<tool id="autospill" name="Autospill" version="0.2.0+galaxy1" profile="19.01" python_template_version="3.5">
    <description>
      calculates spillover coefficients with robust linear models and then refines spillover coefficients iteratively
    </description>
    <requirements>
      <requirement type="package" version="0.2.0">r-autospill</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
      mkdir input_dir;
      #for $fcs in $fcs_list:
        ln -s '$fcs' input_dir/'$fcs.element_identifier';
      #end for

      ## TODO Check that tabular file has the same number of lines that the collection of fcs files.
      ## Check that files given in the tabular file exist in the inputs directory.

      Rscript '$auto_spill_calculate_compensate' input_dir '$fcs_metadata' \${GALAXY_SLOTS:-1};

      #if $get_figure_scatter:
      mkdir all_scatter;
      for suffix in \$(ls | grep figure_scatter | sed 's/figure_scatter_//'); do
        for plot in \$(ls figure_scatter_\$suffix); do
          mv figure_scatter_\$suffix/\$plot all_scatter/\${suffix}__\${plot};
        done;
      done;
      #end if
      ]]></command>
     <configfiles>
      <configfile name="auto_spill_calculate_compensate"><![CDATA[
## calculate_compensation_paper.r
##
## Copyright (c) 2020 VIB (Belgium) and Babraham Institute (United Kingdom)
##
## Software written by Carlos P. Roca, as research funded by the European Union.
##
## This software may be modified and distributed under the terms of the MIT
## license. See the LICENSE file for details.
## Runs a calculation of compensation with autospill, creating all figures and
## tables used in autospill paper.
##
## Requires being called as a batch script with the following two arguments:
##     control.dir    directory with the set of single-color controls
##     control.def.file    csv file defining the names and channels of the
##         single-color controls


library( autospill )


## get directory and csv file with definition of control dataset

args <- commandArgs( TRUE )

if ( length( args ) != 3 ) {
    cat( "ERROR: no arguments with directory, csv file with definition of control dataset and parameter set",
        file = stderr() )
    stop()
}


control.dir <- args[[ 1 ]]
control.def.file <- args[[ 2 ]]

asp <- get.autospill.param()

#if $get_figure_scatter or $get_gates:
## Reduced resolution of plots
asp\$figure.width <- 3.25
asp\$figure.height <- 2.60
asp\$figure.margin <- 1.0

asp\$figure.panel.line.size <- 0.5

asp\$figure.axis.text.size <- 7.0
asp\$figure.axis.title.size <- 7.0

asp\$figure.convergence.point.size <- 1.0
asp\$figure.convergence.line.size <- 0.4

asp\$figure.density.line.size <- 0.4

asp\$figure.gate.scale.expand <- 0.01
asp\$figure.gate.point.size <- 0.4
asp\$figure.gate.line.size <- 0.3
asp\$figure.gate.bar.width <- 0.3
asp\$figure.gate.bar.height <- 10.0
asp\$figure.gate.bar.margin <- 0.0

asp\$figure.matrix.point.size <- 1.2
asp\$figure.matrix.line.size <- 0.4

asp\$figure.scatter.alpha.gate.in <- 0.8
asp\$figure.scatter.alpha.gate.out <- 0.2
asp\$figure.scatter.point.size <- 0.6
asp\$figure.scatter.line.size <- 0.5
asp\$figure.scatter.error.label.size <- 3.0
asp\$figure.scatter.error.label.pos.x <- 0.85
asp\$figure.scatter.error.label.pos.y <- 0.05
asp\$figure.scatter.axis.text.size <- 9.0
asp\$figure.scatter.axis.title.size <- 9.0
## Reduced resolution
#end if

#if $get_figure_scatter:
## triggers generation of compensation plots between pair of channels
asp\$figure.scatter.dir.base <- "figure_scatter"
#end if

#if $get_gates:
## triggers generation of gate figures
asp\$figure.gate.dir <- "figure_gate"
#end if

## triggers generation of a figure with a summary of convergence
asp\$figure.convergence.dir <- "figure_convergence"
asp\$table.spillover.dir <- "table_spillover"

#if $remove_forbidden:
for(c in strsplit('$remove_forbidden', split="")) {
  print(paste0("Removing ",c," from forbidden characters..."))
  asp\$marker.forbidden.char<-gsub(c, "", asp\$marker.forbidden.char)
}
#end if

## Set workers through GALAXY_SLOTS
asp\$worker.process.n<-args[[3]]

flow.control <- read.flow.control( control.dir, control.def.file, asp )

## gate events before calculating spillover

flow.gate <- gate.flow.data( flow.control, asp )


## get initial spillover matrices from untransformed data

marker.spillover.unco.untr <- get.marker.spillover( TRUE, flow.gate,
  flow.control, asp )
#if $get_figure_scatter:
marker.spillover.unco.tran <- get.marker.spillover( FALSE, flow.gate,
  flow.control, asp )
#else:
marker.spillover.unco.tran <- NULL
#end if


## refine spillover matrix iteratively

refine.spillover.result <- refine.spillover( marker.spillover.unco.untr,
  marker.spillover.unco.tran, flow.gate, flow.control, asp )

## Write outputs
write.table(refine.spillover.result\$spillover, file = "spillover.txt", sep="\t", col.names = NA, quote=FALSE)
write.table(refine.spillover.result\$compensation, file = "compensation.txt", sep="\t", col.names = NA, quote=FALSE)
write.table(refine.spillover.result\$convergence, file = "convergence.txt", sep="\t", row.names=FALSE, quote=FALSE)

#if $get_error:
write.table(refine.spillover.result\$error\$inte, file = "error_inte.txt", sep="\t", col.names=NA, quote=FALSE)
write.table(refine.spillover.result\$error\$coef, file = "error_coef.txt", sep="\t", col.names=NA, quote=FALSE)
write.table(refine.spillover.result\$error\$slop, file = "error_slop.txt", sep="\t", col.names=NA, quote=FALSE)
write.table(refine.spillover.result\$error\$skew, file = "error_skew.txt", sep="\t", col.names=NA, quote=FALSE)
#end if

            ]]></configfile>
    </configfiles>

     <inputs>
        <param type="data" name="fcs_list" format="fcs" multiple="true" label="Collection of control FCS files" />
        <param type="data" name="fcs_metadata" format="csv" label="Auxiliary control file" help="Contains metadata for control list. It has to match original names of FCS files uploaded, and those files need to be present in the Collection of control FCS files given." />
        <!-- <param name="param_set" type="select" label="Parameter set" help="Predefined auto-spill parameters set, choose from 'Minimal', 'Final step', 'Paper', or 'Website'">
          <option value="minimal" selected="true">Minimal - no plot generation</option>
          <option value="final.step">Final step - plot generation</option>
          <option value="paper">Paper</option>
          <option value="website">Website</option>
        </param> -->
        <param type="text" name="remove_forbidden" value="" label="Remove characters from autospill's forbidden list of characters" help="Autospill considers all these characters ' !\#$%()*,/:;&amp;?@[\]^{|}~ plus double quotes as forbidden characters. List any of them here to remove them from that list - at a risk of breaking execution." />
        <param type="boolean" name="get_figure_scatter" label="Get scatter" help="If turned On, the tool will produce scatter plots between setups" checked="true"/>
        <param type="boolean" name="get_error" label="Get error matrices/tables" help="If turned On, the tool will produce error matrices for intercepts, coefficients, slope and skewness" checked="false"/>
        <param type="boolean" name="get_gates" label="Get gating information" help="If turned On, gating parameters information will be produced" checked="true"/>
    </inputs>
    <outputs>
      <data name="spillover_matrix" format="tabular" from_work_dir="spillover.txt" label="${tool.name} spillover matrix on ${on_string}"/>
      <data name="compensation_matrix" format="tabular" from_work_dir="compensation.txt" label="${tool.name} compensation matrix on ${on_string}"/>
      <data name="convergence_matrix" format="tabular" from_work_dir="convergence.txt" label="${tool.name} convergence table on ${on_string}"/>
      <data name="convergence_plot" format="png" from_work_dir="figure_convergence/autospill_convergence.png" label="${tool.name} convergence plot on ${on_string}"/>
      <data name="error_inte_matrix" format="tabular" from_work_dir="error_inte.txt" label="${tool.name} error intercepts matrix on ${on_string}">
        <filter>get_error</filter>
      </data>
      <data name="error_coef_matrix" format="tabular" from_work_dir="error_coef.txt" label="${tool.name} error coefficients matrix on ${on_string}">
        <filter>get_error</filter>
      </data>
      <data name="error_slop_matrix" format="tabular" from_work_dir="error_slop.txt" label="${tool.name} error slope matrix on ${on_string}">
        <filter>get_error</filter>
      </data>
      <data name="error_skew_matrix" format="tabular" from_work_dir="error_skew.txt" label="${tool.name} error skewness matrix on ${on_string}">
        <filter>get_error</filter>
      </data>
      <!--
      <collection name="spillover_plots" label="${tool.name} spillover plots on ${on_string}">
        <discover_datasets pattern="__designation_and_ext__" format="png" directory="figure_spillover" visible="true" />
      </collection> -->
      <collection name="gate_plots" label="${tool.name} gate plots on ${on_string}" type="list">
        <discover_datasets pattern="__designation_and_ext__" format="png" directory="figure_gate" />
        <filter>get_gates</filter>
      </collection>
      <collection name="scatter_plots" label="${tool.name} scatter plots on ${on_string}" type="list">
        <discover_datasets pattern="__designation_and_ext__" format="png" directory="all_scatter" />
        <filter>get_figure_scatter</filter>
      </collection>

      <!--
      <collection name="compensation_plots" label="${tool.name} compensation plots on ${on_string}">
        <discover_datasets pattern="__designation_and_ext__" format="png" directory="figure_compensation" visible="true" />
      </collection> -->
    </outputs>
    <tests>
      <test>
        <param name="fcs_list" value="Compensation Controls_FITC Stained Control_001.fcs,Compensation Controls_PE-CF594 Stained Control_025.fcs,Compensation Controls_PE-Cy5.5 Stained Control_027.fcs"/>
        <param name="fcs_metadata" value="fcs_control.csv" ftype="csv"/>
        <param name="get_figure_scatter" value="false"/>
        <param name="get_error" value="false"/>
        <param name="get_gates" value="false"/>
        <output name="spillover_matrix">
          <assert_contents>
            <has_n_lines n="4" />
          </assert_contents>
        </output>
      </test>
    </tests>
    <help><![CDATA[
Autospill: a principled framework that simplifies the analysis of multichromatic flow cytometry data
----------------------------------------------------------------------------------------------------

Calculates spillover coefficients with robust linear models and then refines spillover coefficients iteratively.

**Inputs**

- Collection of control FCS files
- Auxiliary control file: Contains metadata for control list. It has to match original names of FCS files uploaded, and those files need to be present in the Collection of control FCS files given. ​
- Optional list of characters to remove from autospill's forbidden characters (that otherwise autospill replaces with '-').

**Output**

- Spillover matrix
- Compensation matrix
- convergence matrix
- convergence plot
- Gate plots
- Scatter plots between channels

    ]]></help>
    <citations>
        <citation type="bibtex">
@misc{githubautospill,
  author = {Roca, Carlos},
  year = {2020},
  title = {autospill algorithm for calculating spillover coefficients, used to compensate or unmix flow cytometry data.},
  publisher = {GitHub},
  journal = {GitHub repository},
  url = {https://github.com/carlosproca/autospill},
  }</citation>
    <citation type="doi">10.1038/s41467-021-23126-8</citation>
    </citations>
</tool>