annotate cite_seq_count.xml @ 0:3df3d1b51110 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f

<tool name="CITE-seq-Count" id="cite_seq_count" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>Count CMO/HTO</description>
    <macros>
        <token name="@TOOL_VERSION@">1.4.4</token>
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>
    <edam_topics>
        <edam_topic>topic_3170</edam_topic>
        <edam_topic>topic_4028</edam_topic>
        <edam_topic>topic_3308</edam_topic>
    </edam_topics>
    <xrefs>
        <xref type="bio.tools">CITE-seq-Count</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">cite-seq-count</requirement>
        <requirement type="package" version="3.7.12">python</requirement>
        <requirement type="package" version="1.0.0">umi_tools</requirement>
        <requirement type="package" version="0.20.7">python-levenshtein</requirement>
        <requirement type="package" version="0.20.7">levenshtein</requirement>
        <requirement type="package" version="0.25.3">pandas</requirement>
        <requirement type="package" version="1.0.0">umi_tools</requirement>
        <!-- The next dependencies are here to help conda to solve the environment -->
        <requirement type="package" version="1.0.8">bzip2</requirement>
        <requirement type="package" version="2.5.0">expat</requirement>
        <requirement type="package" version="0.70.14">multiprocess</requirement>
        <requirement type="package" version="1.21.6">numpy</requirement>
        <requirement type="package" version="0.16">pysam</requirement>
        <requirement type="package" version="1.7.3">scipy</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" level="fatal"/>
    </stdio>
    <version_command>CITE-seq-Count --version</version_command>
    <command><![CDATA[
## This is taken from the star solo wrapper:
## Check that the input pairs are of the same type.
## We consume either repeats of two inputs R1 + R2
## or a collection of paired reads.
#if str($input_types.use) == "repeat":
    #assert len(str($input_types.input1).split(",")) == len(str($input_types.input2).split(","))
    #set $reads1 = $input_types.input1
    #set $reads2 = $input_types.input2
#elif str($input_types.use) == "list_paired":
    #set $reads1 = $input_types.input_collection.forward
    #set $reads2 = $input_types.input_collection.reverse
#end if
CITE-seq-Count 
--threads \${GALAXY_SLOTS:-4}
--read1 '$reads1'
--read2 '$reads2'
--tags '$tags'
## Chemistry:
#if str($params.chemistry) == "v2":
--cell_barcode_first_base 1
--cell_barcode_last_base 16
--umi_first_base 17
--umi_last_base 26
#else if str($params.chemistry) == "v3":
--cell_barcode_first_base 1
--cell_barcode_last_base 16
--umi_first_base 17
--umi_last_base 28
#else if str($params.chemistry) == "custom":
--cell_barcode_first_base $params.cell_barcode_first_base
--cell_barcode_last_base $params.cell_barcode_last_base
--umi_first_base $params.umi_first_base
--umi_last_base $params.umi_last_base
#end if
--bc_collapsing_dist $bc_collapsing_dist
--umi_collapsing_dist $umi_collapsing_dist
$no_umi_correction
--expected_cells $expected_cells
#if $whitelist:
--whitelist '$whitelist'
#end if
--max-error $max_error
#if str($start_trim) != "0":
--start-trim $start_trim
#end if
$sliding_window
$dense
#if str($first_n) != "0":
--first_n $first_n
#end if
#if str($unmapped.output) == "true":
--unknown-top-tags $unknown_top_tags
#end if

## Outputs are gzip
&& gunzip Results/read_count/barcodes.tsv.gz
&& gunzip Results/read_count/features.tsv.gz
&& gunzip Results/read_count/matrix.mtx.gz
&& gunzip Results/umi_count/barcodes.tsv.gz
&& gunzip Results/umi_count/features.tsv.gz
&& gunzip Results/umi_count/matrix.mtx.gz
]]>
</command>
    <inputs>
        <conditional name="input_types" >
            <param name="use" type="select" label="Input Type" >
                <option value="repeat" >Separate barcode and CMO/HTO reads</option>
                <option value="list_paired" >Paired collection of barcode and CMO/HTO reads</option>
            </param>
            <when value="repeat">
                <param format="fastq.gz,fastqsanger.gz" name="input1" type="data"  multiple="true"
                label="RNA-Seq FASTQ file, Barcode reads" />
                <param format="fastq.gz,fastqsanger.gz" name="input2" type="data"  multiple="true"
                label="RNA-Seq FASTQ file, HTO/CMO reads"/>
            </when>
            <when value="list_paired">
                <param name="input_collection" collection_type="paired" type="data_collection" format="fastq.gz,fastqsanger.gz" label="Collection of Pairs" />
            </when>
        </conditional>
        <param argument="--tags" type="data" format="csv" label="the CMO/HTO barcodes as well as their respective names" help="first column is the sequence and second column is the name" />
        <conditional name="params" >
            <param name="chemistry" type="select" label="Configure Chemistry Options">
                <option value="v2" selected="true">Chromium Chemistry v2</option>
                <option value="v3">Chromium Chemistry v3</option>
                <option value="custom">Custom</option>
            </param>
            <when value="v2" />
            <when value="v3" />
            <when value="custom" >
                <param argument="--cell_barcode_first_base" type="integer" min="1" value="1" label="Cell Barcode First Base" />
                <param argument="--cell_barcode_last_base" type="integer" min="1" value="16" label="Cell Barcode Last Base" />
                <param argument="--umi_first_base" type="integer" min="1" value="17" label="UMI First Base" />
                <param argument="--umi_last_base" type="integer" min="1" value="26" label="UMI Last Base" />
            </when>
        </conditional>
        <param argument="--bc_collapsing_dist" type="integer" min="0" value="1" label="How many errors are allowed between two cell barcodes to collapse them onto one cell." />
        <param argument="--umi_collapsing_dist" type="integer" min="0" value="2" label="How many errors are allowed between two umi within the same cell and TAG to collapse." />
        <param argument="--no_umi_correction" type="boolean" truevalue="--no_umi_correction" falsevalue="" checked="false" label="Deactivate UMI correction" />
        <param argument="--expected_cells" type="integer" min="1" value="3000" label="How many cells you expect in your run" />
        <param argument="--whitelist" type="data" format="txt,csv,tsv" label="Whitelist of cell barcodes" optional="true"/>
        <param name="max_error" type="integer" min="0" value="2" label="Maximum Levenshtein distance allowed for CMO/HTO."/>
        <param name="start_trim" type="integer" min="0" value="0" label="How many bases should be trimmed on CMO/HTO read before starting to map"/>
        <param name="sliding_window" type="boolean" truevalue="--sliding-window" falsevalue="" checked="false" label="Activate sliding window alignement."/>
        <param argument="--dense" type="boolean" truevalue="--dense" falsevalue="" checked="false" label="Output in tsv format (in addition to the dense format)"/>
        <param argument="--first_n" type="integer" value="0" label="Select N reads to run on instead of all." />
        <conditional name="unmapped">
            <param name="output" type="select" label="Write table of unknown TAGs to file.">
                <option value="false">No</option>
                <option value="true">Yes</option>
            </param>
            <when value="false"/>
            <when value="true">
            <param name="unknown_top_tags" type="integer" min="1" value="100" label="Top n unmapped TAGs to output."/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="report" format="yaml" label="${tool.name} on ${on_string}: report" from_work_dir="Results/run_report.yaml" />
        <data format="tsv" name="output_features" label="${tool.name} on ${on_string}: Features raw"
            from_work_dir="Results/read_count/features.tsv" />
        <data format="tsv" name="output_barcodes" label="${tool.name} on ${on_string}: Barcodes raw"
            from_work_dir="Results/read_count/barcodes.tsv" />
        <data format="mtx" name="output_matrix" label="${tool.name} on ${on_string}: Matrix Features Counts raw"
            from_work_dir="Results/read_count/matrix.mtx" />
        <data format="tsv" name="output_features_filtered" label="${tool.name} on ${on_string}: Features filtered"
            from_work_dir="Results/umi_count/features.tsv" />
        <data format="tsv" name="output_barcodes_filtered" label="${tool.name} on ${on_string}: Barcodes filtered"
                from_work_dir="Results/umi_count/barcodes.tsv" />
        <data format="mtx" name="output_matrix_filtered" label="${tool.name} on ${on_string}: Matrix Features Counts filtered (UMI)"
            from_work_dir="Results/umi_count/matrix.mtx" />
        <data format="tsv" name="dense_output_matrix" label="${tool.name} on ${on_string}: Dense Matrix With UMI"
            from_work_dir="Results/dense_umis.tsv" >
            <filter>dense</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="7">
            <!-- test 1 -->
            <param name="tags" value="tags.csv"/>
            <param name="expected_cells" value="2"/>
            <param name="whitelist" value="whitelist.txt"/>
            <conditional name="input_types">
                <param name="use" value="repeat"/>
                <param name="input1" value="correct_R1.fastq.gz" ftype="fastqsanger.gz"/>
                <param name="input2" value="correct_R2.fastq.gz" ftype="fastqsanger.gz"/>
            </conditional>
            <conditional name="params" >
                <param name="chemistry" value="v2"/>
            </conditional>
            <output name="report">
                <assert_contents>
                    <has_line line="CITE-seq-Count Version: @TOOL_VERSION@"/>
                    <has_line line="Reads processed: 200"/>
                    <has_line line="Uncorrected cells: 0"/>
                </assert_contents>
            </output>
            <output name="output_barcodes">
                <assert_contents>
                    <has_line line="TAGAGGGAAGTCAAGC"/>
                    <has_line line="TACATATTCTTTACTG"/>
                    <has_n_lines n="4"/>
                </assert_contents>
            </output>
            <output name="output_features">
                <assert_contents>
                    <has_line line="test2-CGTACGTAGCCTAGC-CGTACGTAGCCTAGC"/>
                    <has_line line="test1-CGTAGCTCG-CGTAGCTCG"/>
                    <has_line line="unmapped"/>
                    <has_n_lines n="3"/>
                </assert_contents>
            </output>
            <output name="output_matrix">
                <assert_contents>
                    <has_line_matching expression="[1-2]\s+[1-4]\s+43"/>
                    <has_n_lines n="9"/>
                </assert_contents>
            </output>
            <output name="output_barcodes_filtered">
                <assert_contents>
                    <has_line line="TAGAGGGAAGTCAAGC"/>
                    <has_line line="TACATATTCTTTACTG"/>
                    <has_n_lines n="4"/>
                </assert_contents>
            </output>
            <output name="output_features_filtered">
                <assert_contents>
                    <has_line line="test2-CGTACGTAGCCTAGC-CGTACGTAGCCTAGC"/>
                    <has_line line="test1-CGTAGCTCG-CGTAGCTCG"/>
                    <has_line line="unmapped"/>
                    <has_n_lines n="3"/>
                </assert_contents>
            </output>
            <output name="output_matrix_filtered">
                <assert_contents>
                    <has_line_matching expression="[1-2]\s+[1-4]\s+36"/>
                    <has_n_lines n="9"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="8">
            <!-- test 2 -->
            <!-- change input style use dense no whitelist-->
            <param name="tags" value="tags.csv"/>
            <param name="expected_cells" value="2"/>
            <conditional name="input_types">
                <param name="use" value="list_paired" />
                <param name="input_collection" >
                    <collection type="paired">
                        <element name="forward" value="correct_R1.fastq.gz" ftype="fastqsanger.gz" />
                        <element name="reverse" value="correct_R2.fastq.gz" ftype="fastqsanger.gz" />
                    </collection>
                </param>
            </conditional>
            <conditional name="params" >
                <param name="chemistry" value="v2"/>
            </conditional>
            <param name="dense" value="true"/>
            <output name="report">
                <assert_contents>
                    <has_line line="CITE-seq-Count Version: @TOOL_VERSION@"/>
                    <has_line line="Reads processed: 200"/>
                    <has_line line="Uncorrected cells: 0"/>
                </assert_contents>
            </output>
            <output name="output_barcodes">
                <assert_contents>
                    <has_line line="TAGAGGGAAGTCAAGC"/>
                    <has_line line="TACATATTCTTTACTG"/>
                    <has_n_lines n="2"/>
                </assert_contents>
            </output>
            <output name="output_features">
                <assert_contents>
                    <has_line line="test2-CGTACGTAGCCTAGC-CGTACGTAGCCTAGC"/>
                    <has_line line="test1-CGTAGCTCG-CGTAGCTCG"/>
                    <has_line line="unmapped"/>
                    <has_n_lines n="3"/>
                </assert_contents>
            </output>
            <output name="output_matrix">
                <assert_contents>
                    <has_line_matching expression="[1-2]\s+[1-2]\s+43"/>
                    <has_n_lines n="9"/>
                </assert_contents>
            </output>
            <output name="output_barcodes_filtered">
                <assert_contents>
                    <has_line line="TAGAGGGAAGTCAAGC"/>
                    <has_line line="TACATATTCTTTACTG"/>
                    <has_n_lines n="2"/>
                </assert_contents>
            </output>
            <output name="output_features_filtered">
                <assert_contents>
                    <has_line line="test2-CGTACGTAGCCTAGC-CGTACGTAGCCTAGC"/>
                    <has_line line="test1-CGTAGCTCG-CGTAGCTCG"/>
                    <has_line line="unmapped"/>
                    <has_n_lines n="3"/>
                </assert_contents>
            </output>
            <output name="output_matrix_filtered">
                <assert_contents>
                    <has_line_matching expression="[1-2]\s+[1-2]\s+36"/>
                    <has_n_lines n="9"/>
                </assert_contents>
            </output>
            <output name="dense_output_matrix">
                <assert_contents>
                    <has_line_matching expression="test2-CGTACGTAGCCTAGC-CGTACGTAGCCTAGC\s+2[79]\s+2[79]"/>
                    <has_line_matching expression="test1-CGTAGCTCG-CGTAGCTCG\s+[23][56]\s+[23][56]"/>
                    <has_line_matching expression="unmapped\s+2[17]\s+2[17]"/>
                    <has_n_lines n="4"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="7">
            <!-- test 3 -->
            <!-- custom chemistry max_error 5 -->
            <param name="tags" value="tags.csv"/>
            <param name="expected_cells" value="2"/>
            <param name="whitelist" value="whitelist.txt"/>
            <conditional name="input_types">
                <param name="use" value="repeat"/>
                <param name="input1" value="correct_R1.fastq.gz" ftype="fastqsanger.gz"/>
                <param name="input2" value="correct_R2.fastq.gz" ftype="fastqsanger.gz"/>
            </conditional>
            <conditional name="params" >
                <param name="chemistry" value="custom"/>
                <param name="cell_barcode_first_base" value="1"/>
                <param name="cell_barcode_last_base" value="16"/>
                <param name="umi_first_base" value="17"/>
                <param name="umi_last_base" value="26"/>
            </conditional>
            <param name="max_error" value="5"/>
            <output name="report">
                <assert_contents>
                    <has_line line="CITE-seq-Count Version: @TOOL_VERSION@"/>
                    <has_line line="Reads processed: 200"/>
                    <has_line line="Uncorrected cells: 0"/>
                </assert_contents>
            </output>
            <output name="output_barcodes">
                <assert_contents>
                    <has_line line="TAGAGGGAAGTCAAGC"/>
                    <has_line line="TACATATTCTTTACTG"/>
                    <has_n_lines n="4"/>
                </assert_contents>
            </output>
            <output name="output_features">
                <assert_contents>
                    <has_line line="test2-CGTACGTAGCCTAGC-CGTACGTAGCCTAGC"/>
                    <has_line line="test1-CGTAGCTCG-CGTAGCTCG"/>
                    <has_line line="unmapped"/>
                    <has_n_lines n="3"/>
                </assert_contents>
            </output>
            <output name="output_matrix">
                <assert_contents>
                    <has_line_matching expression="[1-2]\s+[1-4]\s+68"/>
                    <has_n_lines n="7"/>
                </assert_contents>
            </output>
            <output name="output_barcodes_filtered">
                <assert_contents>
                    <has_line line="TAGAGGGAAGTCAAGC"/>
                    <has_line line="TACATATTCTTTACTG"/>
                    <has_n_lines n="4"/>
                </assert_contents>
            </output>
            <output name="output_features_filtered">
                <assert_contents>
                    <has_line line="test2-CGTACGTAGCCTAGC-CGTACGTAGCCTAGC"/>
                    <has_line line="test1-CGTAGCTCG-CGTAGCTCG"/>
                    <has_line line="unmapped"/>
                    <has_n_lines n="3"/>
                </assert_contents>
            </output>
            <output name="output_matrix_filtered">
                <assert_contents>
                    <has_line_matching expression="[1-2]\s+[1-4]\s+52"/>
                    <has_n_lines n="7"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="7">
            <!-- test 4 -->
            <!-- incompatible whitelist -->
            <param name="tags" value="tags.csv"/>
            <param name="expected_cells" value="2"/>
            <param name="whitelist" value="incompatible_whitelist.txt"/>
            <conditional name="input_types">
                <param name="use" value="repeat"/>
                <param name="input1" value="correct_R1.fastq.gz" ftype="fastqsanger.gz"/>
                <param name="input2" value="correct_R2.fastq.gz" ftype="fastqsanger.gz"/>
            </conditional>
            <conditional name="params" >
                <param name="chemistry" value="v2"/>
            </conditional>
            <output name="report">
                <assert_contents>
                    <has_line line="CITE-seq-Count Version: @TOOL_VERSION@"/>
                    <has_line line="Reads processed: 200"/>
                    <has_line line="Uncorrected cells: 0"/>
                </assert_contents>
            </output>
            <output name="output_barcodes">
                <assert_contents>
                    <has_line line="AAAAAAAAAAAAAAAA"/>
                    <has_line line="TTTTTTTTTTTTTTTT"/>
                    <has_n_lines n="2"/>
                </assert_contents>
            </output>
            <output name="output_features">
                <assert_contents>
                    <has_line line="test2-CGTACGTAGCCTAGC-CGTACGTAGCCTAGC"/>
                    <has_line line="test1-CGTAGCTCG-CGTAGCTCG"/>
                    <has_line line="unmapped"/>
                    <has_n_lines n="3"/>
                </assert_contents>
            </output>
            <output name="output_matrix">
                <assert_contents>
                    <has_n_lines n="3"/>
                </assert_contents>
            </output>
            <output name="output_barcodes_filtered">
                <assert_contents>
                    <has_line line="AAAAAAAAAAAAAAAA"/>
                    <has_line line="TTTTTTTTTTTTTTTT"/>
                    <has_n_lines n="2"/>
                </assert_contents>
            </output>
            <output name="output_features_filtered">
                <assert_contents>
                    <has_line line="test2-CGTACGTAGCCTAGC-CGTACGTAGCCTAGC"/>
                    <has_line line="test1-CGTAGCTCG-CGTAGCTCG"/>
                    <has_line line="unmapped"/>
                    <has_n_lines n="3"/>
                </assert_contents>
            </output>
            <output name="output_matrix_filtered">
                <assert_contents>
                    <has_n_lines n="3"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="7">
            <!-- test 5 -->
            <!-- umi_collapsing_dist 5 -->
            <param name="tags" value="tags.csv"/>
            <param name="expected_cells" value="2"/>
            <param name="whitelist" value="whitelist.txt"/>
            <conditional name="input_types">
                <param name="use" value="repeat"/>
                <param name="input1" value="correct_R1.fastq.gz" ftype="fastqsanger.gz"/>
                <param name="input2" value="correct_R2.fastq.gz" ftype="fastqsanger.gz"/>
            </conditional>
            <conditional name="params" >
                <param name="chemistry" value="v2"/>
            </conditional>
            <param name="umi_collapsing_dist" value="5"/>
            <output name="report">
                <assert_contents>
                    <has_line line="CITE-seq-Count Version: @TOOL_VERSION@"/>
                    <has_line line="Reads processed: 200"/>
                    <has_line line="Uncorrected cells: 0"/>
                </assert_contents>
            </output>
            <output name="output_barcodes">
                <assert_contents>
                    <has_line line="TAGAGGGAAGTCAAGC"/>
                    <has_line line="TACATATTCTTTACTG"/>
                    <has_n_lines n="4"/>
                </assert_contents>
            </output>
            <output name="output_features">
                <assert_contents>
                    <has_line line="test2-CGTACGTAGCCTAGC-CGTACGTAGCCTAGC"/>
                    <has_line line="test1-CGTAGCTCG-CGTAGCTCG"/>
                    <has_line line="unmapped"/>
                    <has_n_lines n="3"/>
                </assert_contents>
            </output>
            <output name="output_matrix">
                <assert_contents>
                    <has_line_matching expression="[1-2]\s+[1-4]\s+43"/>
                    <has_n_lines n="9"/>
                </assert_contents>
            </output>
            <output name="output_barcodes_filtered">
                <assert_contents>
                    <has_line line="TAGAGGGAAGTCAAGC"/>
                    <has_line line="TACATATTCTTTACTG"/>
                    <has_n_lines n="4"/>
                </assert_contents>
            </output>
            <output name="output_features_filtered">
                <assert_contents>
                    <has_line line="test2-CGTACGTAGCCTAGC-CGTACGTAGCCTAGC"/>
                    <has_line line="test1-CGTAGCTCG-CGTAGCTCG"/>
                    <has_line line="unmapped"/>
                    <has_n_lines n="3"/>
                </assert_contents>
            </output>
            <output name="output_matrix_filtered">
                <assert_contents>
                    <has_line_matching expression="[1-2]\s+[1-4]\s+10"/>
                    <has_n_lines n="9"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="7">
            <!-- test 6 -->
            <!-- multiple fastqs -->
            <param name="tags" value="tags.csv"/>
            <param name="expected_cells" value="2"/>
            <param name="whitelist" value="whitelist.txt"/>
            <conditional name="input_types">
                <param name="use" value="repeat"/>
                <param name="input1" value="correct_R1.fastq.gz,correct_R1.fastq.gz" ftype="fastqsanger.gz"/>
                <param name="input2" value="correct_R2.fastq.gz,correct_R2.fastq.gz" ftype="fastqsanger.gz"/>
            </conditional>
            <conditional name="params" >
                <param name="chemistry" value="v2"/>
            </conditional>
            <output name="report">
                <assert_contents>
                    <has_line line="CITE-seq-Count Version: @TOOL_VERSION@"/>
                    <has_line line="Reads processed: 400"/>
                    <has_line line="Uncorrected cells: 0"/>
                </assert_contents>
            </output>
            <output name="output_barcodes">
                <assert_contents>
                    <has_line line="TAGAGGGAAGTCAAGC"/>
                    <has_line line="TACATATTCTTTACTG"/>
                    <has_n_lines n="4"/>
                </assert_contents>
            </output>
            <output name="output_features">
                <assert_contents>
                    <has_line line="test2-CGTACGTAGCCTAGC-CGTACGTAGCCTAGC"/>
                    <has_line line="test1-CGTAGCTCG-CGTAGCTCG"/>
                    <has_line line="unmapped"/>
                    <has_n_lines n="3"/>
                </assert_contents>
            </output>
            <output name="output_matrix">
                <assert_contents>
                    <has_line_matching expression="[1-2]\s+[1-4]\s+86"/>
                    <has_n_lines n="9"/>
                </assert_contents>
            </output>
            <output name="output_barcodes_filtered">
                <assert_contents>
                    <has_line line="TAGAGGGAAGTCAAGC"/>
                    <has_line line="TACATATTCTTTACTG"/>
                    <has_n_lines n="4"/>
                </assert_contents>
            </output>
            <output name="output_features_filtered">
                <assert_contents>
                    <has_line line="test2-CGTACGTAGCCTAGC-CGTACGTAGCCTAGC"/>
                    <has_line line="test1-CGTAGCTCG-CGTAGCTCG"/>
                    <has_line line="unmapped"/>
                    <has_n_lines n="3"/>
                </assert_contents>
            </output>
            <output name="output_matrix_filtered">
                <assert_contents>
                    <has_line_matching expression="[1-2]\s+[1-4]\s+36"/>
                    <has_n_lines n="9"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
CITE-seq-Count is a program that outputs UMI and read counts from raw fastq CITE-seq or hashing data.

Here is an image explaining the expected structure of read1 and read2 from the sequencer:

.. image:: read_structure.png
   :alt: Read1: --barcode--|--umi--|TTTT and Read2: --CMO/HTO--|AAA

]]></help>
    <citations>
        <citation type="doi">10.5281/zenodo.2585469</citation>
    </citations>
</tool>