comparison alevin.xml @ 14:c9944a2600f1 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 20eabb7209eb447bc66450e955291143694b419a

13:e32b215b7c04

<tool id="alevin" name="Alevin" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE_VERSION@">
    <description>Quantification and analysis of 3-prime tagged-end single-cell sequencing data</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        mkdir ./index
        && mkdir ./output
        #if $refTranscriptSource.TranscriptSource != "indexed":

            <section name="optional">
                <param name="keepCBFraction" value="1"/>
                <param name="freqThreshold" value="5"/>
                <param name="dumpMtx" value="true"/>
            </section>
            <output name="quants_mat_mtx" file="alevin_mat_01.mtx" ftype="mtx" sort="true"/>
        </test>
        <test expect_num_outputs="11">
            <conditional name="refTranscriptSource">
                <param name="TranscriptSource" value="history"/>
                <section name="s_index">

                <param name="keepCBFraction" value="1"/>
                <param name="numCellBootstraps" value="2"/>
                <param name="freqThreshold" value="5"/>
                <param name="dumpMtx" value="true"/>
            </section>
            <output name="quants_mat_mtx" file="alevin_mat_02.mtx" ftype="mtx" sort="true"/>
        </test>
        <test expect_num_outputs="8">
            <conditional name="refTranscriptSource">
                <param name="TranscriptSource" value="history"/>
                <section name="s_index">

            <section name="optional">
                <param name="keepCBFraction" value="1"/>
                <param name="freqThreshold" value="5"/>
                <param name="dumpMtx" value="true"/>
            </section>
            <output name="quants_mat_mtx" file="alevin_mat_indropV2.mtx" ftype="mtx" sort="true"/>
        </test>
        <test expect_num_outputs="14">
            <conditional name="refTranscriptSource">
                <param name="TranscriptSource" value="history"/>
                <section name="s_index">

            <param name="tgmap" value="minitxp.tsv"/>
            <param name="output_files" value="dumpFeatures,salmon_log,fragment_length,auxiliar_info,dumpUmiGraph,dumpBfh,commands"/>
            <section name="optional">
                <param name="dumpMtx" value="true"/>
            </section>
            <output name="quants_mat_mtx" file="alevin_mat.mtx" ftype="mtx" sort="true"/>
            <output name="salmon_quant_log" ftype="txt">
                <assert_contents>
                    <has_text text="Index contained 322 targets"/>
                    <has_text text="Counted 14 total reads in the equivalence classes"/>
                </assert_contents>

                </assert_contents>
            </output>
            <output_collection name="umigraphs" type="list" count="14">
                <element name="AGTGGGATCTTAACCT">
                    <assert_contents>
                        <has_size value="4017" delta="1000"/>
                    </assert_contents>
                </element>
            </output_collection>
            <output name="bfh_txt" file="full_data_structure.txt" ftype="txt"/>
        </test>

14:c9944a2600f1

<tool id="alevin" name="Alevin" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE_VERSION@">
    <description>Quantification and analysis of 3-prime tagged-end single-cell sequencing data</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="xrefs"/>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        mkdir ./index
        && mkdir ./output
        #if $refTranscriptSource.TranscriptSource != "indexed":

            <section name="optional">
                <param name="keepCBFraction" value="1"/>
                <param name="freqThreshold" value="5"/>
                <param name="dumpMtx" value="true"/>
            </section>
            <output name="quants_mat_mtx" file="alevin_mat_01.mtx" compare="sim_size" ftype="mtx">
                <assert_contents>
                    <has_text text="MatrixMarket" />
                    <has_n_columns n="5" />
                    <has_n_lines n="105" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="11">
            <conditional name="refTranscriptSource">
                <param name="TranscriptSource" value="history"/>
                <section name="s_index">

                <param name="keepCBFraction" value="1"/>
                <param name="numCellBootstraps" value="2"/>
                <param name="freqThreshold" value="5"/>
                <param name="dumpMtx" value="true"/>
            </section>
            <output name="quants_mat_mtx" file="alevin_mat_02.mtx" compare="sim_size" ftype="mtx" >
                <assert_contents>
                    <has_text text="MatrixMarket" />
                    <has_n_columns n="5" />
                    <has_n_lines n="105" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="8">
            <conditional name="refTranscriptSource">
                <param name="TranscriptSource" value="history"/>
                <section name="s_index">

            <section name="optional">
                <param name="keepCBFraction" value="1"/>
                <param name="freqThreshold" value="5"/>
                <param name="dumpMtx" value="true"/>
            </section>
            <output name="quants_mat_mtx" file="alevin_mat_indropV2.mtx"  compare="sim_size" ftype="mtx">
                <assert_contents>
                    <has_text text="MatrixMarket" />
                    <has_n_columns n="5" />
                    <has_n_lines n="105" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="14">
            <conditional name="refTranscriptSource">
                <param name="TranscriptSource" value="history"/>
                <section name="s_index">

            <param name="tgmap" value="minitxp.tsv"/>
            <param name="output_files" value="dumpFeatures,salmon_log,fragment_length,auxiliar_info,dumpUmiGraph,dumpBfh,commands"/>
            <section name="optional">
                <param name="dumpMtx" value="true"/>
            </section>
            <output name="quants_mat_mtx" file="alevin_mat.mtx"  compare="sim_size" ftype="mtx">
                <assert_contents>
                    <has_text text="MatrixMarket" />
                    <has_n_columns n="5" />
                    <has_n_lines n="17" />
                </assert_contents>
            </output>
            <output name="salmon_quant_log" ftype="txt">
                <assert_contents>
                    <has_text text="Index contained 322 targets"/>
                    <has_text text="Counted 14 total reads in the equivalence classes"/>
                </assert_contents>

                </assert_contents>
            </output>
            <output_collection name="umigraphs" type="list" count="14">
                <element name="AGTGGGATCTTAACCT">
                    <assert_contents>
                        <has_size value="4661" delta="1000"/>
                    </assert_contents>
                </element>
            </output_collection>
            <output name="bfh_txt" file="full_data_structure.txt" ftype="txt"/>
        </test>