comparison autospill.xml @ 2:3293c160f73c draft default tip

"planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/autospill commit 71a5a8cb5b80c7971440a2a1c49a68d311366c6f"

1:7f5bf24d5aeb

<tool id="autospill" name="Autospill" version="0.2.0+galaxy0" 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>

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

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

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

          <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="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>

**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. ​


**Output**

- Spillover matrix
- Compensation matrix

2:3293c160f73c

<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>

## 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 )

          <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>

**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