comparison samtools_view.xml @ 15:6be888be75f9 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a

14:5826298f6a73

<tool id="samtools_view" name="Samtools view" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
    <description>- reformat, filter, or subsample SAM, BAM or CRAM</description>
    <macros>
        <import>macros.xml</import>
        <token name="@REF_DATA@">
            ## additional reference data

                    #if $input.is_of_type('sam') or $std_filters or $reg_filters:
                        ## There is no index or we cannot use it because we are
                        ## not dealing with all of the reads in the indexed
                        ## file. We have to do an extra pass over the input to
                        ## count the reads to subsample.
                        sample_fragment=`samtools view -c $std_filters infile $reg_filters | awk '{s=\$1} END {frac=s/${mode.subsample_config.subsampling_mode.target}; printf("%.8f\n", frac > 1 ? $seed+1/frac : ".0")}'` &&
                    #else:
                        ## We can get the count of reads to subsample using
                        ## an inexpensive call to idxstats.
                        sample_fragment=`samtools idxstats infile | awk '{s+=\$4+\$3} END {frac=s/${mode.subsample_config.subsampling_mode.target}; printf("%.8f\n", frac > 1 ? $seed+1/frac : ".0")}'` &&
                    #end if
                #end if
            #end if

            ## call samtools view

            ## filter options (except regions filter, which is the last parameter)
            $std_filters

            #if $with_subsampling:
                #if str($mode.subsample_config.subsampling_mode.select_subsample) == "target":
                    ##this is calculated at execution time before the main samtools command
                    -s \${sample_fragment}
                #else:
                    #set $fraction = $seed + 1 / float($mode.subsample_config.subsampling_mode.factor)
                    -s $fraction
                #end if
            #end if

            ## output options
            #if str($mode.output_options.reads_report_type) == 'count':

        <data name="outputcnt" format="tabular" from_work_dir="outfile" label="${tool.name} on ${on_string}: Counts">
            <filter>mode['outtype'] != 'header' and mode['output_options']['reads_report_type'] == 'count'</filter>
        </data>
    </outputs>
    <tests>
<!-- 1) sam to bam (copied from the sam_to_bam tool) -->
        <test>
            <param name="input" ftype="sam" value="in_test_1.sam" />
            <output name="outputsam" ftype="bam" file="test_1.bam" lines_diff="4" />
        </test>
        <!-- 2) -->
        <test>
            <param name="input" ftype="sam" dbkey="equCab2" value="in_test_1.sam" />
            <conditional name="addref_cond">
                <param name="addref_select" value="cached" />
                <param name="ref" value="equCab2chrM" />
            </conditional>
            <output name="outputsam" ftype="bam" file="test_2.bam" lines_diff="4" />
        </test>
        <!-- 3) -->
        <test>
            <param name="input" ftype="sam" value="in_test_3.sam" />
            <conditional name="addref_cond">
                <param name="addref_select" value="history" />
                <param name="ref" ftype="fasta" dbkey="equCab2" value="chr_m.fasta" />
            </conditional>
            <output name="outputsam" ftype="bam" file="test_3.bam" lines_diff="4" />
        </test>
        <!-- 4) cram to bam -->
        <test>
            <param name="input" value="in_test_4.cram" ftype="cram" />
            <conditional name="addref_cond">
                <param name="addref_select" value="history" />
                <param name="ref" value="test.fa" />
            </conditional>
            <output name="outputsam" file="test_4.bam" ftype="bam" lines_diff="4" />
        </test>
        <!-- 5) within bam operations expected to result in sorting or not -->
        <test >
            <!-- sorted bam should always result in unmodifed output -->
            <param name="input" ftype="bam" value="in_test_5.bam" />
            <assert_command>
                <not_has_text text="samtools sort" />
            </assert_command>
            <output name="outputsam" ftype="bam" file="test_5.bam" lines_diff="2"/>
        </test>
        <!-- 6) -->
        <test>
            <!-- sorted bam should always result in unmodifed output -->
            <param name="input" ftype="bam" value="in_test_5.bam" />
            <conditional name="mode">
                <conditional name="output_options">
                    <conditional name="output_format">

                <not_has_text text="samtools sort" />
            </assert_command>
            <output name="outputsam" ftype="bam" file="test_5.bam" lines_diff="2"/>
        </test>
        <!-- 7) -->
        <test>
            <!-- qname_sorted.bam should get sorted during "conversion" to bam ... -->
            <param name="input" ftype="qname_sorted.bam" value="in_test_7.bam" />
            <assert_command>
                <has_text text="samtools sort" />
            </assert_command>
            <output name="outputsam" ftype="bam" file="test_7.bam" lines_diff="4" />
        </test>
        <!-- 8) -->
        <test>
            <!-- ... but should be emitted unmodifed when using input format -->
            <param name="input" ftype="qname_sorted.bam" value="in_test_7.bam" />
            <conditional name="mode">
                <conditional name="output_options">
                    <conditional name="output_format">

                <not_has_text text="samtools sort" />
            </assert_command>
            <output name="outputsam" ftype="qname_sorted.bam" file="test_8.bam" lines_diff="2"/>
        </test>
        <!-- 9) -->
        <test>
            <!-- unsorted.bam should get sorted during "conversion" to bam ... -->
            <param name="input" ftype="unsorted.bam" value="in_test_7.bam" />
            <assert_command>
                <has_text text="samtools sort" />
            </assert_command>
            <output name="outputsam" ftype="bam" file="test_7.bam" lines_diff="4" />
        </test>
        <!-- 10) -->
        <test>
            <!-- ... ... but should be emitted unmodifed when using input format -->
            <param name="input" ftype="unsorted.bam" value="in_test_7.bam" />
            <conditional name="mode">
                <conditional name="output_options">
                    <conditional name="output_format">

                <not_has_text text="samtools sort" />
            </assert_command>
            <output name="outputsam" ftype="unsorted.bam" file="test_8.bam" lines_diff="2" />
        </test>
        <!-- 11) bam to sam + header options (adapted from bam_to_sam tool)-->
        <test>
            <param ftype="bam" name="input" value="in_test_11.bam" />
            <conditional name="mode">
                <conditional name="output_options">
                    <conditional name="output_format">
                        <param name="oformat" value="sam" />

                </conditional>
            </conditional>
            <output file="test_11.sam" ftype="sam" name="outputsam" lines_diff="2" />
        </test>
        <!-- 12) -->
        <test>
            <param ftype="bam" name="input" value="in_test_11.bam" />
            <conditional name="mode">
                <param name="outtype" value="header" />
                <conditional name="output_options">
                    <conditional name="output_format">

                </conditional>
            </conditional>
            <output file="test_12.sam" ftype="sam" name="outputsam" lines_diff="2" />
        </test>
        <!-- 13) -->
        <test>
            <param ftype="bam" name="input" value="in_test_11.bam" />
            <conditional name="mode">
                <conditional name="output_options">
                    <conditional name="output_format">
                        <param name="oformat" value="sam" />

                </conditional>
            </conditional>
            <output file="test_13.sam" ftype="sam" name="outputsam" lines_diff="2" />
        </test>
        <!-- 14) count alignments -->
        <test>
            <param name="input" value="in_test_14.bam" ftype="bam" />
            <conditional name="mode">
                <param name="outtype" value="all_reads" />
                <conditional name="output_options">
                    <param name="reads_report_type" value="count" />
                </conditional>
            </conditional>
            <output name="outputcnt" file="test_14.tab" ftype="tabular" lines_diff="2" />
        </test>
        <!-- 15) region filters -->
        <test>
            <param name="input" value="in_test_15.sam" ftype="sam" />
            <conditional name="mode">
                <param name="outtype" value="selected_reads" />
                <section name="filter_config">
                    <conditional name="cond_region">

                <param name="ref" value="test.fa" />
            </conditional>
            <output name="outputsam" file="test_15.cram" ftype="cram" compare="sim_size" delta="250" />
        </test>
        <!-- 16) -->
        <test>
            <param name="input" value="in_test_14.bam" ftype="bam" />
            <conditional name="mode">
                <param name="outtype" value="selected_reads" />
                <section name="filter_config">
                    <conditional name="cond_region">

                <param name="ref" value="test.fa" />
            </conditional>
            <output name="outputsam" file="test_15.cram" ftype="cram" compare="sim_size" delta="250" />
        </test>
        <!-- 17) -->
        <test>
            <param name="input" value="in_test_17.cram" dbkey="equCab2" ftype="cram" />
            <conditional name="mode">
                <param name="outtype" value="selected_reads" />
                <section name="filter_config">
                    <conditional name="cond_region">

                <param name="ref" value="equCab2chrM" />
            </conditional>
            <output name="outputsam" file="test_17.bam" ftype="bam" lines_diff="4" />
        </test>
        <!-- 18) -->
        <test>
            <param name="input" value="in_test_14.bam" ftype="bam" />
            <conditional name="mode">
                <param name="outtype" value="selected_reads" />
                <section name="filter_config">
                    <conditional name="cond_region">

                <param name="ref" value="test.fa" />
            </conditional>
            <output name="outputsam" file="test_15.cram" ftype="cram" compare="sim_size" delta="250" />
        </test>
        <!-- 19) -->
        <test>
            <param name="input" value="test_15.cram" ftype="cram" />
            <conditional name="mode">
                <param name="outtype" value="selected_reads" />
                <section name="filter_config">
                    <conditional name="cond_region">

                <param name="ref" value="test.fa" />
            </conditional>
            <output name="outputsam" file="test_19.bam" ftype="bam" lines_diff="4"/>
        </test>
        <!-- 20) -->
        <test>
            <param name="input" value="test_15.cram" ftype="cram" />
            <conditional name="mode">
                <param name="outtype" value="selected_reads" />
                <section name="filter_config">
                    <conditional name="cond_region">

                <param name="ref" value="test.fa" />
            </conditional>
            <output name="outputsam" file="test_20.bam" ftype="bam" lines_diff="4" />
        </test>
        <!-- 21) sampling options target < total reads -->
        <test>
            <param name="input" value="in_test_15.sam" ftype="sam" />
            <conditional name="mode">
                <param name="outtype" value="selected_reads" />
                <section name="subsample_config">
                    <conditional name="subsampling_mode">

                </conditional>
            </conditional>
            <output name="outputsam" file="test_21.sam" ftype="sam" compare="diff" lines_diff="10" />
        </test>
        <!-- 22) target > total reads -->
        <test>
            <param name="input" value="in_test_15.sam" ftype="sam" />
            <conditional name="mode">
                <param name="outtype" value="selected_reads" />
                <section name="subsample_config">
                    <conditional name="subsampling_mode">

                </conditional>
            </conditional>
            <output name="outputsam" file="test_22.sam" ftype="sam" lines_diff="2"/>
        </test>
        <!-- 23) -->
        <test>
            <!-- subsampling SAM input without reads -->
            <param name="input" value="in_test_23.sam" ftype="sam" />
            <conditional name="mode">
                <param name="outtype" value="selected_reads" />
                <section name="subsample_config">

                </conditional>
            </conditional>
            <output name="outputsam" file="test_23.sam" ftype="sam" lines_diff="2"/>
        </test>
        <!-- 24) -->
        <test>
            <!-- subsampling BAM input without reads -->
            <param name="input" value="in_test_24.bam" ftype="bam" />
            <conditional name="mode">
                <param name="outtype" value="selected_reads" />
                <section name="subsample_config">

                </conditional>
            </conditional>
            <output name="outputsam" file="test_24.bam" ftype="bam" lines_diff="2" />
        </test>
        <!-- 25) -->
        <test>
            <param name="input" value="in_test_15.sam" ftype="sam" />
            <conditional name="mode">
                <param name="outtype" value="selected_reads" />
                <section name="subsample_config">
                    <conditional name="subsampling_mode">

                </conditional>
            </conditional>
            <output name="outputsam" file="test_25.sam" ftype="sam" compare="diff" lines_diff="2" />
        </test>
        <!-- 26) -->
        <test>
            <param name="input" value="in_test_14.bam" ftype="bam" />
            <conditional name="mode">
                <param name="outtype" value="selected_reads" />
                <section name="subsample_config">
                    <conditional name="subsampling_mode">

                </conditional>
            </conditional>
            <output name="outputsam" file="test_26.bam" ftype="bam" lines_diff="2" />
        </test>
        <!-- 27) -->
        <test>
            <param name="input" value="in_test_14.bam" ftype="bam" />
            <conditional name="mode">
                <param name="outtype" value="selected_reads" />
                <section name="subsample_config">
                    <conditional name="subsampling_mode">

                </conditional>
            </conditional>
            <output name="outputsam" file="test_27.bam" ftype="bam" lines_diff="2"/>
        </test>
        <!-- 28) -->
        <test>
            <param name="input" value="in_test_14.bam" ftype="bam" />
            <conditional name="mode">
                <param name="outtype" value="selected_reads" />
                <section name="subsample_config">
                    <conditional name="subsampling_mode">

                </conditional>
            </conditional>
            <output name="outputsam" file="test_28.bam" ftype="bam" lines_diff="2" />
        </test>
        <!-- 29) -->
        <test>
            <param name="input" value="in_test_14.bam" ftype="bam" />
            <conditional name="mode">
                <param name="outtype" value="selected_reads" />
                <section name="subsample_config">
                    <conditional name="subsampling_mode">

                </conditional>
            </conditional>
            <output name="outputsam" file="test_29.bam" ftype="bam" lines_diff="2"/>
        </test>
        <!-- 30) testing tag filtering -->
        <test>
            <param name="input" value="in_test_30.bam" ftype="bam" />
            <conditional name="mode">
                <param name="outtype" value="selected_reads" />
                <section name="filter_config">
                    <param name="tag" value="XS:-18" />

                <has_text text="--tag 'XS:-18'"/>
            </assert_command>
            <output name="outputsam" file="test_30.bam" ftype="bam" lines_diff="2" />
        </test>
        <!-- 31) testing readname filtering -->
        <test>
            <param name="input" value="in_test_30.bam" ftype="bam" />
            <conditional name="mode">
                <param name="outtype" value="selected_reads" />
                <section name="filter_config">
                    <param name="qname_file" value="readnames.txt" />

15:6be888be75f9

<tool id="samtools_view" name="Samtools view" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>- reformat, filter, or subsample SAM, BAM or CRAM</description>
    <macros>
        <import>macros.xml</import>
        <token name="@REF_DATA@">
            ## additional reference data

                    #if $input.is_of_type('sam') or $std_filters or $reg_filters:
                        ## There is no index or we cannot use it because we are
                        ## not dealing with all of the reads in the indexed
                        ## file. We have to do an extra pass over the input to
                        ## count the reads to subsample.
                        sample_fragment=`samtools view -c $std_filters infile $reg_filters | awk '{s=\$1} END {fac=s/${mode.subsample_config.subsampling_mode.target}; printf("%.8f\n", fac > 1 ? 1/fac : 1)}'` &&
                    #else:
                        ## We can get the count of reads to subsample using
                        ## an inexpensive call to idxstats.
                        sample_fragment=`samtools idxstats infile | awk '{s+=\$4+\$3} END {fac=s/${mode.subsample_config.subsampling_mode.target}; printf("%.8f\n", fac > 1 ? 1/fac : 1)}'` &&
                    #end if
                #end if
            #end if

            ## call samtools view

            ## filter options (except regions filter, which is the last parameter)
            $std_filters

            #if $with_subsampling:
                --subsample-seed $seed
                #if str($mode.subsample_config.subsampling_mode.select_subsample) == "target":
                    ##this is calculated at execution time before the main samtools command
                    --subsample \${sample_fragment}
                #else:
                    #set $fraction = 1 / float($mode.subsample_config.subsampling_mode.factor)
                    --subsample $fraction
                #end if
            #end if

            ## output options
            #if str($mode.output_options.reads_report_type) == 'count':

        <data name="outputcnt" format="tabular" from_work_dir="outfile" label="${tool.name} on ${on_string}: Counts">
            <filter>mode['outtype'] != 'header' and mode['output_options']['reads_report_type'] == 'count'</filter>
        </data>
    </outputs>
    <tests>
        <!-- 1) sam to bam (copied from the sam_to_bam tool) -->
        <test expect_num_outputs="1">
            <param name="input" ftype="sam" value="in_test_1.sam" />
            <output name="outputsam" ftype="bam" file="test_1.bam" lines_diff="4" />
        </test>
        <!-- 2) -->
        <test expect_num_outputs="1">
            <param name="input" ftype="sam" dbkey="equCab2" value="in_test_1.sam" />
            <conditional name="addref_cond">
                <param name="addref_select" value="cached" />
                <param name="ref" value="equCab2chrM" />
            </conditional>
            <output name="outputsam" ftype="bam" file="test_2.bam" lines_diff="4" />
        </test>
        <!-- 3) -->
        <test expect_num_outputs="1">
            <param name="input" ftype="sam" value="in_test_3.sam" />
            <conditional name="addref_cond">
                <param name="addref_select" value="history" />
                <param name="ref" ftype="fasta" dbkey="equCab2" value="chr_m.fasta" />
            </conditional>
            <output name="outputsam" ftype="bam" file="test_3.bam" lines_diff="4" />
        </test>
        <!-- 4) cram to bam -->
        <test expect_num_outputs="1">
            <param name="input" value="in_test_4.cram" ftype="cram" />
            <conditional name="addref_cond">
                <param name="addref_select" value="history" />
                <param name="ref" value="test.fa" />
            </conditional>
            <output name="outputsam" file="test_4.bam" ftype="bam" lines_diff="4" />
        </test>
        <!-- 5) within bam operations expected to result in sorting or not -->
        <test expect_num_outputs="1">
            <!-- sorted bam should always result in unmodifed output -->
            <param name="input" ftype="bam" value="in_test_5.bam" />
            <assert_command>
                <not_has_text text="samtools sort" />
            </assert_command>
            <output name="outputsam" ftype="bam" file="test_5.bam" lines_diff="2"/>
        </test>
        <!-- 6) -->
        <test expect_num_outputs="1">
            <!-- sorted bam should always result in unmodifed output -->
            <param name="input" ftype="bam" value="in_test_5.bam" />
            <conditional name="mode">
                <conditional name="output_options">
                    <conditional name="output_format">

                <not_has_text text="samtools sort" />
            </assert_command>
            <output name="outputsam" ftype="bam" file="test_5.bam" lines_diff="2"/>
        </test>
        <!-- 7) -->
        <test expect_num_outputs="1">
            <!-- qname_sorted.bam should get sorted during "conversion" to bam ... -->
            <param name="input" ftype="qname_sorted.bam" value="in_test_7.bam" />
            <assert_command>
                <has_text text="samtools sort" />
            </assert_command>
            <output name="outputsam" ftype="bam" file="test_7.bam" lines_diff="4" />
        </test>
        <!-- 8) -->
        <test expect_num_outputs="1">
            <!-- ... but should be emitted unmodifed when using input format -->
            <param name="input" ftype="qname_sorted.bam" value="in_test_7.bam" />
            <conditional name="mode">
                <conditional name="output_options">
                    <conditional name="output_format">

                <not_has_text text="samtools sort" />
            </assert_command>
            <output name="outputsam" ftype="qname_sorted.bam" file="test_8.bam" lines_diff="2"/>
        </test>
        <!-- 9) -->
        <test expect_num_outputs="1">
            <!-- unsorted.bam should get sorted during "conversion" to bam ... -->
            <param name="input" ftype="unsorted.bam" value="in_test_7.bam" />
            <assert_command>
                <has_text text="samtools sort" />
            </assert_command>
            <output name="outputsam" ftype="bam" file="test_7.bam" lines_diff="4" />
        </test>
        <!-- 10) -->
        <test expect_num_outputs="1">
            <!-- ... ... but should be emitted unmodifed when using input format -->
            <param name="input" ftype="unsorted.bam" value="in_test_7.bam" />
            <conditional name="mode">
                <conditional name="output_options">
                    <conditional name="output_format">

                <not_has_text text="samtools sort" />
            </assert_command>
            <output name="outputsam" ftype="unsorted.bam" file="test_8.bam" lines_diff="2" />
        </test>
        <!-- 11) bam to sam + header options (adapted from bam_to_sam tool)-->
        <test expect_num_outputs="1">
            <param ftype="bam" name="input" value="in_test_11.bam" />
            <conditional name="mode">
                <conditional name="output_options">
                    <conditional name="output_format">
                        <param name="oformat" value="sam" />

                </conditional>
            </conditional>
            <output file="test_11.sam" ftype="sam" name="outputsam" lines_diff="2" />
        </test>
        <!-- 12) -->
        <test expect_num_outputs="1">
            <param ftype="bam" name="input" value="in_test_11.bam" />
            <conditional name="mode">
                <param name="outtype" value="header" />
                <conditional name="output_options">
                    <conditional name="output_format">

                </conditional>
            </conditional>
            <output file="test_12.sam" ftype="sam" name="outputsam" lines_diff="2" />
        </test>
        <!-- 13) -->
        <test expect_num_outputs="1">
            <param ftype="bam" name="input" value="in_test_11.bam" />
            <conditional name="mode">
                <conditional name="output_options">
                    <conditional name="output_format">
                        <param name="oformat" value="sam" />

                </conditional>
            </conditional>
            <output file="test_13.sam" ftype="sam" name="outputsam" lines_diff="2" />
        </test>
        <!-- 14) count alignments -->
        <test expect_num_outputs="1">
            <param name="input" value="in_test_14.bam" ftype="bam" />
            <conditional name="mode">
                <param name="outtype" value="all_reads" />
                <conditional name="output_options">
                    <param name="reads_report_type" value="count" />
                </conditional>
            </conditional>
            <output name="outputcnt" file="test_14.tab" ftype="tabular" lines_diff="2" />
        </test>
        <!-- 15) region filters -->
        <test expect_num_outputs="1">
            <param name="input" value="in_test_15.sam" ftype="sam" />
            <conditional name="mode">
                <param name="outtype" value="selected_reads" />
                <section name="filter_config">
                    <conditional name="cond_region">

                <param name="ref" value="test.fa" />
            </conditional>
            <output name="outputsam" file="test_15.cram" ftype="cram" compare="sim_size" delta="250" />
        </test>
        <!-- 16) -->
        <test expect_num_outputs="1">
            <param name="input" value="in_test_14.bam" ftype="bam" />
            <conditional name="mode">
                <param name="outtype" value="selected_reads" />
                <section name="filter_config">
                    <conditional name="cond_region">

                <param name="ref" value="test.fa" />
            </conditional>
            <output name="outputsam" file="test_15.cram" ftype="cram" compare="sim_size" delta="250" />
        </test>
        <!-- 17) -->
        <test expect_num_outputs="1">
            <param name="input" value="in_test_17.cram" dbkey="equCab2" ftype="cram" />
            <conditional name="mode">
                <param name="outtype" value="selected_reads" />
                <section name="filter_config">
                    <conditional name="cond_region">

                <param name="ref" value="equCab2chrM" />
            </conditional>
            <output name="outputsam" file="test_17.bam" ftype="bam" lines_diff="4" />
        </test>
        <!-- 18) -->
        <test expect_num_outputs="1">
            <param name="input" value="in_test_14.bam" ftype="bam" />
            <conditional name="mode">
                <param name="outtype" value="selected_reads" />
                <section name="filter_config">
                    <conditional name="cond_region">

                <param name="ref" value="test.fa" />
            </conditional>
            <output name="outputsam" file="test_15.cram" ftype="cram" compare="sim_size" delta="250" />
        </test>
        <!-- 19) -->
        <test expect_num_outputs="1">
            <param name="input" value="test_15.cram" ftype="cram" />
            <conditional name="mode">
                <param name="outtype" value="selected_reads" />
                <section name="filter_config">
                    <conditional name="cond_region">

                <param name="ref" value="test.fa" />
            </conditional>
            <output name="outputsam" file="test_19.bam" ftype="bam" lines_diff="4"/>
        </test>
        <!-- 20) -->
        <test expect_num_outputs="1">
            <param name="input" value="test_15.cram" ftype="cram" />
            <conditional name="mode">
                <param name="outtype" value="selected_reads" />
                <section name="filter_config">
                    <conditional name="cond_region">

                <param name="ref" value="test.fa" />
            </conditional>
            <output name="outputsam" file="test_20.bam" ftype="bam" lines_diff="4" />
        </test>
        <!-- 21) sampling options target < total reads -->
        <test expect_num_outputs="1">
            <param name="input" value="in_test_15.sam" ftype="sam" />
            <conditional name="mode">
                <param name="outtype" value="selected_reads" />
                <section name="subsample_config">
                    <conditional name="subsampling_mode">

                </conditional>
            </conditional>
            <output name="outputsam" file="test_21.sam" ftype="sam" compare="diff" lines_diff="10" />
        </test>
        <!-- 22) target > total reads -->
        <test expect_num_outputs="1">
            <param name="input" value="in_test_15.sam" ftype="sam" />
            <conditional name="mode">
                <param name="outtype" value="selected_reads" />
                <section name="subsample_config">
                    <conditional name="subsampling_mode">

                </conditional>
            </conditional>
            <output name="outputsam" file="test_22.sam" ftype="sam" lines_diff="2"/>
        </test>
        <!-- 23) -->
        <test expect_num_outputs="1">
            <!-- subsampling SAM input without reads -->
            <param name="input" value="in_test_23.sam" ftype="sam" />
            <conditional name="mode">
                <param name="outtype" value="selected_reads" />
                <section name="subsample_config">

                </conditional>
            </conditional>
            <output name="outputsam" file="test_23.sam" ftype="sam" lines_diff="2"/>
        </test>
        <!-- 24) -->
        <test expect_num_outputs="1">
            <!-- subsampling BAM input without reads -->
            <param name="input" value="in_test_24.bam" ftype="bam" />
            <conditional name="mode">
                <param name="outtype" value="selected_reads" />
                <section name="subsample_config">

                </conditional>
            </conditional>
            <output name="outputsam" file="test_24.bam" ftype="bam" lines_diff="2" />
        </test>
        <!-- 25) -->
        <test expect_num_outputs="1">
            <param name="input" value="in_test_15.sam" ftype="sam" />
            <conditional name="mode">
                <param name="outtype" value="selected_reads" />
                <section name="subsample_config">
                    <conditional name="subsampling_mode">

                </conditional>
            </conditional>
            <output name="outputsam" file="test_25.sam" ftype="sam" compare="diff" lines_diff="2" />
        </test>
        <!-- 26) -->
        <test expect_num_outputs="1">
            <param name="input" value="in_test_14.bam" ftype="bam" />
            <conditional name="mode">
                <param name="outtype" value="selected_reads" />
                <section name="subsample_config">
                    <conditional name="subsampling_mode">

                </conditional>
            </conditional>
            <output name="outputsam" file="test_26.bam" ftype="bam" lines_diff="2" />
        </test>
        <!-- 27) -->
        <test expect_num_outputs="1">
            <param name="input" value="in_test_14.bam" ftype="bam" />
            <conditional name="mode">
                <param name="outtype" value="selected_reads" />
                <section name="subsample_config">
                    <conditional name="subsampling_mode">

                </conditional>
            </conditional>
            <output name="outputsam" file="test_27.bam" ftype="bam" lines_diff="2"/>
        </test>
        <!-- 28) -->
        <test expect_num_outputs="1">
            <param name="input" value="in_test_14.bam" ftype="bam" />
            <conditional name="mode">
                <param name="outtype" value="selected_reads" />
                <section name="subsample_config">
                    <conditional name="subsampling_mode">

                </conditional>
            </conditional>
            <output name="outputsam" file="test_28.bam" ftype="bam" lines_diff="2" />
        </test>
        <!-- 29) -->
        <test expect_num_outputs="1">
            <param name="input" value="in_test_14.bam" ftype="bam" />
            <conditional name="mode">
                <param name="outtype" value="selected_reads" />
                <section name="subsample_config">
                    <conditional name="subsampling_mode">

                </conditional>
            </conditional>
            <output name="outputsam" file="test_29.bam" ftype="bam" lines_diff="2"/>
        </test>
        <!-- 30) testing tag filtering -->
        <test expect_num_outputs="1">
            <param name="input" value="in_test_30.bam" ftype="bam" />
            <conditional name="mode">
                <param name="outtype" value="selected_reads" />
                <section name="filter_config">
                    <param name="tag" value="XS:-18" />

                <has_text text="--tag 'XS:-18'"/>
            </assert_command>
            <output name="outputsam" file="test_30.bam" ftype="bam" lines_diff="2" />
        </test>
        <!-- 31) testing readname filtering -->
        <test expect_num_outputs="1">
            <param name="input" value="in_test_30.bam" ftype="bam" />
            <conditional name="mode">
                <param name="outtype" value="selected_reads" />
                <section name="filter_config">
                    <param name="qname_file" value="readnames.txt" />