comparison parse.xml @ 15:11149c89ee4f draft

planemo upload for repository https://github.com/open2c/pairtools commit a7612b0f2c0575d6a78fb24dc87192d44817178a

14:bfb00f8fec97

            '$sam_path'
            -c '$chroms_path'
            #if str($assembly_name).strip(): 
                --assembly '$assembly_name'
            #end if
            -o '$output'
            --min-mapq '$min_mapq'
            --max-molecule-size '$max_molecule_size'
            $drop_readid
            $drop_seq
            $output_stats

            #end if
            --walks-policy '$walks_policy'
            --max-inter-align-gap '$max_inter_algn_gap'
            --nproc-in \${GALAXY_SLOTS:-4}
            --nproc-out \${GALAXY_SLOTS:-4}
    ]]></command>
    <inputs>
        <param name="sam_path" type="data" format="sam,qname_input_sorted.bam,qname_sorted.bam" label="Input SAM/BAM file" help="Input SAM or BAM (unsorted/name-sorted) file with paired-end sequence alignments of Hi-C molecules."/>
        <param name="chroms_path" argument="-c" type="data" format="tabular" label="Input a chromosome order file" help="Chromosome order used to flip interchromosomal mates. Any scaffolds not listed will be ordered lexicographically."/>
        <param name="assembly_name" type="text" value="" label="Input a name of genome assembly" help="Name of genome assembly (e.g. hg19, mm10) to store in the pairs header"></param>

        </conditional>
        <param argument="--walks-policy" type="select" label="Walks Policy" help="The policy for reporting unrescuable walks.">
            <expand macro="walks_policy_options"/>
        </param>
        <param name="compress_output" type="boolean" truevalue=".gz" falsevalue="" checked="false" label="Compress output file" />   
        <param argument="max_inter_algn_gap" type="integer" min="0" value="30" label="Max alignment gap" help="read segments that are not covered by any alignment and longer than the specified value are treated as null alignments."/>
    </inputs>
    <outputs>
        <data name="output_parsed_pairs" format="4dn_pairsam" label="${tool.name} on ${on_string}:  .pairs">
            <change_format>

            <param name="sam_path" value="test.sam"/>
            <param name="chroms_path" value="test.genome"/>
            <param name="min_mapq" value="1"/>
            <param name="walks_policy" value="mask"/>
            <param name="max_inter_algn_gap" value="20"/>
            <output name="output_parsed_pairs" ftype="4dn_pairsam" file="output_parsed_pairs_sam.pairs" lines_diff="10"/>
        </test>
        <!--Test 02 with BAM file as input and default parameters-->
        <test expect_num_outputs="1">
            <param name="sam_path" value="test.bam"/>
            <param name="chroms_path" value="test.reduced.chrom.sizes"/>
            <param name="min_mapq" value="1"/>
            <param name="walks_policy" value="mask"/>
            <param name="max_inter_algn_gap" value="20"/>
            <output name="output_parsed_pairs" ftype="4dn_pairsam" file="output_parsed_pairs_bam.pairs" lines_diff="10"/>
        </test>
        <!--Test 03 with BAM file as input and minimal mapq of 40-->
        <test expect_num_outputs="1">
            <param name="sam_path" value="test.bam"/>
            <param name="chroms_path" value="test.reduced.chrom.sizes"/>
            <param name="min_mapq" value="40"/>
            <param name="walks_policy" value="mask"/>
            <param name="max_inter_algn_gap" value="20"/>
            <output name="output_parsed_pairs" ftype="4dn_pairsam" file="output_parsed_pairs_bam_min_mapq_40.pairs" lines_diff="10"/>
        </test>
        <!--Test 04 with BAM file as input and walk policy of 5unique-->
        <test expect_num_outputs="1">
            <param name="sam_path" value="test.bam"/>
            <param name="chroms_path" value="test.reduced.chrom.sizes"/>
            <param name="min_mapq" value="40"/>
            <param name="walks_policy" value="5unique"/>
            <param name="max_inter_algn_gap" value="20"/>
            <output name="output_parsed_pairs" ftype="4dn_pairsam" file="output_parsed_pairs_bam_5unique.pairs" lines_diff="10"/>
        </test>
        <!--Test 05 with BAM file as input and read id dropped-->
        <test expect_num_outputs="1">
            <param name="sam_path" value="test.bam"/>
            <param name="chroms_path" value="test.reduced.chrom.sizes"/>
            <param name="min_mapq" value="40"/>
            <param name="walks_policy" value="5unique"/>
            <param name="max_inter_algn_gap" value="20"/>
            <param name="drop_readid" value="true"></param>
            <output name="output_parsed_pairs" ftype="4dn_pairsam" file="output_parsed_pairs_bam_readid_dropped.pairs" lines_diff="10"/>
        </test>
        <!--Test 06 with SAM file as input and drop_seq enabled-->
        <test expect_num_outputs="1">
            <param name="sam_path" value="test.sam"/>
            <param name="chroms_path" value="test.genome"/>
            <param name="min_mapq" value="40"/>
            <param name="walks_policy" value="5unique"/>
            <param name="max_inter_algn_gap" value="20"/>
            <param name="drop_seq" value="true"></param>
            <output name="output_parsed_pairs" ftype="4dn_pairsam" file="output_parsed_pairs_bam_readid_dropped_seq.pairs" lines_diff="10"/>
        </test>
        <!--Test 07 with SAM file as input and output_stats enabled-->
        <test expect_num_outputs="2">
            <param name="sam_path" value="test.sam"/>
            <param name="chroms_path" value="test.genome"/>
            <param name="min_mapq" value="40"/>
            <param name="walks_policy" value="5unique"/>
            <param name="max_inter_algn_gap" value="20"/>
            <param name="output_stats" value="true"></param>
            <output name="parsed_pairs_stats" file="output_parsed_pairs.stats" lines_diff="10"/>
        </test>
        <!--Test 08 with SAM file as input and default parameters and assembly name -->
        <test expect_num_outputs="1">
            <param name="sam_path" value="test.sam"/>
            <param name="chroms_path" value="test.genome"/>
            <param name="assembly_name" value="test_assembly"/>
            <param name="min_mapq" value="1"/>
            <param name="walks_policy" value="mask"/>
            <param name="max_inter_algn_gap" value="20"/>
            <output name="output_parsed_pairs" ftype="4dn_pairsam" file="output_parsed_pairs_sam_assemblyname.pairs" lines_diff="10"/>
        </test>
        <!--Test 09 with SAM file as input and default parameters and assembly name and compressed output--> 
        <test expect_num_outputs="1">
            <param name="sam_path" value="test.sam"/>
            <param name="chroms_path" value="test.genome"/>
            <param name="assembly_name" value="test_assembly"/>
            <param name="min_mapq" value="1"/>
            <param name="walks_policy" value="mask"/>
            <param name="max_inter_algn_gap" value="20"/>
            <param name="compress_output" value="true"/>
            <output name="output_parsed_pairs" ftype="4dn_pairsam.gz" file="output_parsed_pairs_sam_assemblyname.pairs.gz" decompress="true" lines_diff="10"/>
        </test>
        <!--Test 10 with SAM file as input and add columns-->
        <test expect_num_outputs="1">
            <param name="sam_path" value="test.sam"/>
            <param name="chroms_path" value="test.genome"/>
            <param name="min_mapq" value="1"/>
            <param name="walks_policy" value="mask"/>
            <param name="max_inter_algn_gap" value="20"/>
            <conditional name="select_add_columns">
                <param name="add_columns_selection" value="yes"/>
                <param name="add_columns" value="mapq,seq"/>
            </conditional>
            <output name="output_parsed_pairs" ftype="4dn_pairsam" file="output_parsed_pairs_sam_mapq.pairs" lines_diff="10"/>
        </test>
    </tests>
    <help><![CDATA[
        **Pairtools parse**

        Detects ligation events in the aligned sequences of DNA molecules formed in Hi-C experiments and reports them in the .pairs/.pairsam format.
        
        sam_path : an input .sam/.bam (unsorted/name-sorted) file with paired-end sequence alignments of Hi-C molecules. 
              
    ]]></help>
    <expand macro="citations"/>
    <expand macro="creator"/>
</tool>

15:11149c89ee4f

            '$sam_path'
            -c '$chroms_path'
            #if str($assembly_name).strip(): 
                --assembly '$assembly_name'
            #end if
            --min-mapq '$min_mapq'
            --max-molecule-size '$max_molecule_size'
            $drop_readid
            $drop_seq
            $output_stats

            #end if
            --walks-policy '$walks_policy'
            --max-inter-align-gap '$max_inter_algn_gap'
            --nproc-in \${GALAXY_SLOTS:-4}
            --nproc-out \${GALAXY_SLOTS:-4}
            #if $sort_output:
                |
            pairtools sort -o '$output'
                --nproc-in \${GALAXY_SLOTS:-4}
                --nproc-out \${GALAXY_SLOTS:-4}
            #else
                 -o '$output'
            #end if

    ]]></command>
    <inputs>
        <param name="sam_path" type="data" format="sam,qname_input_sorted.bam,qname_sorted.bam" label="Input SAM/BAM file" help="Input SAM or BAM (unsorted/name-sorted) file with paired-end sequence alignments of Hi-C molecules."/>
        <param name="chroms_path" argument="-c" type="data" format="tabular" label="Input a chromosome order file" help="Chromosome order used to flip interchromosomal mates. Any scaffolds not listed will be ordered lexicographically."/>
        <param name="assembly_name" type="text" value="" label="Input a name of genome assembly" help="Name of genome assembly (e.g. hg19, mm10) to store in the pairs header"></param>

        </conditional>
        <param argument="--walks-policy" type="select" label="Walks Policy" help="The policy for reporting unrescuable walks.">
            <expand macro="walks_policy_options"/>
        </param>
        <param name="compress_output" type="boolean" truevalue=".gz" falsevalue="" checked="false" label="Compress output file" />   
        <param name="sort_output" type="boolean"  checked="true" label="generate sorted output file" />
        <param argument="max_inter_algn_gap" type="integer" min="0" value="30" label="Max alignment gap" help="read segments that are not covered by any alignment and longer than the specified value are treated as null alignments."/>
    </inputs>
    <outputs>
        <data name="output_parsed_pairs" format="4dn_pairsam" label="${tool.name} on ${on_string}:  .pairs">
            <change_format>

            <param name="sam_path" value="test.sam"/>
            <param name="chroms_path" value="test.genome"/>
            <param name="min_mapq" value="1"/>
            <param name="walks_policy" value="mask"/>
            <param name="max_inter_algn_gap" value="20"/>
            <param name="sort_output" value="false"/>
            <output name="output_parsed_pairs" ftype="4dn_pairsam" file="output_parsed_pairs_sam.pairs" lines_diff="10"/>
        </test>
        <!--Test 02 with SAM file as input and sorted output default parameters-->
        <test expect_num_outputs="1">
            <param name="sam_path" value="test.sam"/>
            <param name="chroms_path" value="test.genome"/>
            <param name="min_mapq" value="1"/>
            <param name="walks_policy" value="mask"/>
            <param name="max_inter_algn_gap" value="20"/>
            <param name="sort_output" value="true"/>
            <output name="output_parsed_pairs" ftype="4dn_pairsam" file="output_parsed_pairs_sam.sorted.pairs" lines_diff="10"/>
        </test>
        <!--Test 03 with BAM file as input and default parameters-->
        <test expect_num_outputs="1">
            <param name="sam_path" value="test.bam"/>
            <param name="chroms_path" value="test.reduced.chrom.sizes"/>
            <param name="min_mapq" value="1"/>
            <param name="walks_policy" value="mask"/>
            <param name="max_inter_algn_gap" value="20"/>
            <param name="sort_output" value="false"/>
            <output name="output_parsed_pairs" ftype="4dn_pairsam" file="output_parsed_pairs_bam.pairs" lines_diff="10"/>
        </test>
        <!--Test 04 with BAM file as input and minimal mapq of 40-->
        <test expect_num_outputs="1">
            <param name="sam_path" value="test.bam"/>
            <param name="chroms_path" value="test.reduced.chrom.sizes"/>
            <param name="min_mapq" value="40"/>
            <param name="walks_policy" value="mask"/>
            <param name="max_inter_algn_gap" value="20"/>
            <param name="sort_output" value="false"/>
            <output name="output_parsed_pairs" ftype="4dn_pairsam" file="output_parsed_pairs_bam_min_mapq_40.pairs" lines_diff="10"/>
        </test>
        <!--Test 05 with BAM file as input and walk policy of 5unique-->
        <test expect_num_outputs="1">
            <param name="sam_path" value="test.bam"/>
            <param name="chroms_path" value="test.reduced.chrom.sizes"/>
            <param name="min_mapq" value="40"/>
            <param name="walks_policy" value="5unique"/>
            <param name="max_inter_algn_gap" value="20"/>
            <param name="sort_output" value="false"/>
            <output name="output_parsed_pairs" ftype="4dn_pairsam" file="output_parsed_pairs_bam_5unique.pairs" lines_diff="10"/>
        </test>
        <!--Test 06 with BAM file as input and read id dropped-->
        <test expect_num_outputs="1">
            <param name="sam_path" value="test.bam"/>
            <param name="chroms_path" value="test.reduced.chrom.sizes"/>
            <param name="min_mapq" value="40"/>
            <param name="walks_policy" value="5unique"/>
            <param name="max_inter_algn_gap" value="20"/>
            <param name="drop_readid" value="true"></param>
            <param name="sort_output" value="false"/>
            <output name="output_parsed_pairs" ftype="4dn_pairsam" file="output_parsed_pairs_bam_readid_dropped.pairs" lines_diff="10"/>
        </test>
        <!--Test 07 with SAM file as input and drop_seq enabled-->
        <test expect_num_outputs="1">
            <param name="sam_path" value="test.sam"/>
            <param name="chroms_path" value="test.genome"/>
            <param name="min_mapq" value="40"/>
            <param name="walks_policy" value="5unique"/>
            <param name="max_inter_algn_gap" value="20"/>
            <param name="drop_seq" value="true"></param>
            <param name="sort_output" value="false"/>
            <output name="output_parsed_pairs" ftype="4dn_pairsam" file="output_parsed_pairs_bam_readid_dropped_seq.pairs" lines_diff="10"/>
        </test>
        <!--Test 08 with SAM file as input and output_stats enabled-->
        <test expect_num_outputs="2">
            <param name="sam_path" value="test.sam"/>
            <param name="chroms_path" value="test.genome"/>
            <param name="min_mapq" value="40"/>
            <param name="walks_policy" value="5unique"/>
            <param name="max_inter_algn_gap" value="20"/>
            <param name="output_stats" value="true"></param>
            <output name="parsed_pairs_stats" file="output_parsed_pairs.stats" lines_diff="10"/>
        </test>
        <!--Test 09 with SAM file as input and default parameters and assembly name -->
        <test expect_num_outputs="1">
            <param name="sam_path" value="test.sam"/>
            <param name="chroms_path" value="test.genome"/>
            <param name="assembly_name" value="test_assembly"/>
            <param name="min_mapq" value="1"/>
            <param name="walks_policy" value="mask"/>
            <param name="max_inter_algn_gap" value="20"/>
            <param name="sort_output" value="false"/>
            <output name="output_parsed_pairs" ftype="4dn_pairsam" file="output_parsed_pairs_sam_assemblyname.pairs" lines_diff="10"/>
        </test>
        <!--Test 10 with SAM file as input and default parameters and assembly name and compressed output-->
        <test expect_num_outputs="1">
            <param name="sam_path" value="test.sam"/>
            <param name="chroms_path" value="test.genome"/>
            <param name="assembly_name" value="test_assembly"/>
            <param name="min_mapq" value="1"/>
            <param name="walks_policy" value="mask"/>
            <param name="max_inter_algn_gap" value="20"/>
            <param name="compress_output" value="true"/>
            <param name="sort_output" value="false"/>
            <output name="output_parsed_pairs" ftype="4dn_pairsam.gz" file="output_parsed_pairs_sam_assemblyname.pairs.gz" decompress="true" lines_diff="10"/>
        </test>
        <!--Test 11 with SAM file as input and default parameters and assembly name and sorted, compressed output-->
        <test expect_num_outputs="1">
            <param name="sam_path" value="test.sam"/>
            <param name="chroms_path" value="test.genome"/>
            <param name="assembly_name" value="test_assembly"/>
            <param name="min_mapq" value="1"/>
            <param name="walks_policy" value="mask"/>
            <param name="max_inter_algn_gap" value="20"/>
            <param name="compress_output" value="true"/>
            <output name="output_parsed_pairs" ftype="4dn_pairsam.gz" file="output_parsed_pairs_sam_assemblyname.sorted.pairs.gz" decompress="true" lines_diff="10"/>
        </test>
        <!--Test 12 with SAM file as input and add columns-->
        <test expect_num_outputs="1">
            <param name="sam_path" value="test.sam"/>
            <param name="chroms_path" value="test.genome"/>
            <param name="min_mapq" value="1"/>
            <param name="walks_policy" value="mask"/>
            <param name="max_inter_algn_gap" value="20"/>
            <conditional name="select_add_columns">
                <param name="add_columns_selection" value="yes"/>
                <param name="add_columns" value="mapq,seq"/>
            </conditional>
            <param name="sort_output" value="false"/>
            <output name="output_parsed_pairs" ftype="4dn_pairsam" file="output_parsed_pairs_sam_mapq.pairs" lines_diff="10"/>
        </test>
    </tests>
    <help><![CDATA[
        **Pairtools parse**

        Detects ligation events in the aligned sequences of DNA molecules formed in Hi-C experiments and reports them in the .pairs/.pairsam format.
        
        sam_path : an input .sam/.bam (unsorted/name-sorted) file with paired-end sequence alignments of Hi-C molecules. 

        By default, the generated .pair/.pairsam output is sorted by piping it through pairtools sort. You can disable this behavior by unchecking the “Generate sorted output file” checkbox.

    ]]></help>
    <expand macro="citations"/>
    <expand macro="creator"/>
</tool>