comparison query_tabular.xml @ 8:0c95a3f1654f draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 1647065a8e6e8d8c98cd0d2194b695fb9425f541"

7:33d61c89fb8d

<tool id="query_tabular" name="Query Tabular" version="3.0.0">
    <description>using sqlite sql</description>

    <macros>
         <import>macros.xml</import>
    </macros>

    <requirements>
    </requirements>

    <command detect_errors="exit_code"><![CDATA[
        cat '$query_file' &&
        #if $add_to_database.withdb: 
            #if $save_db:
                cp '$add_to_database.withdb' '$sqlitedb' &&

            <param name="sqlquery" value="SELECT * from PSMs"/>
            <conditional name="query_result">
                <param name="header" value="yes"/>
                <param name="header_prefix" value=""/>
            </conditional>
            <output name="output" file="psm_report_out1.tsv"/>
        </test>

        <test>
            <repeat name="tables">
                <param name="table" ftype="tabular" value="psm_report.tsv"/>

            <param name="sqlquery" value="SELECT Scan,&quot;m/z&quot;, &quot;Precursor m/z Error [ppm]&quot;, Sequence, &quot;Protein(s)&quot; FROM PSMs WHERE NOT re_search(', ',&quot;Protein(s)&quot;)"/>
            <conditional name="query_result">
                <param name="header" value="yes"/>
                <param name="header_prefix" value=""/>
            </conditional>
            <output name="output" file="psm_report_out2.tsv"/>
        </test>

        <test>
            <repeat name="tables">
                <param name="table" ftype="tabular" value="psm_report.tsv"/>

                        <param name="header" value="yes"/>
                        <param name="header_prefix" value=""/>
                    </conditional>
                </repeat>
            </section>
            <output name="output" file="psm_dbmod_output.tsv"/>
            <output name="output1" file="psm_dbmod_output1.tsv"/>
        </test>

    </tests>
    <help><![CDATA[
=============

8:0c95a3f1654f

<tool id="query_tabular" name="Query Tabular" version="3.0.1">
    <description>using sqlite sql</description>

    <macros>
         <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        cat '$query_file' &&
        #if $add_to_database.withdb: 
            #if $save_db:
                cp '$add_to_database.withdb' '$sqlitedb' &&

            <param name="sqlquery" value="SELECT * from PSMs"/>
            <conditional name="query_result">
                <param name="header" value="yes"/>
                <param name="header_prefix" value=""/>
            </conditional>
            <output name="output" file="psm_report_out1.tsv" compare="re_match"/>
        </test>

        <test>
            <repeat name="tables">
                <param name="table" ftype="tabular" value="psm_report.tsv"/>

            <param name="sqlquery" value="SELECT Scan,&quot;m/z&quot;, &quot;Precursor m/z Error [ppm]&quot;, Sequence, &quot;Protein(s)&quot; FROM PSMs WHERE NOT re_search(', ',&quot;Protein(s)&quot;)"/>
            <conditional name="query_result">
                <param name="header" value="yes"/>
                <param name="header_prefix" value=""/>
            </conditional>
            <output name="output" file="psm_report_out2.tsv" compare="re_match"/>
        </test>

        <test>
            <repeat name="tables">
                <param name="table" ftype="tabular" value="psm_report.tsv"/>

                        <param name="header" value="yes"/>
                        <param name="header_prefix" value=""/>
                    </conditional>
                </repeat>
            </section>
            <output name="output" file="psm_dbmod_output.tsv" compare="re_match"/>
            <output name="output1" file="psm_dbmod_output1.tsv" compare="re_match"/>
        </test>

    </tests>
    <help><![CDATA[
=============