comparison pepquery2.xml @ 6:01fd80b15053 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597

5:2045f3b68773

            <conditional name="input_type">
                <param name="input_type_selector" argument="-t" type="select" label="Input Type" help="" >
                    <option value="peptide">peptide</option>
                    <option value="protein">protein</option>
                    <option value="DNA">DNA (translate to protein sequences)</option>
                    <!-- these are not working with pepquery version 1.6
                    <option value="3">VCF (translate to protein sequences)</option>
                    <option value="4">BED (translate to protein sequences)</option>
                    <option value="5">GTF (translate to protein sequences)</option>
                    -->
                </param>
                <when value="peptide">
                    <conditional name="multiple">
                        <param name="peptide_input_selector" type="select" label="Peptides?">
                            <option value="multiple">Peptide list from your history</option>

                        <option value="4">4</option>
                        <option value="5">5</option>
                        <option value="6">6</option>
                    </param>
                </when>
                <!-- these are not working with pepquery version 1.6
                <when value="3">   
                    <param name="input" type="data" format="vcf" label="VCF File" argument="-i" help="" />
                    <param name="anno" type="data_collection" label="Annotation Files" argument="-anno" help="Annotation files for the VCF file. Please follow preparation instructions here: http://bioconductor.org/packages/devel/bioc/html/PGA.html" />
                </when>
                <when value="4">   
                    <param name="input" type="data" format="bed" label="BED File" argument="-i" help="" />
                    <param name="anno" type="data_collection" label="Annotation Files" argument="-anno" help="Annotation files for the BED file. Please follow preparation instructions here: http://bioconductor.org/packages/devel/bioc/html/PGA.html" />
                </when>
                <when value="5">   
                    <param name="input" type="data" format="gtf" label="GTF File" argument="-i" help="" />
                    <param name="anno" type="data_collection" label="Annotation Files" argument="-anno" help="Annotation files for the GTF file. Please follow preparation instructions here: http://bioconductor.org/packages/devel/bioc/html/PGA.html" />
                </when>
                -->
            </conditional>
            <conditional name="db_type">
                <param name="db_type_selector" type="select" label="Protein Reference Database from" help="" >
                    <option value="history">history</option>
                    <option value="download">download</option>

        </data> 

    </outputs>
    <tests>
        <!-- Test-1  PepQueryDB peptide gencode:human -->
        <test>
            <conditional name="validation">
                <param name="task_type" value="novel"/>
            </conditional>
            <section name="req_inputs">
                <conditional name="input_type">

            <output name="psm_rank_txt">
                <assert_contents>
                    <has_text text="LVVVGADGVGK" />
                    <not_has_text text="AHSSMVGVNLPQK" />
                    <has_text text="02CPTAC_LUAD_W_BI_20180518_KR_f15:25149:2" />
                </assert_contents>
            </output>
            <output name="log_txt">
                <assert_contents>
                    <has_text text="Ignore peptide (reason: exist in reference database): AHSSMVGVNLPQK" />
                </assert_contents>
            </output>
        </test>

        <!-- Test-2  PepQueryDB peptide gencode:human pep.txt -->
        <test>
            <conditional name="validation">
                <param name="task_type" value="novel"/>
            </conditional>
            <section name="req_inputs">
                <conditional name="input_type">

            <output name="psm_rank_txt">
                <assert_contents>
                    <has_text text="LVVVGADGVGK" />
                    <not_has_text text="AHSSMVGVNLPQK" />
                    <has_text text="02CPTAC_LUAD_W_BI_20180518_KR_f15:25149:2" />
                </assert_contents>
            </output>
            <output name="log_txt">
                <assert_contents>
                    <has_text text="Ignore peptide (reason: exist in reference database): AHSSMVGVNLPQK" />
                </assert_contents>
            </output>
        </test>

        <!-- Test-3  MGF peptide Uniprot.fasta -->
        <test>
            <conditional name="validation">
                <param name="task_type" value="novel"/>
            </conditional>
            <section name="req_inputs">
                <conditional name="input_type">

                </section>
            </section>
            <output name="psm_rank_txt">
                <assert_contents>
                    <has_text text="ELGSSDLTAR" />
                </assert_contents>
            </output>
            <output name="psm_rank_txt">
                <assert_contents>
                    <has_text text="ELGSSDLTAR" />
                    <has_line_matching expression="ELGSSDLTAR\tiTRAQ 4-plex of peptide N-term@0\[144.1\d+\]\t2\tiTRAQ_f4:3:2\t2\t1191.62\d+\t-3.04\d+\t-0.003\d+\t0.0\t1191.6\d+\t596.8\d+\t24.1\d+\t0\t0\t1\t995\t0.002\d+\t1\t0\tYes\t24.1\d+\t24.1\d+"/>
                </assert_contents>
            </output>
        </test>

        <!-- Test-4  PepQueryDB known peptide gencode:human pep.txt -->
        <test>
            <conditional name="validation">
                <param name="task_type" value="known"/>
            </conditional>
            <section name="req_inputs">
                <conditional name="input_type">

            </section>
            <output name="psm_rank_txt">
                <assert_contents>
                    <has_text text="AHSSMVGVNLPQK" />
                    <has_text text="6CPTAC_LUAD_W_BI_20180718_KL_f12:20286:3" />
                </assert_contents>
            </output>
        </test>

    </tests>

6:01fd80b15053

            <conditional name="input_type">
                <param name="input_type_selector" argument="-t" type="select" label="Input Type" help="" >
                    <option value="peptide">peptide</option>
                    <option value="protein">protein</option>
                    <option value="DNA">DNA (translate to protein sequences)</option>
                    <!-- VCF,BED,GTF input options have not been implemented in this tool -->
                </param>
                <when value="peptide">
                    <conditional name="multiple">
                        <param name="peptide_input_selector" type="select" label="Peptides?">
                            <option value="multiple">Peptide list from your history</option>

                        <option value="4">4</option>
                        <option value="5">5</option>
                        <option value="6">6</option>
                    </param>
                </when>
            </conditional>
            <conditional name="db_type">
                <param name="db_type_selector" type="select" label="Protein Reference Database from" help="" >
                    <option value="history">history</option>
                    <option value="download">download</option>

        </data> 

    </outputs>
    <tests>
        <!-- Test-1  PepQueryDB peptide gencode:human -->
        <test expect_num_outputs="2">
            <conditional name="validation">
                <param name="task_type" value="novel"/>
            </conditional>
            <section name="req_inputs">
                <conditional name="input_type">

            <output name="psm_rank_txt">
                <assert_contents>
                    <has_text text="LVVVGADGVGK" />
                    <not_has_text text="AHSSMVGVNLPQK" />
                    <has_text text="02CPTAC_LUAD_W_BI_20180518_KR_f15:25149:2" />
                    <has_n_columns n="22" />
                </assert_contents>
            </output>
            <output name="log_txt">
                <assert_contents>
                    <has_text text="Ignore peptide (reason: exist in reference database): AHSSMVGVNLPQK" />
                </assert_contents>
            </output>
        </test>

        <!-- Test-2  PepQueryDB peptide gencode:human pep.txt -->
        <test expect_num_outputs="2">
            <conditional name="validation">
                <param name="task_type" value="novel"/>
            </conditional>
            <section name="req_inputs">
                <conditional name="input_type">

            <output name="psm_rank_txt">
                <assert_contents>
                    <has_text text="LVVVGADGVGK" />
                    <not_has_text text="AHSSMVGVNLPQK" />
                    <has_text text="02CPTAC_LUAD_W_BI_20180518_KR_f15:25149:2" />
                    <has_n_columns n="22" />
                </assert_contents>
            </output>
            <output name="log_txt">
                <assert_contents>
                    <has_text text="Ignore peptide (reason: exist in reference database): AHSSMVGVNLPQK" />
                </assert_contents>
            </output>
        </test>

        <!-- Test-3  MGF peptide Uniprot.fasta -->
        <test expect_num_outputs="2">
            <conditional name="validation">
                <param name="task_type" value="novel"/>
            </conditional>
            <section name="req_inputs">
                <conditional name="input_type">

                </section>
            </section>
            <output name="psm_rank_txt">
                <assert_contents>
                    <has_text text="ELGSSDLTAR" />
                    <has_line_matching expression="ELGSSDLTAR\tiTRAQ 4-plex of peptide N-term@0\[144.1\d+\]\t2\tiTRAQ_f4:3:2\t2\t1191.62\d+\t-3.04\d+\t-0.003\d+\t0.0\t1191.6\d+\t596.8\d+\t24.1\d+\t0\t0\t1\t995\t0.002\d+\t1\t0\tYes\t24.1\d+\t24.1\d+"/>
                    <has_n_columns n="22" />
                </assert_contents>
            </output>
        </test>

        <!-- Test-4  PepQueryDB known peptide gencode:human pep.txt -->
        <test expect_num_outputs="2">
            <conditional name="validation">
                <param name="task_type" value="known"/>
            </conditional>
            <section name="req_inputs">
                <conditional name="input_type">

            </section>
            <output name="psm_rank_txt">
                <assert_contents>
                    <has_text text="AHSSMVGVNLPQK" />
                    <has_text text="6CPTAC_LUAD_W_BI_20180718_KL_f12:20286:3" />
                    <has_n_columns n="22" />
                </assert_contents>
            </output>
        </test>

    </tests>