comparison samtools_stats.xml @ 13:c03b52838177 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_stats commit 26763d398d563ccafd2d66ab325f50f5708b5ebc

12:8fecc86e574a

<tool id="samtools_stats" name="Samtools stats" version="2.0.5" profile="@PROFILE@">
    <description>generate statistics for BAM dataset</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

            <param name="input" value="1_map_cigar.sam" ftype="sam" />
            <conditional name="addref_cond">
                <param name="addref_select" value="history" />
                <param name="ref" value="test.fa" ftype="fasta" />
            </conditional>
            <output name="output" file="1.stats.expected" ftype="tabular" lines_diff="4" />
        </test>
        <!-- test_cmd($opts,out=>'stat/1.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/1_map_cigar.sam | tail -n+4", exp_fix=>$efix);-->
        <test expect_num_outputs="1">
            <param name="input" value="2_equal_cigar_full_seq.sam" ftype="sam" />
            <conditional name="addref_cond">
                <param name="addref_select" value="history" />
                <param name="ref" value="test.fa" ftype="fasta" />
            </conditional>
            <output name="output" file="2.stats.expected" ftype="tabular" lines_diff="4" />
        </test>
        <!-- test_cmd($opts,out=>'stat/2.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/2_equal_cigar_full_seq.sam | tail -n+4", exp_fix=>$efix);-->
        <!-- test_cmd($opts,out=>'stat/3.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/3_map_cigar_equal_seq.sam | tail -n+4", exp_fix=>$efix);-->
        <!-- test_cmd($opts,out=>'stat/4.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/4_X_cigar_full_seq.sam | tail -n+4", exp_fix=>$efix);-->
        <!-- test_cmd($opts,out=>'stat/5.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/5_insert_cigar.sam | tail -n+4", exp_fix=>$efix); -->

            <param name="insert_size" value="0" />
            <conditional name="addref_cond">
                <param name="addref_select" value="history" />
                <param name="ref" value="test.fa" ftype="fasta" />
            </conditional>
            <output name="output" file="6.stats.expected" ftype="tabular" lines_diff="4" />
        </test>
        <!-- test_cmd($opts,out=>'stat/6.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa -i 0 $$opts{path}/stat/5_insert_cigar.sam | tail -n+4", exp_fix=>$efix); -->
        <!-- test_cmd($opts,out=>'stat/7.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/7_supp.sam | tail -n+4", exp_fix=>$efix); -->
        <!-- test_cmd($opts,out=>'stat/8.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/8_secondary.sam | tail -n+4", exp_fix=>$efix);-->
        <!-- test_cmd($opts,out=>'stat/9.stats.expected',cmd=>"$$opts{bin}/samtools stats -S RG -r $$opts{path}/stat/test.fa $$opts{path}/stat/1_map_cigar.sam | tail -n+4", exp_fix=>$efix,out_map=>{"stat/1_map_cigar.sam_s1_a_1.bamstat"=>"stat/1_map_cigar.sam_s1_a_1.expected.bamstat"},hskip=>3);-->

            </conditional>
            <conditional name="cond_region">
                <param name="select_region" value="tab"/>
                <param name="targetregions" value="11.stats.targets" ftype="tabular" />
            </conditional>
            <output name="output" file="11.stats.expected" ftype="tabular" lines_diff="4" />
        </test>
        <!-- test_cmd($opts,out=>'stat/11.stats.expected',cmd=>"$$opts{bin}/samtools stats -t $$opts{path}/stat/11.stats.targets $$opts{path}/stat/11_target.sam | tail -n+4", exp_fix=>$efix); -->

        <test expect_num_outputs="1">
            <param name="input" value="11_target.bam" ftype="bam" />

                <param name="select_region" value="text"/>
                <param name="regions_repeat_0|region" value="ref1:10-24"/>
                <param name="regions_repeat_1|region" value="ref1:30-46"/>
                <param name="regions_repeat_2|region" value="ref1:39-56"/>
            </conditional>
            <output name="output" file="11.stats.expected" ftype="tabular" lines_diff="4" />
        </test>
        <!-- test_cmd($opts,out=>'stat/11.stats.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4", exp_fix=>$efix);
-->
        <test expect_num_outputs="1">
            <param name="input" value="11_target.sam" ftype="sam" />

            <conditional name="cond_region">
                <param name="select_region" value="tab"/>
                <param name="targetregions" value="11.stats.targets" ftype="tabular" />
            </conditional>
            <param name="cov_threshold" value="4" />
            <output name="output" file="11.stats.g4.expected" ftype="tabular" lines_diff="4" />
        </test>
        <!-- test_cmd($opts,out=>'stat/11.stats.g4.expected',cmd=>"$$opts{bin}/samtools stats -g 4 -t $$opts{path}/stat/11.stats.targets $$opts{path}/stat/11_target.sam | tail -n+4", exp_fix=>$efix);-->
        <test expect_num_outputs="1">
            <param name="input" value="11_target.bam" ftype="bam" />
            <conditional name="addref_cond">

                <param name="regions_repeat_0|region" value="ref1:10-24"/>
                <param name="regions_repeat_1|region" value="ref1:30-46"/>
                <param name="regions_repeat_2|region" value="ref1:39-56"/>
            </conditional>
            <param name="cov_threshold" value="4" />
            <output name="output" file="11.stats.g4.expected" ftype="tabular" lines_diff="4" />
        </test>
        <!-- test_cmd($opts,out=>'stat/11.stats.g4.expected',cmd=>"$$opts{bin}/samtools stats -g 4 $$opts{path}/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4", exp_fix=>$efix); -->
        <test expect_num_outputs="1">
            <param name="input" value="12_overlaps.bam" ftype="bam" />
            <conditional name="addref_cond">

            </conditional>
            <conditional name="cond_region">
                <param name="select_region" value="tab"/>
                <param name="targetregions" value="12_3reads.bed" ftype="tabular" />
            </conditional>
            <output name="output" file="12.3reads.overlap.expected" ftype="tabular" lines_diff="4" />
        </test>
        <!-- test_cmd($opts,out=>'stat/12.3reads.overlap.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -t $$opts{path}/stat/12_3reads.bed | tail -n+4", exp_fix=>$efix);-->
        <test expect_num_outputs="1">
            <param name="input" value="12_overlaps.bam" ftype="bam" />
            <conditional name="addref_cond">

            </conditional>
            <conditional name="cond_region">
                <param name="select_region" value="tab"/>
                <param name="targetregions" value="12_3reads.bed" ftype="tabular" />
            </conditional>
            <param name="remove_overlaps" value="-p"/>
            <output name="output" file="12.3reads.nooverlap.expected" ftype="tabular" lines_diff="4" />
        </test>
        <!-- test_cmd($opts,out=>'stat/12.3reads.nooverlap.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -p -t $$opts{path}/stat/12_3reads.bed | tail -n+4", exp_fix=>$efix);-->
        <test expect_num_outputs="1">
            <param name="input" value="12_overlaps.bam" ftype="bam" />
            <conditional name="addref_cond">

            </conditional>
            <conditional name="cond_region">
                <param name="select_region" value="tab"/>
                <param name="targetregions" value="12_2reads.bed" ftype="tabular" />
            </conditional>
            <output name="output" file="12.2reads.overlap.expected" ftype="tabular" lines_diff="4" />
        </test>
        <!-- test_cmd($opts,out=>'stat/12.2reads.overlap.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -t $$opts{path}/stat/12_2reads.bed | tail -n+4", exp_fix=>$efix);-->
        <test expect_num_outputs="1">
            <param name="input" value="12_overlaps.bam" ftype="bam" />
            <conditional name="addref_cond">

            </conditional>
            <conditional name="cond_region">
                <param name="select_region" value="tab"/>
                <param name="targetregions" value="12_2reads.bed" ftype="tabular" />
            </conditional>
            <param name="remove_overlaps" value="-p"/>
            <output name="output" file="12.2reads.nooverlap.expected" ftype="tabular" lines_diff="4" />
        </test>
        <!-- test_cmd($opts,out=>'stat/12.2reads.nooverlap.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -p -t $$opts{path}/stat/12_2reads.bed | tail -n+4", exp_fix=>$efix);-->
        <test expect_num_outputs="1">
            <param name="input" value="samtools_stats_input.bam" ftype="bam" />
            <conditional name="addref_cond">
                <param name="addref_select" value="history" />
                <param name="ref" value="samtools_stats_ref.fa" ftype="fasta" />
            </conditional>
            <output name="output" file="samtools_stats_out1.tab" ftype="tabular" lines_diff="4" />
        </test>
        <test expect_num_outputs="1">
            <param name="input" value="samtools_stats_input.bam" ftype="bam" />
            <conditional name="addref_cond">
                <param name="addref_select" value="history" />

                <param name="generate_tables" value="SN,MPC,GCC" />
            </conditional>
            <output_collection name="output_collection" type="list">
                <element name="ACGT content per cycle" ftype="tabular" file="samtools_stats_out1__gcc.tab"/>
                <element name="Mismatches per cycle and quality" ftype="tabular" file="samtools_stats_out1__mpc.tab" />
                <element name="Summary Numbers" ftype="tabular" file="samtools_stats_out1__sn.tab" />
            </output_collection>
        </test>
        <!-- test filtering by read group -->
        <!-- <test>
            <param name="input" value="11_target.sam" ftype="sam" />

13:c03b52838177

<tool id="samtools_stats" name="Samtools stats" version="2.0.9" profile="@PROFILE@">
    <description>generate statistics for BAM dataset</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

            <param name="input" value="1_map_cigar.sam" ftype="sam" />
            <conditional name="addref_cond">
                <param name="addref_select" value="history" />
                <param name="ref" value="test.fa" ftype="fasta" />
            </conditional>
            <output name="output" file="1.stats.expected" ftype="tabular" lines_diff="8" />
        </test>
        <!-- test_cmd($opts,out=>'stat/1.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/1_map_cigar.sam | tail -n+4", exp_fix=>$efix);-->
        <test expect_num_outputs="1">
            <param name="input" value="2_equal_cigar_full_seq.sam" ftype="sam" />
            <conditional name="addref_cond">
                <param name="addref_select" value="cached" />
                <param name="ref" value="test" />
            </conditional>
            <output name="output" file="2.stats.expected" ftype="tabular" lines_diff="8" />
        </test>
        <!-- test_cmd($opts,out=>'stat/2.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/2_equal_cigar_full_seq.sam | tail -n+4", exp_fix=>$efix);-->
        <!-- test_cmd($opts,out=>'stat/3.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/3_map_cigar_equal_seq.sam | tail -n+4", exp_fix=>$efix);-->
        <!-- test_cmd($opts,out=>'stat/4.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/4_X_cigar_full_seq.sam | tail -n+4", exp_fix=>$efix);-->
        <!-- test_cmd($opts,out=>'stat/5.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/5_insert_cigar.sam | tail -n+4", exp_fix=>$efix); -->

            <param name="insert_size" value="0" />
            <conditional name="addref_cond">
                <param name="addref_select" value="history" />
                <param name="ref" value="test.fa" ftype="fasta" />
            </conditional>
            <output name="output" file="6.stats.expected" ftype="tabular" lines_diff="8" />
        </test>
        <!-- test_cmd($opts,out=>'stat/6.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa -i 0 $$opts{path}/stat/5_insert_cigar.sam | tail -n+4", exp_fix=>$efix); -->
        <!-- test_cmd($opts,out=>'stat/7.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/7_supp.sam | tail -n+4", exp_fix=>$efix); -->
        <!-- test_cmd($opts,out=>'stat/8.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/8_secondary.sam | tail -n+4", exp_fix=>$efix);-->
        <!-- test_cmd($opts,out=>'stat/9.stats.expected',cmd=>"$$opts{bin}/samtools stats -S RG -r $$opts{path}/stat/test.fa $$opts{path}/stat/1_map_cigar.sam | tail -n+4", exp_fix=>$efix,out_map=>{"stat/1_map_cigar.sam_s1_a_1.bamstat"=>"stat/1_map_cigar.sam_s1_a_1.expected.bamstat"},hskip=>3);-->

            </conditional>
            <conditional name="cond_region">
                <param name="select_region" value="tab"/>
                <param name="targetregions" value="11.stats.targets" ftype="tabular" />
            </conditional>
            <output name="output" file="11.stats.expected" ftype="tabular" lines_diff="8" />
        </test>
        <!-- test_cmd($opts,out=>'stat/11.stats.expected',cmd=>"$$opts{bin}/samtools stats -t $$opts{path}/stat/11.stats.targets $$opts{path}/stat/11_target.sam | tail -n+4", exp_fix=>$efix); -->

        <test expect_num_outputs="1">
            <param name="input" value="11_target.bam" ftype="bam" />

                <param name="select_region" value="text"/>
                <param name="regions_repeat_0|region" value="ref1:10-24"/>
                <param name="regions_repeat_1|region" value="ref1:30-46"/>
                <param name="regions_repeat_2|region" value="ref1:39-56"/>
            </conditional>
            <output name="output" file="11.stats.expected" ftype="tabular" lines_diff="8" />
        </test>
        <!-- test_cmd($opts,out=>'stat/11.stats.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4", exp_fix=>$efix);
-->
        <test expect_num_outputs="1">
            <param name="input" value="11_target.sam" ftype="sam" />

            <conditional name="cond_region">
                <param name="select_region" value="tab"/>
                <param name="targetregions" value="11.stats.targets" ftype="tabular" />
            </conditional>
            <param name="cov_threshold" value="4" />
            <output name="output" file="11.stats.g4.expected" ftype="tabular" lines_diff="8" />
        </test>
        <!-- test_cmd($opts,out=>'stat/11.stats.g4.expected',cmd=>"$$opts{bin}/samtools stats -g 4 -t $$opts{path}/stat/11.stats.targets $$opts{path}/stat/11_target.sam | tail -n+4", exp_fix=>$efix);-->
        <test expect_num_outputs="1">
            <param name="input" value="11_target.bam" ftype="bam" />
            <conditional name="addref_cond">

                <param name="regions_repeat_0|region" value="ref1:10-24"/>
                <param name="regions_repeat_1|region" value="ref1:30-46"/>
                <param name="regions_repeat_2|region" value="ref1:39-56"/>
            </conditional>
            <param name="cov_threshold" value="4" />
            <output name="output" file="11.stats.g4.expected" ftype="tabular" lines_diff="8" />
        </test>
        <!-- test_cmd($opts,out=>'stat/11.stats.g4.expected',cmd=>"$$opts{bin}/samtools stats -g 4 $$opts{path}/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4", exp_fix=>$efix); -->
        <test expect_num_outputs="1">
            <param name="input" value="12_overlaps.bam" ftype="bam" />
            <conditional name="addref_cond">

            </conditional>
            <conditional name="cond_region">
                <param name="select_region" value="tab"/>
                <param name="targetregions" value="12_3reads.bed" ftype="tabular" />
            </conditional>
            <output name="output" file="12.3reads.overlap.expected" ftype="tabular" lines_diff="8" />
        </test>
        <!-- test_cmd($opts,out=>'stat/12.3reads.overlap.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -t $$opts{path}/stat/12_3reads.bed | tail -n+4", exp_fix=>$efix);-->
        <test expect_num_outputs="1">
            <param name="input" value="12_overlaps.bam" ftype="bam" />
            <conditional name="addref_cond">

            </conditional>
            <conditional name="cond_region">
                <param name="select_region" value="tab"/>
                <param name="targetregions" value="12_3reads.bed" ftype="tabular" />
            </conditional>
            <param name="remove_overlaps" value="true"/>
            <output name="output" file="12.3reads.nooverlap.expected" ftype="tabular" lines_diff="8" />
        </test>
        <!-- test_cmd($opts,out=>'stat/12.3reads.nooverlap.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -p -t $$opts{path}/stat/12_3reads.bed | tail -n+4", exp_fix=>$efix);-->
        <test expect_num_outputs="1">
            <param name="input" value="12_overlaps.bam" ftype="bam" />
            <conditional name="addref_cond">

            </conditional>
            <conditional name="cond_region">
                <param name="select_region" value="tab"/>
                <param name="targetregions" value="12_2reads.bed" ftype="tabular" />
            </conditional>
            <output name="output" file="12.2reads.overlap.expected" ftype="tabular" lines_diff="8" />
        </test>
        <!-- test_cmd($opts,out=>'stat/12.2reads.overlap.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -t $$opts{path}/stat/12_2reads.bed | tail -n+4", exp_fix=>$efix);-->
        <test expect_num_outputs="1">
            <param name="input" value="12_overlaps.bam" ftype="bam" />
            <conditional name="addref_cond">

            </conditional>
            <conditional name="cond_region">
                <param name="select_region" value="tab"/>
                <param name="targetregions" value="12_2reads.bed" ftype="tabular" />
            </conditional>
            <param name="remove_overlaps" value="true"/>
            <output name="output" file="12.2reads.nooverlap.expected" ftype="tabular" lines_diff="8" />
        </test>
        <!-- test_cmd($opts,out=>'stat/12.2reads.nooverlap.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -p -t $$opts{path}/stat/12_2reads.bed | tail -n+4", exp_fix=>$efix);-->
        <test expect_num_outputs="1">
            <param name="input" value="samtools_stats_input.bam" ftype="bam" />
            <conditional name="addref_cond">
                <param name="addref_select" value="history" />
                <param name="ref" value="samtools_stats_ref.fa" ftype="fasta" />
            </conditional>
            <output name="output" file="samtools_stats_out1.tab" ftype="tabular" lines_diff="8" />
        </test>
        <test expect_num_outputs="1">
            <param name="input" value="samtools_stats_input.bam" ftype="bam" />
            <conditional name="addref_cond">
                <param name="addref_select" value="history" />

                <param name="generate_tables" value="SN,MPC,GCC" />
            </conditional>
            <output_collection name="output_collection" type="list">
                <element name="ACGT content per cycle" ftype="tabular" file="samtools_stats_out1__gcc.tab"/>
                <element name="Mismatches per cycle and quality" ftype="tabular" file="samtools_stats_out1__mpc.tab" />
                <element name="Summary Numbers" ftype="tabular" file="samtools_stats_out1__sn.tab" lines_diff="2" />
            </output_collection>
        </test>
        <!-- test filtering by read group -->
        <!-- <test>
            <param name="input" value="11_target.sam" ftype="sam" />