Mercurial > repos > azomics > flowsom_cross_comp
comparison FlowSOMMApIndividualFCS.xml @ 1:a1054bd1060a draft
planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit f2ed3cfcc71ccf61cf6058533d217443318fd024
author | azomics |
---|---|
date | Mon, 25 Sep 2023 22:04:40 +0000 |
parents | e796ed5dfd02 |
children | f611ded6c6df |
comparison
equal
deleted
inserted
replaced
0:e796ed5dfd02 | 1:a1054bd1060a |
---|---|
1 <tool id="flowsom_cross_comp" name="Map individual FCS to reference SOM" version="1.0"> | 1 <tool id="flowsom_cross_comp" name="Map individual FCS to reference SOM" version="1.0+galaxy1"> |
2 <description>using FlowSOM.</description> | 2 <description>using FlowSOM.</description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="1.8.0">bioconductor-flowsom</requirement> | 4 <requirement type="package" version="1.16.0">bioconductor-flowsom</requirement> |
5 </requirements> | 5 </requirements> |
6 <stdio> | 6 <stdio> |
7 <exit_code range="10" level="fatal" description="Please provide valid input files (FCS or flowFrame)." /> | 7 <exit_code range="10" level="fatal" description="Please provide valid input files (FCS or flowFrame)."/> |
8 <exit_code range="11" level="fatal" description="Please provide a valid reference SOM tree." /> | 8 <exit_code range="11" level="fatal" description="Please provide a valid reference SOM tree."/> |
9 <exit_code range="12" level="fatal" description="Input files should all be in the same format." /> | 9 <exit_code range="12" level="fatal" description="Input files should all be in the same format."/> |
10 <exit_code range="13" level="fatal" description="There are inconsistencies in marker names between FCS files." /> | 10 <exit_code range="13" level="fatal" description="There are inconsistencies in marker names between FCS files."/> |
11 <exit_code range="14" level="fatal" description="FCS file and reference tree markers are inconsistent." /> | 11 <exit_code range="14" level="fatal" description="FCS file and reference tree markers are inconsistent."/> |
12 </stdio> | 12 </stdio> |
13 <command><![CDATA[ | 13 <command><![CDATA[ |
14 Rscript $__tool_directory__/FlowSOMMApIndividualFCS.R '${reftree}' 'newDataOutput' '${cluster}' '${tablecontent}' '${mfi}' '${stats}' '${mfistats}' '${allstats}' | 14 Rscript $__tool_directory__/FlowSOMMApIndividualFCS.R '${reftree}' 'newDataOutput' '${cluster}' '${tablecontent}' '${mfi}' '${stats}' '${mfistats}' '${allstats}' |
15 #if $plot == "TRUE" | 15 #if $plot == "TRUE" |
16 'newDataTrees' | 16 'newDataTrees' |
28 <param format="fsom" name="reftree" type="data" label="Reference SOM tree"/> | 28 <param format="fsom" name="reftree" type="data" label="Reference SOM tree"/> |
29 <param name="tablecontent" type="select" label="Associate each event to SOM clusters or meta-clusters?"> | 29 <param name="tablecontent" type="select" label="Associate each event to SOM clusters or meta-clusters?"> |
30 <option value="FlowSOM">FlowSOM Clusters</option> | 30 <option value="FlowSOM">FlowSOM Clusters</option> |
31 <option value="meta">Meta-Clusters</option> | 31 <option value="meta">Meta-Clusters</option> |
32 </param> | 32 </param> |
33 <param name="cluster" type="integer" value="10" optional="true" label="Number of expected metaclusters" help="By default, the number of expected metaclusters is set to 10" /> | 33 <param name="cluster" type="integer" value="10" optional="true" label="Number of expected metaclusters" help="By default, the number of expected metaclusters is set to 10"/> |
34 <param name="plot" type="boolean" label="Plot SOM Tree?" checked="false" truevalue="TRUE" falsevalue="FALSE" /> | 34 <param name="plot" type="boolean" label="Plot SOM Tree?" checked="false" truevalue="TRUE" falsevalue="FALSE"/> |
35 <param name="mplot" type="boolean" label="Plot individual marker trees?" checked="false" truevalue="TRUE" falsevalue="FALSE" /> | 35 <param name="mplot" type="boolean" label="Plot individual marker trees?" checked="false" truevalue="TRUE" falsevalue="FALSE"/> |
36 <param name="mfi" type="select" label="Calculate centroids using:"> | 36 <param name="mfi" type="select" label="Calculate centroids using:"> |
37 <option value="mfi" selected="true">Mean Fluorescence Intensity</option> | 37 <option value="mfi" selected="true">Mean Fluorescence Intensity</option> |
38 <option value="mdfi">Median Fluorescence Intensity</option> | 38 <option value="mdfi">Median Fluorescence Intensity</option> |
39 <option value="gmfi">Geometric Mean Fluorescence Intensity</option> | 39 <option value="gmfi">Geometric Mean Fluorescence Intensity</option> |
40 </param> | 40 </param> |
41 </inputs> | 41 </inputs> |
42 <outputs> | 42 <outputs> |
43 <collection type="list" label="Mapping of ${input.name} to ${reftree.name}" name="output"> | 43 <collection type="list" label="Mapping of ${input.name} to ${reftree.name}" name="output"> |
44 <discover_datasets pattern="(?P<name>.*)" directory="newDataOutput" format="flowclr" /> | 44 <discover_datasets pattern="(?P<name>.*)" directory="newDataOutput" format="flowclr"/> |
45 </collection> | 45 </collection> |
46 <data format="flowstat1" name="stats" label="${tablecontent} cluster distribution in ${input.name}"/> | 46 <data format="flowstat1" name="stats" label="${tablecontent} cluster distribution in ${input.name}"/> |
47 <data format="flowstat2" name="mfistats" label="${tablecontent} cluster ${mfi} centroids in ${input.name}"/> | 47 <data format="flowstat2" name="mfistats" label="${tablecontent} cluster ${mfi} centroids in ${input.name}"/> |
48 <data format="flowstat3" name="allstats" label="${tablecontent} cluster descriptive stats of ${input.name}"/> | 48 <data format="flowstat3" name="allstats" label="${tablecontent} cluster descriptive stats of ${input.name}"/> |
49 <collection type="list" label="Tree representations of mapping ${input.name} to ${reftree.name}" name="trees"> | 49 <collection type="list" label="Tree representations of mapping ${input.name} to ${reftree.name}" name="trees"> |
50 <discover_datasets pattern="(?P<name>.*)" directory="newDataTrees" format="png" /> | 50 <discover_datasets pattern="(?P<name>.*)" directory="newDataTrees" format="png"/> |
51 <filter>(plot)</filter> | 51 <filter>(plot)</filter> |
52 </collection> | 52 </collection> |
53 <collection type="list" label="Marker trees from mapping ${input.name} to ${reftree.name}" name="mtrees"> | 53 <collection type="list" label="Marker trees from mapping ${input.name} to ${reftree.name}" name="mtrees"> |
54 <discover_datasets pattern="(?P<name>.*)" directory="newDataMarkers" format="pdf" /> | 54 <discover_datasets pattern="(?P<name>.*)" directory="newDataMarkers" format="pdf"/> |
55 <filter>(mplot)</filter> | 55 <filter>(mplot)</filter> |
56 </collection> | 56 </collection> |
57 </outputs> | 57 </outputs> |
58 <tests> | 58 <tests> |
59 <test> | 59 <test> |
68 <param name="tablecontent" value="meta"/> | 68 <param name="tablecontent" value="meta"/> |
69 <param name="cluster" value="10"/> | 69 <param name="cluster" value="10"/> |
70 <param name="plot" value="FALSE"/> | 70 <param name="plot" value="FALSE"/> |
71 <param name="mplot" value="FALSE"/> | 71 <param name="mplot" value="FALSE"/> |
72 <param name="mfi" value="mfi"/> | 72 <param name="mfi" value="mfi"/> |
73 <output name="stats" file="out1.flowstat1" compare="sim_size"/> | 73 <output name="stats" file="out1.flowstat1" compare="sim_size"/> |
74 <output name="mfistats" file="out1.flowstat2" compare="sim_size"/> | 74 <output name="mfistats" file="out1.flowstat2" compare="sim_size"/> |
75 <output name="allstats" file="out1.flowstat3" compare="sim_size"/> | 75 <output name="allstats" file="out1.flowstat3" compare="sim_size"/> |
76 <output_collection name="output" type="list" count="3"> | 76 <output_collection name="output" type="list" count="3"> |
77 <element name="input1.flowframe_clustered.flowclr" file="run1/input1.flowclr" compare="sim_size"/> | 77 <element name="input1.flowframe_clustered.flowclr" file="run1/input1.flowclr" compare="sim_size"/> |
78 <element name="input2.flowframe_clustered.flowclr" file="run1/input2.flowclr" compare="sim_size"/> | 78 <element name="input2.flowframe_clustered.flowclr" file="run1/input2.flowclr" compare="sim_size"/> |