comparison scpred_preprocess_data.xml @ 1:39b208cca9f1 draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 59503a4ae6f53a7782336df4f82fbd755cfb2933"

0:0cd6c851ccfe

<tool id="scpred_preprocess_data" name="Scpred pre-process" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
    <description>Pre-process input dataset (no train/test split)</description>
    <macros>
        <import>scpred_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        scpred_preprocess_data.R --input-sce-object "${input_sce_object}" --normalised-counts-slot "${norm_counts_slot}" --output-matrix-object "${output_mat_object}" --output-labels "${output_labels}" ]]></command>
    <inputs>
         <param type="data" name="input_sce_object" label="SCE object containing expression data" format="rdata" help="File with serialized SingleCellExperiment object that contains expression matrix" />
         <param type="text" name="norm_counts_slot" value="normcounts" label="Normalised counts slot" help="Slot containing normalised counts in input SCE object" />
    </inputs> 
    <outputs>

1:39b208cca9f1

<tool id="scpred_preprocess_data" name="Scpred pre-process" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
    <description>Pre-process input dataset (no train/test split)</description>
    <macros>
        <import>scpred_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        scpred_preprocess_data.R --input-sce-object "${input_sce_object}" --output-matrix-object "${output_mat_object}" 

        #if $norm_counts_slot
        --normalised-counts-slot "${norm_counts_slot}"
        #end if
        #if $output_labels
        --output-labels "${output_labels}"
        #end if

         ]]></command>
    <inputs>
         <param type="data" name="input_sce_object" label="SCE object containing expression data" format="rdata" help="File with serialized SingleCellExperiment object that contains expression matrix" />
         <param type="text" name="norm_counts_slot" value="normcounts" label="Normalised counts slot" help="Slot containing normalised counts in input SCE object" />
    </inputs> 
    <outputs>