
41 <help><![CDATA[
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
42
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
43
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
44 This Galaxy tool can be used to run any possible YAML-based immuneML analysis in Galaxy.
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
45
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
46 It is typically recommended to use the analysis-specific Galaxy tools for
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
47 `creating datasets <https://galaxy.immuneml.uio.no/root?tool_id=immune_ml_dataset>`_,
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
48 `simulating synthetic data <https://galaxy.immuneml.uio.no/root?tool_id=immuneml_simulate_dataset>`_,
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
49 `implanting synthetic immune signals <https://galaxy.immuneml.uio.no/root?tool_id=immuneml_simulation>`_ or
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
50 `training <https://galaxy.immuneml.uio.no/root?tool_id=immuneml_train_ml_model>`_ and
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
51 `applying <https://galaxy.immuneml.uio.no/root?tool_id=immuneml_apply_ml_model>`_ ML models instead of this tool.
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
52 These other tools are able to export the relevant output files to Galaxy history elements.
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
53
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
54 However, when you want to run the `ExploratoryAnalysis <https://docs.immuneml.uio.no/specification.html#exploratoryanalysis>`_ instruction,
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
55 or other analyses that do not have a corresponding Galaxy tool, this generic tool can be used.
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
56
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
57 For the exhaustive documentation of this tool and an example YAML specification for exploratory analysis, see the tutorial `How to run any AIRR ML analysis in Galaxy <https://docs.immuneml.uio.no/galaxy/galaxy_general_yaml.html>`_.
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
58
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
59
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
60 **Tool output**
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
61
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
62 This Galaxy tool will produce the following history elements:
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
63
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
64 - Summary: immuneML analysis: a HTML page that allows you to browse through all results.
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
65
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
66 - ImmuneML Analysis Archive: a .zip file containing the complete output folder as it was produced by immuneML. This folder
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
67 contains the output of the instruction that was used, including all raw data files.
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
68 Furthermore, the folder contains the complete YAML specification file for the immuneML run, the HTML output and a log file.
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
69
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
70
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
71 ]]>
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
72 </help>
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
73
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
74 </tool>