comparison scpred_predict.xml @ 2:051f5801c819 draft

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

1:f0862eb4f999

<tool id="scpred_predict_labels" name="Scpred predict" version="@TOOL_VERSION@+galaxy0">
    <description>Make cell type predictions using trained model.</description>
     <macros>
        <import>scpred_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        scpred_predict.R --input-object "${input_object}" --pred-data "${pred_data}" --test-labels "${test_labels}" --cell-types-column "${cell_types_column}" --output-path "${output_tbl_path}" --plot-path "${plot_path}" --confusion-table "${confusion_table}"
        ]]></command>
    <inputs>
        <param type="data" name="input_object" label="Input SCE object" format="rdata" help="Input SCE object in .rds format" />
        <param type="data" name="pred_data" label="Matrix with query data" format="rdata" help="Path to the input prediction matrix in .rds format"/>
        <param type="data" name="test_labels" format="txt" label="Test labels" help="Path to the test labels file for evalutation of model performance in text format" />

2:051f5801c819

<tool id="scpred_predict_labels" name="Scpred predict" version="@TOOL_VERSION@+galaxy1">
    <description>Make cell type predictions using trained model.</description>
     <macros>
        <import>scpred_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        scpred_predict.R --input-object "${input_object}" --pred-data "${pred_data}" --output-path "${output_tbl_path}"  

        #if $test_labels
        --test-labels "${test_labels}" 
        #end if
        #if $cell_types_column
        --cell-types-column "${cell_types_column}"
        #end if
        #if $plot_path
        --plot-path "${plot_path}"
        #end if
        #if $confusion_table
        --confusion-table "${confusion_table}"
        #end if

        ]]></command>
    <inputs>
        <param type="data" name="input_object" label="Input SCE object" format="rdata" help="Input SCE object in .rds format" />
        <param type="data" name="pred_data" label="Matrix with query data" format="rdata" help="Path to the input prediction matrix in .rds format"/>
        <param type="data" name="test_labels" format="txt" label="Test labels" help="Path to the test labels file for evalutation of model performance in text format" />