Mercurial > repos > azomics > flowsom_cross_comp

comparison FlowSOMMApIndividualFCS.xml @ 1:a1054bd1060a draft

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/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 ${reftree.name}" name="output">
44 <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="newDataOutput" format="flowclr" /> 44 <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="newDataOutput" format="flowclr"/>
45 </collection> 45 </collection>
46 <data format="flowstat1" name="stats" label="${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&lt;name&gt;.*)" directory="newDataTrees" format="png" /> 50 <discover_datasets pattern="(?P&lt;name&gt;.*)" 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&lt;name&gt;.*)" directory="newDataMarkers" format="pdf" /> 54 <discover_datasets pattern="(?P&lt;name&gt;.*)" 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"/>