comparison aplcms_macros.xml @ 3:bb4ffaeba411 draft

"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms commit 1852a90740a2e1e98f576d68164100c46daaf71a"

2:ec8d56a91335

<macros>
    <token name="@TOOL_VERSION@">6.6.6</token>

    <xml name="requirements">
        <requirements>
            <container type="docker">recetox/aplcms:latest</container>
        </requirements>
    </xml>

    <xml name="inputs">
        <inputs>

            <yield />
        </inputs>
    </xml>

    <xml name="history_db">
        <param name="known_table" type="data" format="aplcms_history.feather" label="known_table"
               help="A data table containing the known metabolite ions and previously found features. The table must contain these 18 columns: chemical_formula (optional), HMDB_ID (optional), KEGG_compound_ID (optional), neutral.mass (optional), ion.type (the ion form - optional), m.z (either theoretical or mean observed m/z value of previously found features), Number_profiles_processed (the total number of processed samples to build this database), Percent_found (the percentage of historically processed samples in which the feature appeared), mz_min (minimum  observed m/z value), mz_max (maximum observed m/z value), RT_mean (mean observed retention time), RT_sd (standard deviation of observed retention time), RT_min (minimum observed retention time), RT_max (maximum observed retention time), int_mean.log. (mean observed log intensity), int_sd.log. (standard deviation of observed log intensity), int_min.log. (minimum observed log intensity), int_max.log. (maximum observed log intensity)." />
        <section name="history_db" title="Known-Table settings">
            <param name="match_tol_ppm" type="integer" optional="true" min="0" label="match_tol_ppm (optional)"
                   help="The ppm tolerance to match identified features to known metabolites/features." />
            <param name="new_feature_min_count" type="integer" value="2" min="1" label="new_feature_min_count"

3:bb4ffaeba411

<macros>
    <token name="@TOOL_VERSION@">6.6.6</token>

    <xml name="requirements">
        <requirements>
            <container type="docker">recetox/aplcms:6.6.6-recetox1</container>
        </requirements>
    </xml>

    <xml name="inputs">
        <inputs>

            <yield />
        </inputs>
    </xml>

    <xml name="history_db">
        <param name="known_table" type="data" format="h5" label="known_table"
               help="A data table containing the known metabolite ions and previously found features. The table must contain these 18 columns: chemical_formula (optional), HMDB_ID (optional), KEGG_compound_ID (optional), neutral.mass (optional), ion.type (the ion form - optional), m.z (either theoretical or mean observed m/z value of previously found features), Number_profiles_processed (the total number of processed samples to build this database), Percent_found (the percentage of historically processed samples in which the feature appeared), mz_min (minimum  observed m/z value), mz_max (maximum observed m/z value), RT_mean (mean observed retention time), RT_sd (standard deviation of observed retention time), RT_min (minimum observed retention time), RT_max (maximum observed retention time), int_mean.log. (mean observed log intensity), int_sd.log. (standard deviation of observed log intensity), int_min.log. (minimum observed log intensity), int_max.log. (maximum observed log intensity)." />
        <section name="history_db" title="Known-Table settings">
            <param name="match_tol_ppm" type="integer" optional="true" min="0" label="match_tol_ppm (optional)"
                   help="The ppm tolerance to match identified features to known metabolites/features." />
            <param name="new_feature_min_count" type="integer" value="2" min="1" label="new_feature_min_count"