view macros.xml @ 0:10257d6d545b draft

"planemo upload for repository commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
author bgruening
date Thu, 26 Mar 2020 16:38:48 -0400
children c956182d4e2c
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    <token name="@CP_VERSION@">3.1.9</token>
    <token name="@PY_VERSION@">2.7.16</token>
    <token name="@FORMATS@">jpg,png,tiff,bmp,gif,pcx,ppm,psd,pbm,pgm,eps</token>

    <token name="@SPACES@">"    "</token> <!-- four spaces needed for CP pipeline file -->

    <xml name="output_pipeline_macro">
        <data name="out_file" from_work_dir="output" format="txt" label="Output pipeline" />

    <xml name="input_pipeline_macro">
        <param name="input_pipeline" type="data" format="data" label="Pipeline to select"/>

    <xml name="cp_requirements">
            <requirement type="package" version="@CP_VERSION@">cellprofiler</requirement>

    <xml name="py_requirements">
            <requirement type="package" version="@PY_VERSION@">python</requirement>

    <xml name="citations">
            <citation type="bibtex">
            author = {Sun, Yi},
            year = {2020},
            title = {Cellprofiler Galaxy tools},
            publisher = {Github},
            journal = {Github repository},
            url = {},

    <xml name="cmd_modules">
        <command detect_errors="aggressive"><![CDATA[
            python '$script_file' '$inputs' '$input_pipeline'

    <xml name="text_validator">
        <validator type="regex" message="Only numbers, letters, hyphen, underscore and spaces are allowed">^[A-Za-z0-9 _-]*$</validator>

    <xml name="test_input_pipeline_param">
        <param name="input_pipeline" value="common.txt" />

    <xml name="test_out_file" token_file="common.txt">
        <output name="out_file" ftype="txt" file="@FILE@" lines_diff="0"/>
    <xml name="help" token_module="common">
           This tool appends the inputs of the @MODULE@ module to an existing pipeline file (.cppipe)

           Input: existing pipeline file

           Output: new pipeline file

           Combine this tool with "Common" tool and "CellProfiler" tool together to run the current module alone.