Mercurial > repos > azomics > cs_overview_2

annotate crossSampleOverview.xml @ 0:09114b034834 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/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
author azomics
date Wed, 20 May 2020 15:37:35 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
1 <tool id="cross_sample_overview" name="Generate overview information" version="1.1">
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
2 <description>of a multi-sample analysis.</description>
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
3 <requirements>
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
4 <requirement type="package" version="2.0.2">ig-flowtools</requirement>
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
5 </requirements>
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
6 <stdio>
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
7 <exit_code range="1" level="fatal" description="There are too many populations in the input files. The maximum number of populations is 40." />
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
8 <exit_code range="2" level="fatal" description="There are populations inconsistencies between provided inputs." />
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
9 </stdio>
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
10 <command><![CDATA[
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
11 mkdir templates &&
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
12 mkdir -p static/flowtools &&
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
13 mkdir -p static/images/flowtools &&
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
14 export FLOWTOOL='which crossSampleOverview.py' &&
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
15 FLOWTOOLDIR=\$(dirname $FLOWTOOL) &&
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
16 cp $FLOWTOOLDIR/../share/templates/* templates/ &&
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
17 cp -r $FLOWTOOLDIR/../share/static/flowtools/* static/flowtools/ &&
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
18 cp $FLOWTOOLDIR/../share/static/images/flowtools/* static/images/flowtools/ &&
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
19 crossSampleOverview.py -i '${input}' -I '${inputmfi}' -o '${html_file}' -m '${mfi}' -d '${html_file.files_path}' -t 'templates/'
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
20 #for $f in $cs_outputs
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
21 -s $f
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
22 #end for
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
23 ]]>
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
24 </command>
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
25 <inputs>
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
26 <param format="flowstat1" name="input" type="data" label="CrossSample Population Summary Table"/>
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
27 <param format="flowstat2" name="inputmfi" type="data" label="Centroids MFI Summary Table"/>
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
28 <param format="flowmfi" name="mfi" type="data" label="Centroids File from FLOCK"/>
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
29 <param format="flowclr" name="cs_outputs" type="data_collection" collection_type="list" label="Clustered flow files" help="output from a Cross Sample analysis or from mapping individual files to a FlowSOM reference tree."/>
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
30 </inputs>
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
31 <outputs>
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
32 <data format="html" name="html_file" label="Overview of ${input.name}">
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
33 </data>
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
34 </outputs>
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
35 <tests>
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
36 <test>
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
37 <param name="input" value="input.flowstat1"/>
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
38 <param name="inputmfi" value="input.flowstat2"/>
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
39 <param name="mfi" value="input.mfi"/>
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
40 <param name="cs_outputs">
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
41 <collection type="list">
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
42 <element name="input1.flowclr" value="input1.flowclr"/>
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
43 <element name="input2.flowclr" value="input2.flowclr"/>
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
44 <element name="input3.flowclr" value="input3.flowclr"/>
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
45 </collection>
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
46 </param>
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
47 <output name="html_file" file="out.html" compare="sim_size">
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
48 <extra_files type="file" name="csAllMFIs.tsv" value="csAllMFIs.tsv"/>
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
49 <extra_files type="file" name="csOverview.tsv" value="csOverview.tsv"/>
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
50 <extra_files type="file" name="csBoxplotData.json" value="csBoxplotData.json" compare="contains"/>
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
51 </output>
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
52 </test>
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
53 </tests>
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
54 <help><![CDATA[
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
55 This tool generates an overview of the flow analysis results.
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
56
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
57 -----
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
58
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
59 **Input**
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
60
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
61 Input files are tab-separated files containing counts of events in each population for each file compared to reference population patterns, MFI for each marker in each population for each file, and individual files used in the comparison. The output from a Cross Sample analysis as well as from mapping individual files to a FlowSOM reference tree are suitable files.
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
62 The Centroids file can be generated with the following Flow Analysis tool:
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
63
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
64 - Generate the centroids from a flow result file
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
65
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
66 .. class:: warningmark
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
67
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
68 The number of populations or clusters this tool can handle is limited to 40.
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
69
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
70 **Output**
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
71
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
72 The output is a page that allows visualization of the data.
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
73
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
74 .. class:: warningmark
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
75
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
76 *The output of this tool is interactive. However, comments or any other modifications made are not saved when exiting the view.*
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
77
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
78 -----
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
79
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
80 **Example**
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
81
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
82 *Input*
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
83
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
84 Clustered Flow Data - fluorescence intensities per marker and population ID per event::
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
85
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
86 Marker1 Marker2 Marker3 ... Population
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
87 33 47 11 ... 1
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
88 31 64 11 ... 6
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
89 21 62 99 ... 2
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
90 14 34 60 ... 7
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
91 ... ... ... ... ...
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
92
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
93
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
94 Population distribution table::
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
95
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
96 Filename SampleName Pop1 Pop2 Pop3 ...
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
97 File1 Biosample1 0.1 0.25 0.14 ...
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
98 File2 Biosample2 0.02 0.1 0.17 ...
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
99 File3 Biosample3 0.4 0.05 0.21 ...
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
100 File4 Biosample4 0.05 0.3 0.08 ...
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
101 ... ... ... ... ... ...
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
102
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
103 Centroids MFI Summary table::
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
104
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
105 Marker1 Marker2 Marker3 ... Population Percentage SampleName
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
106 154 885 24 ... 1 0.2 Biosample1
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
107 458 74 574 ... 2 0.3 Biosample1
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
108 3 210 86 ... 3 0.05 Biosample1
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
109 ... ... ... ... ... ... ...
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
110 140 921 19 ... 1 0.1 Biosample2
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
111 428 79 508 ... 2 0.25 Biosample2
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
112 9 225 90 ... 3 0.3 Biosample2
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
113 ... ... ... ... ... ... ...
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
114
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
115 Centroids file::
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
116
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
117 Population Marker1 Marker2 Marker3 ...
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
118 1 38 49 10 ...
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
119 2 21 63 100 ...
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
120 3 31 52 45 ...
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
121 4 11 78 25 ...
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
122 ... ... ... ... ...
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
123
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
124 *Output*
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
125
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
126 Summary of the population distribution:
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
127
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
128 The comment field of this table is editable, as well as the population names. The edited values are used to populate the legends of the other graphs. The columns are re-orderable. The 'col visibility' button allows to choose which columns to display. 'CSV', 'PDF' and 'Copy' respectively allow to download a comma-separated values file, a pdf version or to copy to your clipboard in a tab-separated format the current view of the table.
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
129
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
130 .. image:: ./static/images/flowtools/popdistrib.png
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
131
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
132 .. image:: ./static/images/flowtools/edit_popdistrib.png
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
133
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
134
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
135 Stacked plot of the population distribution in each sample:
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
136
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
137 The user can choose which populations to display, and whether to see the data as a bar plot or area plot. The graph displays the proportion of each population within the set of selected populations. The Plotly toolbar allows more control over the display of the graph. There is an option to save the plot as a png file.
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
138
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
139 .. image:: ./static/images/flowtools/stackedA.png
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
140
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
141 .. image:: ./static/images/flowtools/stackedB.png
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
142
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
143
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
144 Parallel coordinates representation of populations:
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
145
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
146 The user can reorder the populations, and choose which samples to display either by selecting them in the legend via checkboxes or by selecting them on the graph. Data selected for display is shown in the table below the graph. Mousing over a line in that table highlights the corresponding line on the graph. The 'col visibility' button allows to choose which columns to display. 'CSV', 'PDF' and 'Copy' respectively allow to download a comma-separated values file, a pdf version or to copy to your clipboard in a tab-separated format the current view of the table.
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
147
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
148 .. image:: ./static/images/flowtools/pcpop.png
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
149
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
150
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
151 Parallel coordinates representation of the data:
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
152
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
153 The user can reorder the markers, and choose which samples and/or populations to display either by selecting them in the legends via checkboxes or by selecting them on the graph. Data selected for display is shown in the table below the graph. Mousing over a line in that table highlights the corresponding line on the graph. The 'col visibility' button allows to choose which columns to display. 'CSV', 'PDF' and 'Copy' respectively allow to download a comma-separated values file, a pdf version or to copy to your clipboard in a tab-separated format the current view of the table.
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
154
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
155 .. image:: ./static/images/flowtools/pcmfi.png
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
156
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
157
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
158 Summary Statistics Boxplots:
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
159
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
160 The user can choose whether to group the boxplots per marker or per population. By default, the values displayed are the 25th, median and 75th percentiles. The whiskers represent 1.5 times the interquartile range. The MFI or the values can be displayed by checking the corresponding checkboxes. The number of markers that can be plotted simultaneously is limited to 5. The number of outliers per data point is limited to 100. If there are more than 100 outliers, they are downsampled randomly to a 100 and a warning message is displayed.
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
161
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
162 .. image:: ./static/images/flowtools/cs_bpt.png
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
163 ]]>
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
164 </help>
09114b034834 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit d572546e2a1a28b33df2f908652e85dd86f5916f"
azomics
parents:
diff changeset
165 </tool>