Mercurial > repos > azomics > flowsom_compare
diff FlowSOMCompare.xml @ 0:bd35f3b66a1e draft
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
| author | azomics |
|---|---|
| date | Mon, 22 Jun 2020 17:54:03 -0400 |
| parents | |
| children | 33b8673272cf |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/FlowSOMCompare.xml Mon Jun 22 17:54:03 2020 -0400 @@ -0,0 +1,195 @@ +<tool id="flowsom_compare" name="Compare Samples" version="1.0+galaxy1"> + <description>using a FlowSOM tree</description> + <requirements> + <requirement type="package" version="1.18.0">bioconductor-flowsom</requirement> + </requirements> + <stdio> + <exit_code range="10" level="fatal" description="Please provide valid input FCS files." /> + <exit_code range="11" level="fatal" description="Please provide a valid reference SOM tree." /> + <exit_code range="12" level="fatal" description="There are inconsistencies in markers and/or channels between FCS files." /> + <exit_code range="13" level="fatal" description="FCS file and reference tree markers and/or channels are inconsistent." /> + <exit_code range="14" level="fatal" description="Some FCS files are used more than once." /> + </stdio> + <command><![CDATA[ + Rscript $__tool_directory__/FlowSOMCompare.R '${reftree}' '${groups}' '${plot}' '${thresh}' + #if $count == "TRUE" + 'counts' '${count_out}' + #end if + #if $mean == "TRUE" + 'means' '${mean_out}' + #end if + #if $med == "TRUE" + 'medians' '${med_out}' + #end if + #if $prctg == "TRUE" + 'pctgs' '${p_out}' + #end if + '${name1}' + #for $f in $group1 + '${f}' '${f.name}' + #end for + 'DONE' '${name2}' + #for $ff in $group2 + '${ff}' '${ff.name}' + #end for + ]]> + </command> + <inputs> + <param format="fsom" name="reftree" type="data" label="FlowSOM Reference Tree"/> + <param name="name1" value="Group 1" type="text" label="Label for first group of files" help="This label will be used in the output tables."/> + <param format="fcs" name="group1" type="data_collection" collection_type="list" label="FCS files Collection"/> + <param name="name2" value="Group 2" type="text" label="Label for second group of files" help="This label will be used in the output tables."/> + <param format="fcs" name="group2" type="data_collection" collection_type="list" label="FCS files Collection"/> + <param name="thresh" type="float" value="0.05" label="Wilcox-test threshold for differential" help="By default, the threshold is set to 0.05" /> + <param name="count" type="boolean" label="Output counts of events in clusters for each file?" checked="false" truevalue="TRUE" falsevalue="FALSE" /> + <param name="prctg" type="boolean" label="Output proportions of events in clusters for each file?" checked="false" truevalue="TRUE" falsevalue="FALSE" /> + <param name="mean" type="boolean" label="Output means of proportions for each group?" checked="false" truevalue="TRUE" falsevalue="FALSE" /> + <param name="med" type="boolean" label="Output medians of proportions for each group?" checked="false" truevalue="TRUE" falsevalue="FALSE" /> + </inputs> + <outputs> + <data format="tabular" name="groups" label="Comparison of '${name1}' and '${name2}' to ${reftree.name}"/> + <data format="pdf" name="plot" label="Plot of comparison of '${name1}' and '${name2}' to ${reftree.name}"/> + <data format="tabular" name="count_out" label="Counts of events in samples of '${name1}' and '${name2}' in comparison to ${reftree.name}"> + <filter>(count)</filter> + </data> + <data format="tabular" name="med_out" label="Median of proportions of event in '${name1}' and '${name2}' in comparison to ${reftree.name}"> + <filter>(med)</filter> + </data> + <data format="tabular" name="mean_out" label="Means of proportions of events in '${name1}' and '${name2}' in comparison to ${reftree.name}"> + <filter>(mean)</filter> + </data> + <data format="tabular" name="p_out" label="Proportions of events in samples of '${name1}' and '${name2}' in comparison to ${reftree.name}"> + <filter>(prctg)</filter> + </data> + </outputs> + <tests> + <test> + <param name="reftree" value="reftree.fsom"/> + <param name="name1" value="Group 1"/> + <param name="thresh" value="0.05"/> + <param name="group1"> + <collection type="list"> + <element name="input1.fcs" value="input1.fcs"/> + </collection> + </param> + <param name="name2" value="Group 2"/> + <param name="group2"> + <collection type="list"> + <element name="input2.fcs" value="input2.fcs"/> + <element name="input3.fcs" value="input3.fcs"/> + </collection> + </param> + <param name="count" value="FALSE"/> + <param name="mean" value="FALSE"/> + <param name="med" value="FALSE"/> + <param name="prctg" value="FALSE"/> + <output name="groups" file="out1.tabular" compare="sim_size"/> + <output name="plot" file="out1.pdf" compare="sim_size" delta="100000"/> + </test> + <test> + <param name="reftree" value="reftree.fsom"/> + <param name="name1" value="Group 1"/> + <param name="thresh" value="0.05"/> + <param name="group1"> + <collection type="list"> + <element name="input1.fcs" value="input1.fcs"/> + </collection> + </param> + <param name="name2" value="Group 2"/> + <param name="group2"> + <collection type="list"> + <element name="input2.fcs" value="input2.fcs"/> + <element name="input3.fcs" value="input3.fcs"/> + </collection> + </param> + <param name="count" value="TRUE"/> + <param name="mean" value="TRUE"/> + <param name="med" value="TRUE"/> + <param name="prctg" value="TRUE"/> + <output name="groups" file="out2.tabular" compare="sim_size"/> + <output name="plot" file="out2.pdf" compare="sim_size" delta="100000"/> + <output name="count_out" file="count.tabular" compare="sim_size"/> + <output name="mean_out" file="mean.tabular" compare="sim_size"/> + <output name="med_out" file="median.tabular" compare="sim_size"/> + <output name="p_out" file="prop.tabular" compare="sim_size"/> + </test> + </tests> + <help><![CDATA[ +Compare sample +------------------- + +This tool uses FlowSOM to compare two or more groups of files to a reference FlowSOM tree. + +**Input** + +This tool requires a reference FlowSOM tree, as well as two dataset collections of FCS files. Each group is compared to the reference tree. The statistical differential threshold is based on a Wilcox-test, with a p-value of 0.05 by default. + +.. class:: infomark + +If there is only one group to compare to the tree, the first set of FCS files should be the one used to generate the reference tree. + +**Output** + +This tool generates a table with groups attribution to each FlowSOM node, as well as a plot per comparison. Tables of counts, mean, median, proportion and normalized mean per node and files or groups are optionally produced. + +----- + +**Example** + +*Output* - Node Table:: + + Node Group1-Group2 + 1 group1 + 2 -- + 3 group2 + 4 group1 + ... ... + +*Output* - Counts of events in file per node Table:: + + Filename filename1 filename2 filename3 filename4 ... + Group group1 group1 group2 group2 ... + 1 17 2230 18 5054 ... + 2 760 9 249 178 ... + 3 155 9 1337 4 ... + 4 53 2 1754 0 ... + 5 42 1739 140 1320 ... + ... ... ... ... ... ... + +*Output* - Proportion of events in file per node Table:: + + Filename filename1 filename2 filename3 filename4 ... + Group group1 group1 group2 group2 ... + 1 0.0002528 0.0346386 0.0003068 0.0905507 ... + 2 0.0113029 0.0001397 0.0042441 0.0031891 ... + 3 0.0023052 0.0001397 0.0227888 7.1666606 ... + 4 0.0007882 3.1066030 0.0298965 0.00017 ... + 5 0.0006246 0.0270119 0.0023862 0.2365714 ... + ... ... ... ... ... ... + +*Output* - Means of proportions of events in group per node Table:: + + Nodes group1 group2 + 1 0.00025 0.01747 + 2 0.01130 0.00219 + 3 0.00230 0.01146 + 4 0.00078 0.01496 + 5 0.00062 0.01469 + ... ... ... + +*Output* - Medians of proportions of events in group per node Table:: + + Nodes group1 group2 + 1 0.00025 0.01747 + 2 0.01130 0.00219 + 3 0.00230 0.01146 + 4 0.00078 0.01496 + 5 0.00062 0.01469 + ... ... ... + + ]]> + </help> + <citations> + <citation type="doi">10.1002/cyto.a.22625</citation> + </citations> +</tool>